Contacts of the helix formed by residues 113 - 139 (chain G) in PDB entry 1F33
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 ASN 113 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G ARG 3.5 8.2 - - - +
56G GLY* 5.1 4.7 - - - -
57G ALA 5.6 0.9 + - - -
112G HIS* 1.3 81.8 - - - +
114G VAL* 1.3 64.9 + - - +
115G GLN* 2.7 48.1 - - - +
116G ASP* 3.2 32.7 + - - +
117G HIS* 3.2 12.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 114 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G MET* 4.4 12.8 - - + -
55G ARG 3.0 37.1 + - - +
56G GLY 3.8 5.4 - - - +
57G ALA 3.4 27.4 - - - +
58G ASN* 4.4 1.6 - - + +
59G PHE* 4.2 11.0 - - - -
62G VAL* 4.3 23.8 - - + -
112G HIS 4.2 1.3 - - - -
113G ASN* 1.3 74.2 - - - +
115G GLN* 1.3 62.8 + - + +
117G HIS* 3.2 4.4 + - - +
118G LEU* 2.8 46.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 115 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G ALA* 5.3 4.4 + - + +
58G ASN* 5.9 3.0 - - - +
113G ASN* 2.7 23.3 - - - +
114G VAL* 1.3 78.1 - - + +
116G ASP* 1.3 61.3 + - - +
118G LEU* 3.4 14.2 - - - +
119G LYS* 3.0 42.2 + - - +
165G ASN 3.2 21.2 + - - -
166G ILE* 3.3 13.2 - - - +
167G GLU* 2.7 54.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 116 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G ILE* 4.1 28.7 - - + +
112G HIS 4.8 0.5 + - - -
113G ASN* 3.2 31.3 + - - +
115G GLN* 1.3 79.2 - - - +
117G HIS* 1.3 62.4 + - - +
119G LYS* 3.2 15.8 + - - +
120G GLU* 2.9 26.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 117 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G GLN* 4.5 5.2 - - - -
50G ALA* 3.4 24.2 - - + -
53G ASN* 3.4 16.7 + - + -
54G MET* 3.7 27.8 - - + -
107G TYR* 2.6 33.0 + + - +
108G PRO 5.0 1.3 - - - -
111G ILE* 3.3 39.1 + - + +
112G HIS 3.4 24.0 - - - -
113G ASN 3.2 8.7 + - - -
114G VAL 3.6 5.6 - - - +
116G ASP* 1.3 78.3 - - - +
118G LEU* 1.3 55.0 + - - +
120G GLU 3.2 0.3 + - - -
121G LEU* 2.7 40.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G MET* 5.0 0.9 - - + -
58G ASN* 5.8 0.4 - - - +
62G VAL* 3.8 28.7 - - + -
65G MET* 5.1 4.3 - - + -
66G LEU* 5.5 0.4 - - + -
114G VAL* 2.8 33.6 + - + +
115G GLN* 3.4 15.7 - - - +
116G ASP 3.2 0.2 - - - -
117G HIS* 1.3 76.8 - - - +
119G LYS* 1.3 58.0 + - - +
121G LEU* 3.6 9.6 - - + +
122G ALA* 2.8 25.6 + - - +
162G ILE* 3.3 40.2 - - + +
165G ASN* 3.7 34.1 - - + +
166G ILE* 3.9 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 119 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115G GLN* 3.0 34.6 + - - +
116G ASP* 3.7 12.7 + - - +
118G LEU* 1.3 72.7 - - - +
120G GLU* 1.3 67.9 + - + +
122G ALA* 3.3 3.7 + - - +
123G ASP* 3.1 30.0 + - - +
166G ILE* 4.0 37.0 - - + -
167G GLU 5.7 0.7 - - - -
18K ARG* 4.5 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 120 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107G TYR* 3.5 22.0 - - + +
108G PRO* 3.9 10.8 - - + +
111G ILE* 3.7 21.6 - - + +
116G ASP* 2.9 20.3 + - + +
117G HIS 3.6 2.5 - - - +
119G LYS* 1.3 77.5 - - - +
121G LEU* 1.3 61.1 + - - +
123G ASP* 3.5 13.4 + - - +
124G ARG* 2.9 52.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G ILE* 3.8 27.6 - - + +
47G THR* 4.3 8.3 - - - -
50G ALA* 3.6 32.3 - - + -
54G MET* 4.7 0.7 - - + -
66G LEU* 3.7 32.5 - - + -
107G TYR* 4.0 2.9 - - + +
117G HIS 2.7 29.4 + - - +
118G LEU* 3.6 12.6 - - + +
120G GLU* 1.3 72.0 - - - +
122G ALA* 1.3 66.3 + - - +
124G ARG* 3.1 3.8 + - - -
125G TYR* 2.8 39.4 + - + -
162G ILE* 4.1 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 122 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G LEU 2.8 17.6 + - - +
119G LYS* 3.3 8.0 + - - +
121G LEU* 1.3 76.2 - - - +
123G ASP* 1.3 57.5 + - - +
125G TYR* 4.5 0.9 - - - -
126G ALA* 2.9 31.7 + - - +
159G LEU* 3.4 10.9 - - - +
162G ILE* 3.8 15.7 - - + +
163G GLU* 4.3 6.1 - - + -
166G ILE* 4.2 4.7 - - + -
18K ARG* 3.5 31.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 123 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119G LYS* 3.1 13.4 + - - +
120G GLU* 3.6 16.4 - - - +
121G LEU 3.1 0.6 - - - -
122G ALA* 1.3 78.7 - - - +
124G ARG* 1.3 69.3 + - - +
126G ALA* 3.3 4.7 + - - +
127G ILE* 3.1 29.8 + - + +
18K ARG* 2.9 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 124 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G LEU* 3.8 17.7 - - + -
46G ILE* 4.1 12.8 - - + +
104G LEU* 3.7 18.5 - - + +
105G LYS* 2.9 54.8 + - - +
106G SER 3.6 4.2 + - - -
107G TYR* 2.9 36.1 - - - +
108G PRO* 3.6 14.8 - - - +
120G GLU* 2.9 40.7 + - - +
121G LEU* 3.1 6.8 + - - +
123G ASP* 1.3 77.8 - - - +
125G TYR* 1.3 65.9 + - + +
127G ILE* 3.3 8.6 + - - +
128G VAL* 3.1 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 125 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G LEU* 3.5 35.0 - - + -
47G THR* 2.6 38.8 + - + +
66G LEU* 5.5 0.2 - - + -
69G PHE* 3.6 16.9 - + - +
73G LEU* 3.5 11.5 - - + +
121G LEU* 2.8 41.2 + - + +
122G ALA 3.9 3.1 - - - +
124G ARG* 1.3 73.7 - - - +
126G ALA* 1.3 53.7 + - - +
128G VAL* 3.3 1.4 + - - +
129G ALA* 2.6 38.8 + - - +
155G LEU* 4.2 9.9 - - + +
158G PHE* 3.7 36.1 - + + -
159G LEU* 4.1 13.0 - - + -
162G ILE* 3.5 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 126 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122G ALA 2.9 20.0 + - - +
123G ASP* 3.4 6.1 - - - +
125G TYR* 1.3 77.8 - - - +
127G ILE* 1.3 58.8 + - + +
130G ASN* 2.7 45.6 + - - +
159G LEU* 3.9 14.8 - - + +
18K ARG* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 127 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G GLN* 4.3 10.5 - - - +
103G PRO* 4.4 17.7 - - + +
104G LEU* 3.8 24.0 - - + -
105G LYS* 5.5 3.4 - - + +
123G ASP* 3.1 18.5 + - + +
124G ARG* 3.3 13.0 + - - +
126G ALA* 1.3 76.3 - - + +
128G VAL* 1.3 62.1 + - - +
130G ASN* 4.0 3.5 - - - +
131G ASP* 3.0 27.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 128 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G GLN* 3.4 35.9 - - + +
40G PHE* 3.6 28.7 - - + -
43G LEU* 4.0 17.3 - - + -
104G LEU* 3.8 17.5 - - + -
124G ARG 3.1 14.6 + - - +
125G TYR 3.9 2.2 - - - +
127G ILE* 1.3 72.8 - - - +
129G ALA* 1.3 66.4 + - - +
131G ASP* 3.8 0.2 - - - +
132G VAL* 2.9 24.4 + - - +
155G LEU* 3.6 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G TYR 2.6 25.9 + - - +
126G ALA* 3.7 5.4 - - - +
128G VAL* 1.3 74.1 - - - +
130G ASN* 1.3 63.3 + - - +
132G VAL* 3.2 10.1 - - - +
133G ARG* 3.0 30.9 + - - +
152G SER* 4.8 0.2 + - - -
155G LEU* 3.9 21.7 - - + +
156G ASP* 3.7 17.4 - - - +
159G LEU* 4.4 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 130 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126G ALA* 2.7 32.2 + - - +
127G ILE* 4.1 3.7 - - - +
129G ALA* 1.3 74.9 - - - +
131G ASP* 1.3 62.1 + - - +
133G ARG* 2.4 36.7 + - - +
134G LYS* 3.3 33.9 + - - +
18K ARG 3.2 20.0 + - - -
19K ASN* 3.7 4.0 - - - -
20K ASP* 2.9 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 131 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G ARG* 2.8 41.1 + - - -
36G GLN* 3.7 2.3 - - - +
39G GLN* 3.0 25.2 + - - +
103G PRO* 5.4 0.3 - - - +
127G ILE* 3.0 21.4 + - + +
128G VAL 3.8 2.5 - - - +
130G ASN* 1.3 74.1 - - - +
132G VAL* 1.3 66.8 + - - +
134G LYS* 3.0 12.2 + - - +
135G ALA 3.0 15.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 132 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G GLN* 3.6 28.3 - - - +
40G PHE* 4.3 19.1 - - + -
128G VAL 2.9 25.2 + - - +
129G ALA* 3.2 11.7 - - - +
131G ASP* 1.3 74.9 + - - +
133G ARG* 1.3 66.8 + - - +
135G ALA* 3.2 9.0 + - - +
136G ILE* 3.4 13.5 + - - +
148G LEU* 3.9 34.0 - - + +
151G ALA* 4.7 2.0 - - + -
152G SER* 4.0 20.6 - - - +
155G LEU* 4.8 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 133 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129G ALA* 3.0 19.3 + - - +
130G ASN* 2.4 34.5 + - - +
131G ASP 3.1 0.2 - - - -
132G VAL* 1.3 76.8 - - - +
134G LYS* 1.3 64.4 + - + +
136G ILE* 3.4 24.0 - - + +
137G GLY 4.4 0.3 + - - -
152G SER* 3.7 14.6 - - - +
156G ASP* 2.6 42.4 + - - -
19K ASN* 3.1 21.3 + - - +
20K ASP* 3.1 15.5 + - - -
21K VAL* 3.4 21.3 - - - +
83K ARG* 4.2 5.2 - - - +
141K ASP* 4.3 7.2 - - - +
142K ASP* 4.3 8.5 - - + +
143K ASP* 3.9 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 134 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G ASN* 3.3 23.1 + - - +
131G ASP* 3.0 10.5 + - - +
133G ARG* 1.3 76.7 - - + +
135G ALA* 1.3 65.8 + - - +
136G ILE 3.0 3.6 + - - -
137G GLY* 3.1 12.0 + - - -
138G GLU* 3.2 14.0 + - - +
20K ASP* 2.5 40.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 135 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G LEU* 3.9 19.8 - - + +
35G ARG* 4.3 3.6 - - - +
36G GLN* 3.5 23.8 - - - +
131G ASP 3.0 8.7 + - - +
132G VAL* 3.2 10.3 + - - +
134G LYS* 1.3 76.4 - - - +
136G ILE* 1.3 56.0 + - - +
138G GLU* 3.1 14.5 + - - +
139G ALA* 2.8 30.8 + - - +
148G LEU* 3.8 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 136 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G VAL 3.5 9.0 - - - +
133G ARG* 3.4 19.7 - - + +
134G LYS 3.0 0.8 - - - -
135G ALA* 1.3 77.2 - - - +
137G GLY* 1.3 62.8 + - - +
139G ALA* 3.2 21.0 + - - +
145G ALA* 4.0 14.2 - - + +
148G LEU* 3.9 21.5 - - + +
149G THR* 3.5 38.6 - - - +
152G SER* 3.7 11.9 - - - +
142K ASP* 3.8 28.0 - - + +
143K ASP* 3.6 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 137 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G ARG 4.4 0.8 + - - -
134G LYS 3.1 7.6 + - - -
136G ILE* 1.3 81.7 - - - +
138G GLU* 1.3 59.4 + - - +
139G ALA 3.5 5.1 + - - +
142K ASP* 4.4 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G LEU* 3.6 30.6 - - + +
35G ARG* 3.9 12.4 + - - -
134G LYS* 3.2 13.4 + - - +
135G ALA* 3.1 12.9 + - - +
137G GLY* 1.3 75.7 - - - +
139G ALA* 1.3 60.6 + - - +
140G LYS* 3.5 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G LEU* 4.0 15.5 - - + -
135G ALA 2.8 11.3 + - - +
136G ILE 3.2 17.6 + - - +
137G GLY 4.2 4.2 - - - +
138G GLU* 1.3 75.3 - - - +
140G LYS* 1.3 63.9 + - - +
141G ASP 4.4 1.3 - - - +
144G THR* 4.4 6.3 - - + -
145G ALA* 3.9 31.6 - - - +
148G LEU* 4.2 5.6 - - + -
----------------------------------------------------------
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