Contacts of the helix formed by residues 102 - 131 (chain F) in PDB entry 1O9R
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 102 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLU* 3.5 29.4 - - + +
161A LYS 5.7 1.1 - - - +
162A SER* 3.5 35.5 + - - +
2E LYS* 5.7 5.8 - - - +
44F LYS 3.5 3.6 - - - -
101F TYR* 1.3 80.2 - - - +
103F ILE* 1.3 65.7 + - - +
104F HIS* 5.0 1.1 - - + -
105F ASP* 3.0 40.5 + - - +
106F HIS* 3.1 11.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 103 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A SER* 3.0 13.7 + - - +
43F LEU* 3.8 21.5 - - + -
44F LYS 3.1 16.2 + - - +
45F GLY* 3.7 11.2 - - - +
46F PRO* 4.1 1.1 - - + -
47F GLN* 3.5 22.7 - - + +
48F PHE* 3.5 32.5 - - - +
51F VAL* 4.3 16.8 - - + -
101F TYR 4.2 0.9 - - - -
102F LYS* 1.3 70.9 - - - +
104F HIS* 1.3 59.6 + - - +
106F HIS* 3.1 3.9 + - - +
107F LEU* 2.7 49.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 104 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A SER* 2.8 30.0 + - - +
102F LYS* 3.2 1.5 - - + -
103F ILE* 1.3 73.1 - - - +
105F ASP* 1.3 61.2 + - - +
107F LEU* 3.4 7.9 + - - +
108F ASP* 3.0 51.4 + - - -
158F VAL* 3.7 34.7 - - + +
161F LYS* 6.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 105 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F ILE* 3.6 33.7 - - + +
101F TYR 5.0 0.5 + - - -
102F LYS* 3.0 37.1 + - + +
104F HIS* 1.3 79.0 - - - +
106F HIS* 1.3 65.0 + - - +
108F ASP* 3.4 10.8 + - - +
109F ALA* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 106 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F GLN* 4.4 1.6 - - + -
39F ALA* 3.5 28.5 - - + -
42F ASN* 4.0 15.5 - - + -
43F LEU* 3.7 20.4 - - + -
55F LEU* 6.1 0.2 - - + -
96F TYR* 2.8 31.5 + + - +
97F PRO 5.1 0.9 - - - -
100F ILE* 2.9 39.9 + - + +
101F TYR* 3.5 28.0 - - - -
102F LYS 3.1 13.1 + - - -
103F ILE* 3.6 6.1 - - - +
105F ASP* 1.3 74.4 - - - +
107F LEU* 1.3 61.0 + - + +
109F ALA 3.3 0.5 + - - -
110F LEU* 2.8 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F VAL* 4.4 18.2 - - + -
103F ILE* 2.7 43.5 + - + +
104F HIS* 3.8 6.3 - - + +
106F HIS* 1.3 72.8 - - + +
108F ASP* 1.3 57.8 + - - +
110F LEU* 3.7 6.4 - - + +
111F ILE* 2.8 38.9 + - + +
154F LEU* 3.7 35.4 - - + +
157F HIS* 3.8 24.2 - - + +
158F VAL* 3.7 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 108 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104F HIS* 3.0 44.7 + - - +
105F ASP* 3.6 11.4 - - - +
106F HIS 3.2 0.4 - - - -
107F LEU* 1.3 76.5 - - - +
109F ALA* 1.3 61.9 + - - +
111F ILE* 3.4 9.6 + - - +
112F GLU* 3.1 29.9 + - + +
158F VAL* 4.7 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F TYR* 3.5 30.1 - - + +
97F PRO* 4.5 7.2 - - + -
100F ILE* 4.2 7.0 - - + -
105F ASP 3.1 15.2 + - - +
108F ASP* 1.3 80.7 - - - +
110F LEU* 1.4 63.0 + - - +
112F GLU* 3.5 4.5 + - - +
113F ARG* 2.9 43.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F VAL* 3.6 28.7 - - + +
36F THR* 4.3 6.3 - - - -
39F ALA* 3.8 27.4 - - + -
51F VAL* 5.9 0.2 - - + -
55F LEU* 3.9 24.7 - - + -
96F TYR* 3.9 6.3 - - - +
106F HIS* 2.8 26.5 + - + +
107F LEU* 3.7 8.7 - - + +
109F ALA* 1.4 76.9 - - - +
111F ILE* 1.3 55.5 + - - +
113F ARG* 3.2 2.8 + - - +
114F TYR* 2.7 55.2 + - + -
154F LEU* 4.1 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 111 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107F LEU* 2.8 31.2 + - + +
108F ASP* 3.8 9.6 - - - +
109F ALA 3.4 0.2 - - - -
110F LEU* 1.3 71.2 - - - +
112F GLU* 1.3 66.6 + - + +
115F GLY* 2.8 22.9 + - - -
151F LEU* 3.9 8.1 - - + +
154F LEU* 3.6 34.5 - - + +
155F GLU* 3.8 31.6 - - + +
158F VAL* 3.7 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 112 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108F ASP* 3.1 16.5 + - - +
109F ALA* 3.6 10.8 - - - +
111F ILE* 1.3 80.3 - - + +
113F ARG* 1.3 72.1 + - + +
115F GLY* 3.9 0.9 - - - -
116F GLU* 3.1 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 113 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F LEU* 3.6 18.4 - - + -
35F VAL* 4.1 14.1 - - + +
93F LEU* 4.0 19.0 - - + +
94F LYS* 3.0 42.2 + - - +
95F ALA 3.0 18.0 + - - -
96F TYR* 3.7 26.4 - - - +
97F PRO* 4.0 5.5 - - - +
109F ALA* 2.9 41.5 + - - +
110F LEU* 3.2 4.0 + - - +
112F GLU* 1.3 88.3 + - + +
114F TYR* 1.4 62.3 + - - +
115F GLY 3.2 1.1 - - - -
116F GLU* 3.3 11.5 + - - +
117F VAL* 3.0 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 114 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F LEU* 3.6 33.9 - - + -
36F THR* 2.7 29.3 + - + +
55F LEU* 5.6 0.2 - - + -
58F PHE* 3.3 33.0 - + + +
62F LEU* 3.5 9.1 - - + +
110F LEU* 2.7 44.8 + - + +
113F ARG* 1.4 72.5 - - - +
115F GLY* 1.4 58.5 + - - +
117F VAL* 4.1 0.3 - - - +
118F ALA* 2.8 32.7 + - - +
147F LEU* 4.3 13.9 - - + +
150F SER* 3.9 30.1 - - - -
151F LEU* 4.2 15.9 - - + +
154F LEU* 3.6 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 115 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111F ILE 2.8 19.1 + - - -
112F GLU 3.9 1.1 - - - -
114F TYR* 1.4 78.7 - - - +
116F GLU* 1.4 56.2 + - - +
118F ALA* 3.8 0.5 - - - +
119F ASN* 2.9 43.0 + - - -
151F LEU* 3.8 21.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 116 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F LYS* 4.4 6.5 - - + +
93F LEU* 3.4 30.4 - - + +
94F LYS* 4.9 7.1 + - - +
112F GLU* 3.1 23.4 + - - +
113F ARG* 3.3 12.9 + - - +
115F GLY* 1.4 76.9 - - - +
117F VAL* 1.3 58.4 + - - +
119F ASN* 3.8 5.2 - - - +
120F MET* 2.9 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F SER* 3.9 34.1 - - - +
29F VAL* 4.1 22.2 - - + +
32F LEU* 3.9 19.1 - - + -
62F LEU* 5.5 0.2 - - + -
93F LEU* 4.1 10.3 - - + -
113F ARG 3.0 17.1 + - - +
114F TYR 4.1 1.3 - - - +
116F GLU* 1.3 73.5 - - - +
118F ALA* 1.3 66.1 + - - +
120F MET* 3.2 7.5 + - + +
121F ILE* 2.9 26.5 + - + +
147F LEU* 3.9 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 118 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F TYR 2.8 23.4 + - - +
115F GLY 3.8 3.4 - - - +
117F VAL* 1.3 72.7 - - - +
119F ASN* 1.3 59.5 + - - +
121F ILE* 3.4 2.9 + - - +
122F ARG* 3.0 35.4 + - - +
144F SER* 5.1 1.7 + - - -
147F LEU* 3.9 29.3 - - + +
148F ASP* 3.6 21.2 - - - +
151F LEU* 4.4 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 119 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F GLY* 2.9 26.9 + - - +
116F GLU* 3.9 5.3 - - - +
118F ALA* 1.3 76.8 - - - +
120F MET* 1.3 63.9 + - - +
122F ARG* 2.9 34.4 + - - +
123F LYS* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 120 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F GLU* 4.3 20.4 - - - +
25F SER* 3.8 31.2 - - - +
28F SER* 3.8 35.4 - - - +
92F LYS* 4.1 20.6 - - + -
93F LEU* 5.7 0.4 - - + -
116F GLU* 2.9 24.3 + - + +
117F VAL* 3.5 10.8 - - + +
119F ASN* 1.3 77.9 - - - +
121F ILE* 1.4 59.0 + - + +
123F LYS* 3.2 7.7 + - - +
124F ALA* 3.0 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F SER* 3.3 34.1 - - - +
29F VAL* 4.6 7.2 - - + -
69F ILE* 4.5 9.4 - - + -
117F VAL* 2.9 25.2 + - + +
118F ALA 3.7 3.6 - - - +
120F MET* 1.4 76.9 - - + +
122F ARG* 1.3 64.0 + - - +
124F ALA* 3.1 12.9 + - - +
125F ILE* 3.2 14.2 + - - +
140F PHE* 3.3 39.9 - - + +
143F ALA* 4.1 6.7 - - + -
144F SER* 3.6 19.5 - - - +
147F LEU* 3.6 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 122 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F ALA* 3.0 21.5 + - - +
119F ASN* 2.9 34.1 + - - +
120F MET 3.3 0.2 - - - -
121F ILE* 1.3 76.7 - - - +
123F LYS* 1.4 62.4 + - - +
125F ILE* 3.4 29.0 + - + +
126F ASP* 3.7 10.9 + - - +
144F SER* 4.2 9.8 + - - +
148F ASP* 2.9 42.2 + - - -
151F LEU* 5.4 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 123 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F ASN 3.1 13.4 + - - +
120F MET* 3.6 10.3 - - - +
121F ILE 3.2 0.2 - - - -
122F ARG* 1.4 76.7 - - - +
124F ALA* 1.3 58.6 + - - +
126F ASP* 3.2 11.0 + - + +
127F ASP* 2.6 57.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 124 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F ILE* 3.7 24.0 - - + -
25F SER* 4.3 4.3 - - - +
120F MET 3.0 14.3 + - - +
121F ILE* 3.1 11.4 + - - +
123F LYS* 1.3 74.6 - - - +
125F ILE* 1.3 64.7 + - - +
127F ASP* 4.1 3.8 - - - +
128F SER* 2.9 30.0 + - - -
140F PHE* 3.7 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 125 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121F ILE 3.2 12.2 + - - +
122F ARG* 3.5 17.7 - - + +
124F ALA* 1.3 75.1 - - - +
126F ASP* 1.3 67.3 + - - +
129F ASP* 3.0 30.0 + - + +
137F ALA* 3.6 15.3 - - + +
140F PHE* 3.7 21.7 - - + +
141F THR* 3.5 37.9 - - + +
144F SER* 3.9 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 126 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122F ARG* 3.7 11.5 + - - +
123F LYS* 3.2 11.6 + - + +
125F ILE* 1.3 88.6 - - - +
127F ASP* 1.3 61.2 + - - +
129F ASP* 3.3 5.8 + - - +
130F GLU* 2.8 45.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 127 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F THR* 5.3 0.7 - - - +
21F ILE* 3.7 25.4 - - + +
123F LYS* 2.6 55.0 + - - +
124F ALA* 4.1 4.6 + - - +
126F ASP* 1.3 79.1 - - - +
128F SER* 1.4 62.0 + - - +
130F GLU* 3.5 17.0 + - - +
131F ALA* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 128 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F VAL* 4.1 13.9 - - - +
21F ILE* 4.2 5.5 - - - +
124F ALA 2.9 19.2 + - - -
125F ILE 3.7 3.6 - - - -
127F ASP* 1.4 75.6 - - - +
129F ASP* 1.3 65.5 + - - +
131F ALA* 3.2 9.5 + - - +
132F GLY 3.4 0.2 + - - -
133F ASP* 3.0 24.5 + - - +
136F THR* 3.6 9.1 - - - +
137F ALA* 3.8 24.0 - - - -
140F PHE* 3.4 19.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 129 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F ILE* 3.0 19.7 + - + +
126F ASP* 3.8 5.8 - - - +
128F SER* 1.3 76.7 - - - +
130F GLU* 1.3 58.3 + - + +
132F GLY* 2.9 20.4 + - - -
133F ASP 3.9 3.5 + - - +
134F PRO* 3.7 27.5 - - - +
137F ALA* 4.0 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 130 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F ASP* 2.8 32.4 + - - +
127F ASP* 3.8 18.1 - - - +
128F SER 3.3 0.2 - - - -
129F ASP* 1.3 72.9 - - + +
131F ALA* 1.3 59.5 + - - +
132F GLY* 3.3 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 131 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F ALA* 3.3 26.1 - - + +
17F THR* 4.2 19.3 - - + -
18F VAL* 3.8 22.0 - - + -
127F ASP 3.1 17.1 + - - +
128F SER 3.6 6.1 - - - +
129F ASP 3.1 0.6 - - - -
130F GLU* 1.3 75.4 - - - +
132F GLY* 1.3 57.5 + - - +
133F ASP 3.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il