Contacts of the helix formed by residues 25 - 38 (chain C) in PDB entry 3VJR
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 25 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C LEU 3.7 3.6 - - - -
13C ALA* 3.4 11.0 - - + +
14C ASN* 2.8 48.5 + - - +
19C TYR 3.2 22.5 + - - +
20C ALA* 3.8 20.4 + - - +
22C THR* 2.9 16.5 + - - +
24C HIS* 1.3 80.2 - - - +
26C ALA* 1.3 62.2 + - - +
27C GLY 3.3 3.1 - - - -
28C ALA* 2.9 18.6 + - + +
29C TRP* 3.0 16.5 + - + +
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Residues in contact with ALA 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C THR 4.0 0.8 + - - -
23C ARG* 3.0 19.6 + - - +
24C HIS 3.4 1.4 - - - -
25C ASN* 1.3 76.1 - - - +
27C GLY* 1.3 63.0 + - - +
29C TRP* 3.0 18.8 + - + +
30C PHE* 2.9 22.3 + - - +
97C ASP* 4.1 13.0 - - + +
138C ILE* 4.0 24.7 - - + -
140C ILE* 4.6 6.5 - - + -
165C ILE* 4.6 9.9 - - + -
169C ILE* 3.8 3.5 - - - +
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Residues in contact with GLY 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLY* 3.3 14.1 - - - -
12C LEU 3.8 5.6 + - - -
24C HIS 5.1 0.4 + - - -
25C ASN 3.3 1.2 - - - -
26C ALA* 1.3 76.9 - - - +
28C ALA* 1.3 56.1 + - - +
30C PHE* 3.1 6.1 + - - +
31C VAL* 3.1 22.5 + - - +
95C ALA* 3.2 35.2 - - - +
96C HIS* 3.9 7.1 - - - +
97C ASP* 4.2 0.8 + - - +
138C ILE* 4.0 3.7 - - - +
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Residues in contact with ALA 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C GLY* 3.6 7.6 - - - +
12C LEU 3.3 5.2 + - - +
13C ALA* 3.8 18.2 - - + -
25C ASN* 2.9 14.5 + - + +
27C GLY* 1.3 72.0 - - - +
29C TRP* 1.3 58.3 + - + +
30C PHE 3.0 1.3 - - - -
31C VAL* 4.1 0.8 - - - +
32C ASP* 2.7 47.5 + - - +
66C VAL* 3.8 28.0 - - + -
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Residues in contact with TRP 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ALA 2.9 22.4 + - - -
21C ALA* 3.7 26.9 - - + -
22C THR 4.0 8.1 - - - -
23C ARG* 5.6 1.3 - - - -
25C ASN* 3.0 26.6 + - + +
26C ALA* 3.3 12.3 - - + +
28C ALA* 1.3 76.2 - - + +
30C PHE* 1.3 57.9 + - - +
32C ASP* 3.4 8.6 + - - +
33C LEU* 2.9 30.1 + - - +
157C PRO* 4.2 21.5 - - + -
162C GLN* 4.2 14.8 - - + -
165C ILE* 3.9 33.9 - - + -
166C ASP* 4.0 27.1 - - - +
169C ILE* 3.8 11.8 - - + +
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Residues in contact with PHE 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ILE* 4.0 15.9 - - + -
26C ALA 2.9 11.0 + - - +
27C GLY 3.3 7.2 - - - +
28C ALA 3.0 0.2 - - - -
29C TRP* 1.3 76.7 - - - +
31C VAL* 1.3 62.5 + - + +
33C LEU* 3.1 5.4 + - - +
34C LEU* 2.9 53.2 + - + +
93C LEU* 5.1 3.4 - - + -
95C ALA* 3.5 18.6 - - + -
136C LEU* 3.5 25.1 - - + -
138C ILE* 3.8 12.8 - - + -
169C ILE* 3.8 26.9 - - + +
172C ALA* 3.7 2.2 - - + -
173C ALA* 3.4 30.9 - - + +
176C THR* 3.4 21.8 - - + -
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Residues in contact with VAL 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ILE* 4.1 14.4 - - + +
10C VAL 3.7 6.3 - - - +
11C GLY* 3.4 29.8 - - - +
27C GLY 3.1 7.1 + - - +
30C PHE* 1.3 87.5 - - + +
32C ASP* 1.3 57.4 + - - +
34C LEU* 3.2 5.5 + - + +
35C ALA* 2.8 29.1 + - - +
42C LEU* 4.4 5.4 - - + -
64C LEU* 4.0 30.3 - - + -
65C LEU 4.4 4.3 - - - +
66C VAL* 3.7 25.8 - - + -
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Residues in contact with ASP 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ALA* 2.7 33.8 + - - +
29C TRP* 3.7 7.7 + - - +
31C VAL* 1.3 73.3 - - - +
33C LEU* 1.3 61.8 + - - +
35C ALA* 3.4 6.4 + - - +
36C GLU* 3.2 21.8 + - - +
42C LEU* 3.2 24.1 - - - +
66C VAL* 4.0 6.9 - - - +
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Residues in contact with LEU 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C TRP 2.9 13.8 + - - +
30C PHE 3.1 8.3 + - - +
32C ASP* 1.3 75.4 - - - +
34C LEU* 1.3 58.3 + - - +
36C GLU* 3.2 23.0 + - - +
37C ARG* 2.9 41.1 + - + +
166C ASP* 5.4 2.9 - - - +
169C ILE* 3.8 24.2 - - + -
170C ASP* 3.8 25.4 - - + +
173C ALA* 4.1 14.6 - - + -
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Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ILE* 4.0 26.2 - - + -
30C PHE* 2.9 41.5 + - + +
31C VAL* 3.6 6.7 - - - +
33C LEU* 1.3 77.2 - - - +
35C ALA* 1.3 55.8 + - - +
37C ARG* 3.3 5.0 + - + +
38C LEU* 2.9 57.6 + - + +
57C LEU* 5.7 0.9 - - + -
64C LEU* 4.3 13.7 - - + -
173C ALA* 4.1 32.1 - - + +
176C THR* 4.4 7.4 - - + -
177C GLU* 4.4 12.1 - - + +
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Residues in contact with ALA 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C VAL 2.8 19.7 + - - +
32C ASP* 3.7 6.5 - - - +
34C LEU* 1.3 74.0 - - - +
36C GLU* 1.3 56.8 + - - +
38C LEU* 3.6 1.5 + - - -
39C ARG 3.0 5.9 + - - -
40C ALA* 2.8 49.5 + - - +
41C PRO* 4.1 3.8 - - + -
42C LEU* 3.9 18.4 - - + +
64C LEU* 3.7 19.4 - - + +
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Residues in contact with GLU 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ASP 3.2 9.9 + - - +
33C LEU* 3.2 26.3 + - - +
35C ALA* 1.3 77.3 - - - +
37C ARG* 1.3 66.4 + - - +
39C ARG* 2.9 28.6 + - - +
41C PRO* 5.9 1.8 - - - -
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Residues in contact with ARG 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C LEU* 2.9 36.5 + - + +
34C LEU* 3.3 5.8 + - - +
36C GLU* 1.3 73.6 - - - +
38C LEU* 1.3 62.6 + - + +
39C ARG* 3.2 8.2 + - - +
170C ASP* 4.5 3.8 + - - -
173C ALA* 3.8 26.5 - - - +
174C ARG* 3.4 54.5 - - - +
177C GLU* 2.8 39.3 + - - +
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Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LEU* 2.9 42.4 + - + +
35C ALA* 4.3 1.8 - - - +
37C ARG* 1.3 78.3 - - - +
39C ARG* 1.3 71.1 + - - +
40C ALA* 3.3 3.4 + - - +
55C VAL* 3.9 41.8 - - + +
56C THR 5.4 0.7 - - - +
57C LEU* 3.8 31.4 - - + -
64C LEU* 5.0 2.5 - - + -
177C GLU* 4.0 25.8 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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