Contacts of the strand formed by residues 21 - 30 (chain C) in PDB entry 2W2X
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 LYS 21 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C TRP* 3.6 8.7 - - - -
16C ASP* 2.9 30.8 + - + +
19C ASP* 3.3 15.7 - - + +
20C GLN* 1.3 79.8 - - - +
22C TRP* 1.3 68.1 + - - +
23C THR* 5.0 7.3 - - + +
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Residues in contact with TRP 22 (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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13C TYR* 3.5 26.5 - - + -
14C MET 3.2 23.1 - - - -
15C TRP* 3.4 39.7 - + + -
21C LYS* 1.3 77.6 - - - +
23C THR* 1.3 68.9 + - - +
72C LYS* 3.7 18.8 - - + -
73C ASN* 3.2 28.5 + - + -
75C LYS* 3.6 35.1 - - + +
78C VAL* 4.5 7.0 - - + -
92C GLU* 3.5 27.1 - - + -
93C PHE 3.7 11.2 - - - -
94C ALA* 3.6 22.4 - - + -
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Residues in contact with THR 23 (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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13C TYR* 3.2 3.5 - - - -
14C MET* 2.7 34.1 + - - +
16C ASP* 5.8 5.5 - - + +
21C LYS* 5.0 8.8 + - + +
22C TRP* 1.3 81.7 - - - +
24C ARG* 1.3 64.8 + - - +
25C HIS* 2.7 31.0 + - - -
39C ASP* 3.6 24.0 - - + +
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Residues in contact with ARG 24 (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 GLU* 2.6 48.7 + - + +
12C LEU 3.5 4.7 - - - +
13C TYR* 3.5 33.9 - - + -
23C THR* 1.3 71.9 - - - +
25C HIS* 1.3 68.6 + - - +
39C ASP* 3.4 5.6 + - - -
40C ILE* 3.1 54.8 + - + +
41C GLU* 4.6 22.0 - - + +
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Residues in contact with HIS 25 (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 GLU* 3.3 1.7 - - - -
12C LEU 2.9 31.4 + - - +
14C MET* 3.5 32.3 - - + +
23C THR* 2.7 49.5 + - - -
24C ARG* 1.3 78.6 - - - +
26C PHE* 1.3 61.5 + - - +
27C CYS* 3.4 17.1 + - - -
36C PHE* 4.8 2.0 - + - -
37C SER* 3.0 31.8 + - - +
38C ASP* 3.4 5.2 + - - -
39C ASP* 3.7 21.3 - - + -
40C ILE* 3.8 6.1 - - - -
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Residues in contact with PHE 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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9C GLN* 4.0 19.5 - - + -
10C GLY* 3.6 29.8 - - - -
11C GLU* 4.3 4.9 - - + +
25C HIS* 1.3 70.8 - - - +
27C CYS* 1.3 64.0 + - - +
28C ALA* 4.3 13.9 - - + -
35C SER 4.7 0.2 - - - -
36C PHE* 3.6 0.3 - - - -
37C SER* 2.8 44.8 + - - +
40C ILE* 3.6 14.3 - - + +
53C LEU* 3.7 32.7 - - + +
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Residues in contact with CYS 27 (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 GLN* 3.2 2.1 - - - +
10C GLY 2.7 44.9 + - - +
12C LEU* 3.8 32.5 - - + -
14C MET* 4.8 0.2 - - - -
25C HIS* 3.6 16.6 - - - -
26C PHE* 1.3 82.8 - - - +
28C ALA* 1.3 60.1 + - - +
34C LEU* 4.6 0.9 - - + -
35C SER 2.9 18.8 - - - +
36C PHE* 3.6 24.2 - - - -
93C PHE* 4.4 8.1 - - - -
104C TRP* 3.7 4.2 - - + -
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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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8C GLN 3.5 10.3 - - - +
9C GLN* 4.1 9.6 - - + -
26C PHE* 4.3 14.4 - - + -
27C CYS* 1.3 75.5 - - - +
29C ILE* 1.3 64.8 + - - +
34C LEU* 3.3 1.9 - - - -
35C SER* 2.5 56.3 + - - +
104C TRP* 4.3 0.9 - - - -
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Residues in contact with ILE 29 (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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7C LYS* 4.5 14.8 - - + +
8C GLN* 2.9 35.3 + - + +
28C ALA* 1.3 79.8 - - - +
30C ALA* 1.3 65.3 + - - +
31C ASP 4.2 5.8 - - - +
33C LYS 2.7 17.5 - - - +
34C LEU* 4.4 8.7 - - + -
60C LEU* 4.4 7.2 - - + -
104C TRP* 3.6 30.7 - - + -
107C SER* 4.1 7.2 - - - -
108C ILE* 4.1 19.3 - - + -
111C ILE* 3.8 24.7 - - + -
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Residues in contact with ALA 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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29C ILE* 1.3 75.6 - - - +
31C ASP* 1.3 61.8 + - - +
32C ALA 2.7 17.0 + - - -
33C LYS* 2.7 27.1 + - - +
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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