Contacts of the helix formed by residues 22 - 30 (chain A) in PDB entry 2W3S
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 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A THR 3.1 6.3 + - - -
21A GLN* 1.3 81.6 - - - +
23A LEU* 1.3 63.0 + - - +
24A LEU* 3.2 7.5 + - - +
25A GLU* 2.2 48.6 + - - +
26A TRP* 3.2 18.1 + - - +
40A ASN* 5.6 1.3 - - - -
62A ALA 4.0 0.2 - - - -
63A CYS* 3.7 23.3 - - - -
65A MET 3.3 7.6 - - - -
66A MET* 4.3 2.5 - - - +
67A LEU* 5.4 0.2 - - - -
209A SER* 6.5 0.2 - - - -
213A THR* 5.6 5.2 - - - -
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLN 3.7 1.0 + - - -
22A SER* 1.3 72.1 - - - +
24A LEU* 1.3 61.3 + - - +
26A TRP* 4.6 7.0 - - + -
27A LEU* 3.0 36.8 + - + +
49A VAL* 3.8 29.4 - - + -
62A ALA* 3.2 17.0 + - + +
65A MET* 2.7 26.1 + - + +
66A MET* 4.3 1.5 - - - +
67A LEU* 4.4 17.5 - - + +
70A ILE* 3.8 39.5 - - + -
75A LEU* 3.9 23.1 - - + -
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Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A SER* 3.1 7.6 - - - +
23A LEU* 1.3 76.8 - - - +
25A GLU* 1.3 71.5 + - - +
26A TRP 3.1 0.9 + - - -
27A LEU* 3.2 8.7 + - - +
28A ARG* 3.3 29.0 + - + +
35A THR* 4.1 13.5 - - + -
36A LYS 3.6 21.1 - - - +
37A GLU* 3.4 37.0 - - + +
40A ASN* 3.4 22.2 - - - +
47A CYS* 3.9 13.0 - - + -
62A ALA* 2.7 19.0 + - - +
63A CYS* 3.8 11.2 - - + -
1464A FES 5.1 0.9 - - - -
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Residues in contact with GLU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLN* 3.6 26.2 - - + +
22A SER* 2.2 46.9 + - - +
24A LEU* 1.3 80.5 - - - +
26A TRP* 1.3 58.6 + - - +
28A ARG* 3.9 3.1 - - - +
29A ALA* 2.9 31.4 + - - +
37A GLU* 4.2 12.9 - - - +
40A ASN* 4.3 12.0 + - - +
213A THR* 5.9 1.2 - - - +
107B ARG* 5.4 13.1 - - + +
256B ARG* 5.8 1.2 + - - -
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Residues in contact with TRP 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PHE* 4.0 15.0 - + - -
7A LEU* 3.7 22.0 - - + -
12A ARG* 3.9 13.5 - - - -
14A VAL* 3.5 38.4 - - + +
21A GLN* 3.1 31.2 - - + +
22A SER 3.2 11.7 + - - +
23A LEU* 3.9 6.7 - - + +
24A LEU 3.1 1.0 - - - -
25A GLU* 1.3 77.7 - - - +
27A LEU* 1.3 95.0 + - + +
29A ALA* 3.3 5.2 + - + +
30A GLU* 3.0 60.0 + - + +
67A LEU* 3.5 27.8 - - + -
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 4.3 7.0 - - + -
23A LEU* 3.0 34.6 + - + +
24A LEU* 3.2 3.1 + - - +
26A TRP* 1.3 99.1 - - + +
28A ARG* 1.3 57.5 + - - +
30A GLU* 3.1 10.6 + - - +
32A LEU* 2.8 62.4 + - + +
35A THR* 3.9 18.2 - - + +
49A VAL* 4.1 13.9 - - + -
62A ALA* 4.8 0.4 - - + -
75A LEU* 4.6 6.1 - - + -
77A THR* 3.5 28.3 - - + -
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Residues in contact with ARG 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 3.3 29.5 + - + +
25A GLU* 4.2 2.9 - - - +
27A LEU* 1.3 73.6 - - - +
29A ALA* 1.3 61.8 + - - +
30A GLU 3.0 1.3 - - - -
31A GLY* 2.8 19.3 + - - +
32A LEU 4.0 11.4 - - - +
33A THR* 2.5 40.9 + - - +
35A THR* 2.9 33.0 + - - +
36A LYS* 3.9 7.6 - - - +
37A GLU* 4.8 14.2 + - - +
24B ASP* 3.3 41.4 + - - +
25B ASP* 2.5 23.8 + - - +
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLN* 4.8 7.2 - - - +
25A GLU 2.9 20.2 + - - +
26A TRP* 3.7 8.1 - - + +
28A ARG* 1.3 76.2 - - - +
30A GLU* 1.3 63.8 + - - +
31A GLY 3.1 0.9 + - - -
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Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 5.7 0.2 - - + -
12A ARG* 2.9 32.5 + - - +
26A TRP* 3.0 59.4 + - + +
27A LEU* 3.2 11.9 - - - +
28A ARG 3.0 0.4 - - - -
29A ALA* 1.3 78.9 - - - +
31A GLY* 1.3 58.4 + - - +
32A LEU* 4.3 11.4 - - + +
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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