Contacts of the helix formed by residues 35 - 55 (chain V) in PDB entry 6GYK
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 SER 35 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27V ILE* 5.3 0.6 - - - +
34V ALA* 1.3 77.1 - - - +
36V LEU* 1.3 62.5 + - - -
37V ALA* 3.2 5.4 - - - +
38V MET* 3.1 37.3 + - - +
39V ARG* 3.4 5.2 + - - +
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Residues in contact with LEU 36 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21U VAL* 5.3 2.7 - - + -
24U ASP* 3.8 34.3 - - + +
25U PHE* 3.6 38.6 - - + -
28U ALA* 5.2 8.3 - - + -
30U ILE* 5.9 2.0 - - + -
32V ILE* 6.0 3.6 - - + -
33V GLU* 4.2 17.9 - - + +
34V ALA 2.5 16.1 + - - +
35V SER* 1.3 69.4 - - - +
37V ALA* 1.3 60.7 + - - +
39V ARG* 3.0 19.6 + - + +
40V VAL* 2.9 37.1 + - + +
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Residues in contact with ALA 37 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23V LEU* 3.4 35.4 - - + +
24V ASP* 6.0 0.4 - - - +
27V ILE* 3.8 28.3 - - + -
32V ILE* 6.4 1.1 - - + -
33V GLU 4.7 1.8 + - - +
34V ALA 4.5 1.0 - - - -
35V SER 3.2 3.0 - - - +
36V LEU* 1.3 78.4 - - - +
38V MET* 1.3 56.9 + - - +
40V VAL* 3.2 6.6 + - - -
41V LEU* 2.9 32.3 + - + +
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Residues in contact with MET 38 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11V ARG* 5.3 5.4 - - - +
35V SER* 3.1 25.2 + - - +
37V ALA* 1.3 75.9 - - - +
39V ARG* 1.3 59.8 + - - +
41V LEU* 3.0 16.9 + - + +
42V GLU* 2.9 46.6 + - + +
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Residues in contact with ARG 39 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21U VAL* 5.7 3.8 - - + -
24U ASP* 3.7 33.2 + - - +
35V SER 3.4 3.5 + - - +
36V LEU* 3.0 26.7 + - + +
38V MET* 1.3 79.7 - - - +
40V VAL* 1.3 57.7 + - - +
42V GLU* 3.3 22.4 + - - +
43V THR* 2.9 42.0 + - - +
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Residues in contact with VAL 40 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17U VAL* 4.3 20.1 - - + +
21U VAL* 4.3 24.7 - - + -
25U PHE* 5.7 1.3 - - + -
38U LEU* 5.4 9.2 - - + -
42U TRP* 6.0 0.2 - - + -
19V LEU* 4.0 23.6 - - + -
23V LEU* 4.0 20.6 - - + -
36V LEU* 2.9 20.4 + - + +
37V ALA* 3.2 13.2 + - - +
39V ARG* 1.3 76.3 - - - +
41V LEU* 1.3 58.0 + - - +
43V THR* 3.9 5.5 - - - -
44V PHE* 2.9 28.1 + - - +
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Residues in contact with LEU 41 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11V ARG* 3.4 44.1 + - + +
16V GLY 5.5 0.2 - - - +
19V LEU* 4.3 13.2 - - + -
20V VAL* 4.1 25.4 - - + -
23V LEU* 3.9 18.6 - - + -
37V ALA* 2.9 20.0 + - + +
38V MET* 3.0 17.0 + - + +
40V VAL* 1.3 75.2 - - - +
42V GLU* 1.3 59.9 + - - +
44V PHE* 3.3 6.9 + - + +
45V ASP* 2.9 32.6 + - - +
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Residues in contact with GLU 42 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6V TYR* 5.4 1.0 - - - +
8V GLU* 5.7 1.3 - - - +
11V ARG* 4.3 9.6 - - - +
38V MET* 2.9 36.5 + - + +
39V ARG* 3.8 25.9 + - - +
41V LEU* 1.3 75.2 - - - +
43V THR* 1.3 65.1 + - - +
45V ASP* 3.0 10.6 + - - +
46V LYS* 2.9 23.6 + - - +
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Residues in contact with THR 43 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17U VAL* 4.3 14.1 - - + -
20U GLU* 3.4 34.2 - - + +
21U VAL* 4.7 10.2 - - + +
39V ARG* 2.9 28.0 + - - +
40V VAL* 4.0 7.0 - - - -
42V GLU* 1.3 76.2 - - - +
44V PHE* 1.3 57.4 + - - +
46V LYS* 3.4 13.5 + - - +
47V VAL* 2.9 37.7 + - + +
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Residues in contact with PHE 44 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13U ILE* 4.6 12.8 - - + -
17U VAL* 4.9 5.4 - - + +
42U TRP* 5.0 3.6 - + - -
10V TYR* 3.8 24.7 - - + -
11V ARG* 4.3 8.5 - - + -
15V ILE* 4.0 29.8 - - + -
16V GLY* 3.6 29.4 - - - -
19V LEU* 3.5 26.5 - - + -
40V VAL 2.9 21.2 + - - +
41V LEU* 3.4 8.7 - - + +
42V GLU 3.1 0.4 - - - -
43V THR* 1.3 76.8 - - - +
45V ASP* 1.3 67.7 + - - +
47V VAL* 4.6 3.1 - - - -
48V VAL* 2.9 61.0 + - + +
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Residues in contact with ASP 45 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6V TYR* 4.1 16.4 - - + +
7V TYR 3.5 23.3 - - - +
8V GLU* 3.5 8.2 - - - +
10V TYR* 4.7 7.8 - - - +
11V ARG* 2.9 52.9 + - - +
41V LEU 2.9 15.8 + - - +
42V GLU* 3.0 9.6 + - - +
44V PHE* 1.3 81.4 - - - +
46V LYS* 1.3 57.4 + - - +
48V VAL* 3.9 3.1 - - - +
49V ALA* 2.9 30.7 + - - +
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Residues in contact with LYS 46 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20U GLU* 3.9 25.0 + - - -
6V TYR* 3.6 42.1 - - + +
42V GLU 2.9 14.7 + - - +
43V THR* 3.8 13.2 + - - +
45V ASP* 1.3 78.7 - - - +
47V VAL* 1.3 59.5 + - - +
49V ALA* 3.3 0.3 + - - +
50V GLU* 2.9 48.3 + - - +
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Residues in contact with VAL 47 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12U ILE* 5.2 1.3 - - + +
13U ILE* 3.7 41.5 - - + +
16U SER* 4.2 20.2 - - - +
17U VAL* 4.3 10.1 - - + -
20U GLU* 4.5 7.0 - - - +
43V THR* 2.9 34.3 + - + +
44V PHE* 4.0 2.9 - - - +
46V LYS* 1.3 80.6 - - + +
48V VAL* 1.3 56.8 + - - +
50V GLU* 5.1 3.6 - - - -
51V THR* 2.4 43.7 + - - +
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Residues in contact with VAL 48 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13U ILE* 4.4 14.8 - - + -
266U VAL* 6.0 1.1 - - + -
10V TYR* 3.6 34.1 - - + -
15V ILE* 5.5 3.4 - - + -
44V PHE* 2.9 55.8 + - + +
45V ASP 4.1 2.5 - - - +
47V VAL* 1.3 74.4 - - + +
49V ALA* 1.3 59.5 + - - +
51V THR* 4.4 3.6 - - - -
52V LEU* 2.9 46.6 + - + +
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Residues in contact with ALA 49 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264U ASP* 5.6 0.7 - - - +
6V TYR* 3.8 23.1 - - + -
10V TYR* 4.3 15.9 - - + -
45V ASP 2.9 20.2 + - - +
46V LYS 3.3 4.2 + - - +
48V VAL* 1.3 77.4 - - - +
50V GLU* 1.3 57.7 + - + +
52V LEU* 3.8 1.6 - - - +
53V LYS* 2.9 32.5 + - - +
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Residues in contact with GLU 50 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6V TYR* 3.9 14.8 + - + +
46V LYS* 2.9 44.9 + - + +
47V VAL* 4.5 3.7 - - - +
49V ALA* 1.3 72.8 - - + +
51V THR* 1.3 58.4 + - - +
53V LYS* 3.3 16.9 + - - +
54V ASP* 2.9 41.2 + - - +
55V ASN* 4.2 0.4 + - - -
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Residues in contact with THR 51 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9U VAL* 3.6 33.2 - - + +
12U ILE* 5.3 10.9 - - + +
13U ILE* 4.4 6.5 - - + +
47V VAL* 2.4 38.5 + - - +
48V VAL* 4.1 3.4 - - - -
50V GLU* 1.3 77.3 - - - +
52V LEU* 1.3 60.5 + - + +
55V ASN* 2.6 61.7 + - + +
56V THR* 6.4 0.2 - - + -
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Residues in contact with LEU 52 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9U VAL* 5.6 5.2 - - + -
264U ASP* 2.9 24.0 - - + +
265U GLY* 4.1 20.4 - - - +
266U VAL* 4.3 8.3 - - + +
275U THR* 4.0 23.1 - - + -
10V TYR* 3.9 25.1 - - + +
48V VAL* 2.9 41.6 + - + +
49V ALA 4.2 1.8 - - - +
51V THR* 1.3 81.0 - - + +
53V LYS* 1.3 56.2 + - - +
54V ASP 3.5 0.2 - - - -
56V THR* 2.6 44.2 + - + +
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Residues in contact with LYS 53 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264U ASP* 3.4 18.6 - - + +
277U GLN* 3.9 15.7 + - - +
49V ALA 2.9 18.1 + - - +
50V GLU* 3.6 20.6 - - - +
51V THR 3.1 0.6 - - - -
52V LEU* 1.3 78.6 - - - +
54V ASP* 1.3 93.2 + - - +
56V THR* 4.5 1.2 + - - -
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Residues in contact with ASP 54 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277U GLN* 6.2 0.2 - - - -
50V GLU* 2.9 20.1 + - - +
53V LYS* 1.3 113.3 + - - +
55V ASN* 1.3 67.6 + - - +
56V THR 3.5 6.7 + - - +
57V GLN* 4.4 7.3 + - - -
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Residues in contact with ASN 55 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5U GLU* 3.4 12.3 - - - +
9U VAL* 4.1 17.2 - - + +
12U ILE* 4.8 16.3 - - - +
275U THR* 5.3 0.2 + - - -
50V GLU 4.2 0.4 + - - -
51V THR* 2.6 50.0 + - + +
54V ASP* 1.3 84.0 - - - +
56V THR* 1.3 65.4 + - - +
57V GLN* 4.0 10.3 - - - +
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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