Contacts of the strand formed by residues 21 - 30 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14D MET 3.9 0.3 - - - +
15D TRP* 3.5 10.2 - - - -
16D ASP* 2.9 30.1 + - + +
19D ASP* 3.3 16.6 - - + +
20D GLN* 1.3 79.2 - - - +
22D TRP* 1.3 66.3 + - - +
23D THR* 4.9 7.2 - - + -
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Residues in contact with TRP 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D TYR* 3.5 27.1 - - + -
14D MET 3.2 23.8 - - - -
15D TRP* 3.4 45.5 - + + -
21D LYS* 1.3 75.6 - - - +
23D THR* 1.3 72.5 + - - +
72D LYS* 3.8 17.9 - - + -
73D ASN* 3.2 28.8 + - + -
75D LYS* 3.5 32.6 - - + +
78D VAL* 4.5 7.2 - - + -
92D GLU* 3.4 21.1 - - + -
93D PHE 3.7 10.8 - - - -
94D ALA* 3.6 21.8 - - + -
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Residues in contact with THR 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D TYR* 3.3 2.9 - - - -
14D MET* 2.7 36.8 + - - +
16D ASP* 5.7 6.3 - - + +
21D LYS* 4.9 9.6 + - + +
22D TRP* 1.3 86.3 - - - +
24D ARG* 1.3 63.6 + - - +
25D HIS* 2.7 31.5 + - - -
39D ASP* 3.6 24.0 - - + +
41D GLU* 6.5 0.4 - - - -
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Residues in contact with ARG 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D GLU* 2.8 43.1 + - + +
12D LEU 3.5 4.3 - - - -
13D TYR* 3.5 34.8 - - + -
23D THR* 1.3 72.7 - - - +
25D HIS* 1.3 68.6 + - - +
39D ASP* 3.4 5.3 - - - -
40D ILE* 3.1 52.3 + - + +
41D GLU* 2.8 53.4 + - + +
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Residues in contact with HIS 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D GLU* 3.4 1.6 - - - +
12D LEU 2.9 31.9 + - - +
14D MET* 3.5 30.7 - - + +
23D THR* 2.7 49.5 + - - -
24D ARG* 1.3 78.6 + - - +
26D PHE* 1.3 62.0 + - - +
27D CYS* 3.4 17.4 + - - -
36D PHE* 4.3 6.9 - + + -
37D SER* 3.0 30.4 + - - +
38D ASP* 3.5 3.6 + - - -
39D ASP* 3.7 21.1 - - + -
40D ILE* 3.8 6.0 - - - +
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Residues in contact with PHE 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D GLN* 4.0 20.4 - - + -
10D GLY* 3.6 29.2 - - - -
11D GLU* 4.3 4.7 - - + +
25D HIS* 1.3 71.0 - - - +
27D CYS* 1.3 68.5 + - - +
28D ALA* 4.3 11.0 - - + -
35D SER* 3.9 1.1 - - - +
36D PHE* 3.5 0.3 - - - -
37D SER* 2.7 45.9 + - - +
40D ILE* 3.5 14.0 - - + +
53D LEU* 3.9 33.4 - - + +
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Residues in contact with CYS 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D GLN* 3.3 1.9 - - - +
10D GLY 2.7 41.7 + - - +
12D LEU* 3.7 33.2 - - + -
14D MET* 4.8 0.2 - - - -
25D HIS* 3.5 19.3 - - - -
26D PHE* 1.3 78.4 - - - +
28D ALA* 1.3 63.8 + - - +
34D LEU* 4.5 6.5 - - + -
35D SER 3.0 10.5 - - - +
36D PHE* 3.6 22.7 - - - -
93D PHE* 4.4 8.7 - - - -
104D TRP* 3.8 7.2 - - + -
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Residues in contact with ALA 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D GLN 3.5 10.8 - - - +
9D GLN* 4.0 10.5 - - + +
26D PHE* 4.3 12.3 - - + -
27D CYS* 1.3 78.3 - - - +
29D ILE* 1.3 67.1 + - - +
33D LYS 3.8 0.2 - - - +
34D LEU* 3.2 4.9 - - - +
35D SER* 2.8 43.8 + - - +
104D TRP* 4.0 1.3 - - - -
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Residues in contact with ILE 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D LYS* 4.4 15.2 - - + +
8D GLN* 3.0 35.4 + - + +
28D ALA* 1.3 81.9 - - - +
30D ALA* 1.3 67.5 + - - +
31D ASP 3.5 22.4 - - - +
33D LYS 3.4 8.7 - - - +
34D LEU* 4.3 12.1 - - + -
60D LEU* 4.5 6.3 - - + -
104D TRP* 3.5 31.2 - - + -
107D SER* 4.2 8.1 - - - -
108D ILE* 4.0 19.7 - - + -
111D ILE* 3.8 11.7 - - + -
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Residues in contact with ALA 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ILE* 1.3 77.5 - - - +
31D ASP* 1.3 60.3 + - - +
32D ALA 2.7 20.4 + - - -
33D LYS* 2.9 21.1 + - + +
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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