Contacts of the strand formed by residues 5 - 17 (chain C) in PDB entry 2V1C
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 THR 5 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B ARG* 5.4 11.2 + - - +
3C SER* 3.5 24.1 + - - +
4C ARG* 1.3 80.7 - - - +
6C ALA* 1.3 62.6 + - - +
59C GLN* 3.8 27.2 + - - +
60C VAL 3.1 15.9 - - - -
61C TYR* 4.2 19.5 - - + +
72C LYS* 5.3 5.6 - - + -
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Residues in contact with ALA 6 (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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3C SER 5.6 1.8 - - - +
4C ARG 5.5 0.7 - - - +
5C THR* 1.3 76.4 - - - +
7C ASN* 1.3 70.8 + - - +
8C ARG* 3.9 10.3 + - + +
58C VAL 3.7 0.5 - - - +
59C GLN* 3.5 4.4 - - - -
60C VAL* 2.8 40.6 + - + +
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Residues in contact with ASN 7 (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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6C ALA* 1.3 75.3 - - - +
8C ARG* 1.3 68.6 + - - +
31C GLN* 5.4 2.8 + - - -
58C VAL 3.4 5.5 + - - +
59C GLN* 3.4 41.4 + - - +
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Residues in contact with ARG 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ALA* 3.9 13.6 + - + +
7C ASN* 1.3 78.7 - - - +
9C SER* 1.3 60.2 + - - +
27C LEU* 5.9 0.7 - - + -
29C THR* 2.9 41.4 + - + +
31C GLN* 3.7 38.4 + - - +
32C GLY* 4.2 2.2 - - - +
33C LYS* 4.4 10.5 + - - +
34C LEU* 3.9 36.4 - - + +
56C VAL 4.1 0.2 - - - +
57C GLY* 3.4 1.9 - - - -
58C VAL* 2.7 53.9 + - + +
60C VAL* 5.5 5.6 - - + -
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Residues in contact with SER 9 (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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8C ARG* 1.3 74.9 - - - +
10C GLY* 1.3 58.7 + - - +
27C LEU* 5.3 0.9 - - - -
29C THR* 3.3 10.7 - - - -
30C PRO* 3.2 30.3 - - - +
31C GLN* 4.8 4.8 + - - +
55C HIS* 4.2 10.4 + - - -
56C VAL 3.3 5.2 - - - -
77C GLU* 3.7 23.1 - - - -
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Residues in contact with GLY 10 (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 SER* 1.3 75.1 - - - +
11C ILE* 1.3 63.5 + - - -
27C LEU* 4.6 7.9 - - - +
28C LEU 3.1 13.5 - - - -
29C THR* 4.1 4.7 - - - -
54C HIS 3.8 0.2 - - - +
55C HIS* 3.4 7.6 + - - -
56C VAL* 2.8 36.7 + - - +
113C PHE* 4.1 10.3 - - - -
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Residues in contact with ILE 11 (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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10C GLY* 1.3 77.0 - - - +
12C VAL* 1.3 75.9 + - - +
13C ILE* 3.3 4.5 + - + +
27C LEU* 3.3 4.7 - - - -
28C LEU 2.7 35.0 + - - +
53C PHE* 3.8 20.4 - - - +
54C HIS 3.6 2.5 - - - -
55C HIS* 3.9 22.7 - - + +
113C PHE* 4.0 13.0 - - + -
116C PHE* 3.9 20.6 - - + -
117C ALA* 3.9 35.0 - - + -
120C LEU* 3.9 17.7 - - + -
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Residues in contact with VAL 12 (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 ILE* 1.3 73.0 - - - +
13C ILE* 1.3 58.9 + - - +
14C ARG 3.6 23.8 - - - +
15C ARG* 4.8 0.7 - - + -
25C VAL* 4.0 8.3 - - + -
26C THR 4.4 1.6 - - - +
27C LEU* 3.5 19.7 - - + -
50C LEU* 4.0 24.0 - - + +
51C ASN 3.3 31.2 - - - +
52C LEU* 3.6 4.7 - - + +
53C PHE* 2.6 32.7 + - - +
54C HIS* 3.2 16.1 + - + +
56C VAL* 4.2 12.6 - - + -
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Residues in contact with ILE 13 (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 ILE* 3.3 11.9 + - + +
12C VAL* 1.3 76.1 - - - +
14C ARG* 1.3 67.5 + - - +
26C THR* 3.1 34.3 + - + +
28C LEU* 3.6 35.2 - - + +
52C LEU* 4.0 14.7 - - - +
53C PHE* 5.1 0.4 - - + -
96C ALA* 3.7 26.7 - - + +
97C GLU* 4.6 7.4 - - - +
100C ASP* 4.0 24.9 - - + -
116C PHE* 3.6 34.5 - - + -
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Residues in contact with ARG 14 (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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114A MET* 4.5 18.5 - - + +
12C VAL* 3.6 4.9 - - - +
13C ILE* 1.3 85.2 - - + +
15C ARG* 1.3 68.6 + - - +
24C ILE 4.6 0.2 - - - -
25C VAL* 3.3 10.7 - - - +
26C THR* 3.2 48.5 + - - +
35C LYS* 5.9 2.0 - - - +
52C LEU* 3.8 7.2 - - + +
97C GLU* 2.8 39.2 + - - +
100C ASP* 2.9 32.1 + - - +
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Residues in contact with ARG 15 (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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144A THR* 5.0 9.6 - - - -
175B GLY 3.7 6.5 + - - -
176B GLY* 6.1 0.2 - - - -
12C VAL* 4.8 0.2 - - + -
14C ARG* 1.3 84.8 - - - +
16C ARG* 1.3 66.2 + - - +
17C VAL* 3.2 30.5 - - - +
23C ILE* 3.8 29.0 - - + +
24C ILE 3.4 4.9 - - - -
25C VAL* 4.1 5.8 - - + -
48C SER* 3.6 28.9 + - - +
50C LEU* 3.0 34.0 + - - +
51C ASN* 3.3 26.5 + - - +
52C LEU* 3.8 16.6 - - + +
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Residues in contact with ARG 16 (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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18A PRO* 5.4 10.0 - - - +
114A MET* 6.2 3.4 - - - +
15C ARG* 1.3 75.3 - - - +
17C VAL* 1.3 75.6 + - - +
18C THR* 3.8 20.9 - - + +
19C PRO* 5.7 1.8 - - - -
22C ASP 3.6 0.2 - - - +
23C ILE* 3.1 10.4 - - - +
24C ILE* 2.6 52.5 + - + +
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Residues in contact with VAL 17 (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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177B SER* 5.8 3.8 - - - +
180B TYR* 5.0 19.5 - - + -
15C ARG* 3.2 35.2 - - - +
16C ARG* 1.3 79.1 - - - +
18C THR* 1.3 66.8 + - - +
19C PRO* 4.8 0.2 - - - +
21C GLY 5.9 1.1 - - - +
22C ASP 3.3 9.9 - - - +
23C ILE* 4.3 5.8 - - + -
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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