Contacts of the helix formed by residues 103 - 127 (chain F) in PDB entry 5SV1
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 ASP 103 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F SER* 3.3 16.8 + - - +
102F ASP* 1.3 74.7 - - - +
104F ASN* 1.3 62.3 + - - +
105F GLU* 3.1 29.6 + - - +
106F GLY* 3.1 19.8 + - - +
107F ILE* 3.5 21.0 + - - +
110F ARG* 5.1 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 104 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F SER 5.1 3.3 - - - +
102F ASP 3.4 9.3 + - - +
103F ASP* 1.3 71.0 + - - +
105F GLU* 1.3 66.7 + - - +
106F GLY 3.0 2.9 + - - -
107F ILE* 3.2 11.9 + - - +
108F MLY 3.2 46.9 + - - +
224F LEU* 3.4 48.3 + - + +
225F ASP* 5.2 1.4 + - - +
227F GLU* 5.8 2.0 + - - +
228F ALA* 4.0 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 105 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F ASP* 3.1 15.2 + - - +
104F ASN* 1.3 77.9 - - - +
106F GLY* 1.3 59.8 + - - +
108F MLY 3.9 20.8 - - - +
109F GLU* 3.2 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 106 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F ASP* 3.1 24.7 + - - -
104F ASN 3.0 1.0 - - - -
105F GLU* 1.3 74.7 - - - +
107F ILE* 1.3 67.4 + - - +
109F GLU* 3.0 24.1 + - - +
110F ARG* 3.1 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 107 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F GLU* 4.4 7.1 - - + +
95F LEU* 4.1 21.5 - - + +
98F SER* 3.6 35.4 - - - +
101F SER* 5.1 7.4 - - - +
103F ASP 3.5 14.5 + - - +
104F ASN* 3.2 18.2 + - - +
106F GLY* 1.3 71.0 - - - +
108F MLY 1.3 65.6 + - - +
110F ARG* 3.0 19.2 + - - +
111F THR* 2.9 22.1 + - - +
220F GLN* 3.4 25.1 - - - +
224F LEU* 3.9 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MLY 108 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104F ASN* 3.2 20.4 + - - +
105F GLU* 3.9 30.1 - - - +
107F ILE* 1.3 76.2 + - - +
109F GLU* 1.3 67.8 + - + +
111F THR* 3.0 13.4 + - - -
112F SER* 3.0 16.2 + - - +
217F LEU* 5.3 0.2 - - - +
220F GLN* 4.6 8.7 - - - +
221F SER* 3.4 41.7 - - - +
224F LEU* 4.4 18.6 - - + -
225F ASP* 2.9 31.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 109 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F GLU* 3.2 39.3 + - + +
106F GLY* 3.0 12.9 + - - +
108F MLY 1.3 79.8 + - + +
110F ARG* 1.3 67.1 + - + +
112F SER* 3.0 6.2 + - - -
113F PHE* 3.0 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 110 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F GLU* 3.3 27.3 + - - +
98F SER* 2.8 28.9 + - - -
101F SER* 4.8 11.9 + - - -
103F ASP* 5.1 2.2 + - - +
106F GLY* 3.1 22.6 + - - +
107F ILE* 3.0 33.9 + - - +
109F GLU* 1.3 78.5 - - + +
111F THR* 1.3 63.4 + - - +
113F PHE* 3.0 12.2 + - + +
114F ARG* 2.9 26.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 111 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F ALA* 3.9 26.6 + - + -
94F GLU* 3.7 18.4 - - - +
107F ILE 2.9 9.9 + - - -
108F MLY 3.0 5.6 + - - -
110F ARG* 1.3 74.2 - - - +
112F SER* 1.3 65.8 + - - +
114F ARG* 3.0 7.5 + - + +
115F LEU* 2.7 26.3 + - + +
217F LEU* 3.6 15.7 - - + -
220F GLN* 2.9 43.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 112 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108F MLY 3.0 11.6 + - - +
109F GLU* 3.0 10.1 + - - -
111F THR* 1.3 74.9 - - - +
113F PHE* 1.3 66.2 + - - +
115F LEU 3.0 0.9 + - - +
116F GLU* 2.9 34.5 + - - +
217F LEU* 3.3 35.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109F GLU 3.0 12.2 + - - +
110F ARG* 3.3 14.6 - - + +
112F SER* 1.3 75.3 - - - +
114F ARG* 1.3 66.3 + - + +
116F GLU* 4.5 1.9 - - - +
117F ARG* 3.1 57.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 114 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F GLU* 2.3 64.6 + - + +
93F ASN* 3.2 23.0 + - - +
94F GLU* 3.2 36.3 + - - +
97F LEU* 4.5 5.1 - - - +
110F ARG* 2.9 18.6 + - + +
111F THR* 3.6 5.7 - - + +
113F PHE* 1.3 77.1 - - + +
115F LEU* 1.3 57.5 + - + +
117F ARG* 2.9 8.5 + - - +
118F ARG* 2.7 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F LEU* 3.7 43.3 - - + +
90F GLU* 3.9 20.0 - - + -
91F ALA* 4.5 1.8 - - + +
111F THR* 2.7 29.4 + - + +
112F SER* 4.0 1.6 - - - +
114F ARG* 1.3 73.9 - - + +
116F GLU* 1.3 65.5 + - - +
118F ARG* 2.9 11.7 + - + +
119F VAL* 3.0 17.8 + - - +
213F ALA* 4.2 13.0 - - + +
216F VAL* 3.8 27.8 - - + -
217F LEU* 3.7 32.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
112F SER* 2.9 30.6 + - - +
113F PHE* 4.5 2.2 - - - +
115F LEU* 1.3 71.3 - - - +
117F ARG* 1.3 65.3 + - - +
119F VAL* 3.0 25.9 + - - +
120F ALA* 3.1 10.4 + - - +
210F GLY* 5.7 2.6 - - - +
213F ALA* 4.8 7.4 - - - +
217F LEU* 4.4 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 117 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F PHE* 3.1 49.4 + - + +
114F ARG* 2.9 6.6 + - - +
116F GLU* 1.3 77.2 - - - +
118F ARG* 1.3 67.6 + - - +
120F ALA* 3.0 19.9 + - + +
121F ALA* 3.2 11.3 + - + +
124F ARG* 5.3 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 118 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F HIS* 6.3 3.8 - - + -
87F LEU* 4.7 15.7 - - + -
90F GLU* 3.3 38.5 + - + +
114F ARG 2.7 16.5 + - - +
115F LEU* 3.4 11.0 - - - +
117F ARG* 1.3 74.6 - - - +
119F VAL* 1.3 64.2 + - - +
121F ALA* 3.0 24.1 + - + +
122F VAL* 3.2 17.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 119 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F LEU* 4.9 3.8 - - + +
115F LEU 3.0 16.5 + - - +
116F GLU* 3.2 15.3 - - - +
118F ARG* 1.3 76.0 - - - +
120F ALA* 1.3 66.5 + - - +
122F VAL* 3.0 19.0 + - - +
123F GLY* 3.2 8.0 + - - -
206F LYS* 4.8 26.0 - - + +
209F LEU* 3.6 37.5 - - + +
210F GLY* 5.0 4.0 - - - +
213F ALA* 4.1 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 120 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F GLU 3.1 5.3 + - - +
117F ARG* 3.0 15.9 + - + +
119F VAL* 1.3 79.4 - - - +
121F ALA* 1.3 63.1 + - - +
123F GLY* 3.0 13.7 + - - -
124F ARG* 3.2 20.4 + - - +
206F LYS* 5.2 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 121 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F ARG* 3.2 7.1 + - + +
118F ARG* 3.0 20.0 + - + +
120F ALA* 1.3 78.3 - - - +
122F VAL* 1.3 65.3 + - + +
124F ARG* 2.9 47.7 + - - +
125F GLN* 3.1 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 122 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F LEU* 4.5 19.1 - - + -
118F ARG* 3.2 15.0 + - + +
119F VAL 3.0 9.9 + - - +
121F ALA* 1.3 74.4 - - + +
123F GLY* 1.3 65.8 + - - +
125F GLN* 2.9 24.7 + - + +
126F MET* 3.0 17.5 + - + +
205F PHE* 4.1 21.8 - - + -
206F LYS* 6.3 2.0 - - + -
209F LEU* 3.7 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 123 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F VAL 3.2 4.8 + - - -
120F ALA 3.0 8.8 + - - -
122F VAL* 1.3 78.9 - - - +
124F ARG* 1.3 62.9 + - - +
126F MET* 2.9 20.5 + - - +
127F GLY* 3.2 10.4 + - - -
202F ILE* 5.0 4.2 - - - +
206F LYS* 3.7 31.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 124 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F ARG* 5.3 6.5 + - - +
120F ALA* 3.2 14.3 + - - +
121F ALA* 2.9 41.1 + - - +
123F GLY* 1.3 75.5 - - - +
125F GLN* 1.3 61.6 + - + +
127F GLY* 4.0 1.9 + - - -
128F ARG* 3.9 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 125 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F GLU* 5.6 0.9 - - - +
121F ALA* 3.1 17.7 + - - +
122F VAL* 2.9 20.3 + - + +
124F ARG* 1.3 80.2 - - + +
126F MET* 1.3 71.8 + - + +
127F GLY 3.5 0.2 - - - -
128F ARG* 3.9 13.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 126 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F LYS* 5.7 5.5 - - - +
47F GLU* 4.6 13.7 - - + +
48F PHE* 4.8 16.8 - - - -
51F GLN* 3.5 26.0 - - - +
122F VAL* 3.3 19.3 - - + +
123F GLY* 2.9 8.8 + - - +
125F GLN* 1.3 86.0 - - + +
127F GLY* 1.3 60.9 + - - +
128F ARG 3.3 4.6 + - - +
130F ASN* 4.7 4.5 + - - -
202F ILE* 3.5 27.5 - - + +
205F PHE* 3.2 39.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 127 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F GLY 3.2 9.9 + - - -
124F ARG* 4.0 3.7 + - - -
125F GLN 3.5 0.2 - - - -
126F MET* 1.3 77.1 - - - +
128F ARG* 1.3 64.1 + - - +
129F GLY 3.3 0.9 + - - -
130F ASN* 3.1 27.3 + - - +
131F GLY 4.2 2.9 + - - -
202F ILE* 3.8 11.6 - - - +
----------------------------------------------------------
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