Contacts of the strand formed by residues 26 - 37 (chain B) in PDB entry 2WV4
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 26 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B ILE* 3.6 3.5 - - - +
23B LEU 3.0 30.3 + - - +
24B ASP* 3.1 10.5 + - + +
25B GLY* 1.3 83.5 - - - +
27B THR* 1.3 65.5 + - - +
28B VAL* 3.3 7.3 + - + +
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Residues in contact with THR 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLU* 4.3 13.0 - - + +
21B LEU 3.5 8.1 - - - +
22B ILE* 4.6 8.9 - - - +
25B GLY 4.2 1.0 + - - -
26B LYS* 1.3 73.7 - - - +
28B VAL* 1.3 63.6 + - - +
29B ALA 3.9 17.9 - - - +
30B ILE* 4.3 11.0 - - + -
10D PHE* 3.2 30.1 - - + +
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Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU* 2.9 32.3 + - + +
23B LEU* 4.0 24.0 - - + +
26B LYS* 3.4 18.6 - - + +
27B THR* 1.3 74.8 - - - +
29B ALA* 1.3 63.7 + - + +
50B GLU* 5.9 1.3 - - + -
51B LYS 4.1 17.0 - - - +
9D ASN* 3.6 6.2 + - - -
10D PHE* 3.1 38.1 + - + +
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Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLU* 3.3 7.5 - - - +
21B LEU* 3.1 53.8 + - + -
27B THR* 3.7 2.4 - - - +
28B VAL* 1.3 84.0 - - + +
30B ILE* 1.3 67.7 + - - +
47B LEU* 6.1 0.2 - - - -
50B GLU* 5.1 0.4 - - + -
7D LEU* 4.6 11.0 - - + -
8D LEU 3.0 12.8 - - - +
9D ASN* 3.9 11.2 - - - +
10D PHE* 4.0 3.1 - - - -
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Residues in contact with ILE 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL* 3.6 9.9 - - - +
20B GLU* 4.5 4.3 - - + -
27B THR* 4.3 13.2 - - + -
29B ALA* 1.3 81.1 - - - +
31B CYS* 1.3 69.2 + - - +
121B ASN* 3.7 32.8 - - + +
122B ALA* 3.7 24.5 - - + +
123B ASP* 4.1 14.8 - - + +
161B GLY* 3.7 2.6 - - - -
7D LEU* 3.7 1.2 - - - +
8D LEU* 2.8 49.6 + - + +
10D PHE* 4.1 22.9 - - + -
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Residues in contact with CYS 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B PRO 3.8 0.2 - - - -
19B VAL* 2.8 50.8 + - - +
30B ILE* 1.3 80.6 - - - +
32B CYS* 1.3 72.3 + - - +
44B PRO* 4.1 7.0 - - - -
47B LEU* 4.0 15.0 - - - -
121B ASN* 3.7 9.5 - - - +
161B GLY 3.4 12.6 - - - +
163B ALA* 3.4 16.2 - - + +
7D LEU* 3.5 25.1 - - + -
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Residues in contact with CYS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B THR* 4.2 9.4 - - + -
17B LYS 3.6 8.1 - - - +
19B VAL* 3.9 3.7 - - - +
31B CYS* 1.3 82.5 - - - +
33B ALA* 1.3 62.6 + - - +
43B VAL* 4.2 1.2 - - - +
44B PRO* 3.8 11.3 - - - +
119B VAL* 3.7 15.0 - - - -
120B ASN 3.6 25.1 - - - +
121B ASN* 4.0 5.4 - - - -
161B GLY 3.5 17.9 - - - -
162B TYR 4.2 5.8 - - - -
163B ALA 3.0 10.3 + - - +
164B GLY* 3.5 16.7 - - - +
165B GLY* 3.9 13.9 - - - +
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Residues in contact with ALA 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ASN 3.7 0.9 - - - +
16B THR* 3.3 4.5 - - - +
17B LYS* 2.8 35.8 + - - +
19B VAL* 3.5 21.1 - - + -
32B CYS* 1.3 78.8 - - - +
34B THR* 1.3 62.9 + - - +
35B GLY 3.9 0.4 - - - -
41B TYR* 4.2 11.4 - - + -
42B LEU 3.4 5.2 - - - -
43B VAL* 3.7 13.2 - - + -
57B LEU* 3.6 16.2 - - + -
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Residues in contact with THR 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL* 4.7 6.7 - - + -
15B ASN* 4.1 4.7 - - + -
16B THR* 3.8 13.0 + - - +
33B ALA* 1.3 74.1 - - - +
35B GLY* 1.3 71.0 + - - +
36B VAL* 3.4 7.3 + - + +
41B TYR* 4.2 0.9 - - - -
42B LEU* 2.9 36.8 + - + +
99B ILE* 4.8 8.3 - - + -
103B PHE* 5.7 3.1 - - + -
164B GLY 2.9 20.9 + - - -
165B GLY* 3.9 0.9 - - - -
166B ALA* 3.4 31.2 + - + -
177B ILE* 6.1 0.4 - - + -
180B THR* 4.4 11.7 - - + -
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Residues in contact with GLY 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ASN* 2.9 44.5 + - - +
34B THR* 1.3 73.2 - - - +
36B VAL* 1.3 58.3 + - - -
37B PHE 3.8 0.7 - - - -
40B ALA 3.5 11.0 - - - -
41B TYR* 3.6 18.7 - - - -
96B VAL* 4.0 8.5 - - - -
99B ILE* 3.7 10.0 - - - +
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Residues in contact with VAL 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B THR* 3.9 4.9 - - + +
35B GLY* 1.3 78.4 - - - +
37B PHE* 1.3 86.6 + - + +
40B ALA* 2.9 16.8 + - + +
41B TYR 4.3 0.4 - - - +
42B LEU* 3.8 29.4 - - + -
87B LEU* 3.6 26.2 - - + -
97B ARG 3.8 4.5 - - - -
99B ILE* 3.2 26.8 + - + -
100B THR* 3.8 4.8 + - + +
103B PHE* 3.9 22.7 - - + -
199B LEU* 4.3 10.3 - - + -
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Residues in contact with PHE 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B VAL* 1.3 94.9 - - + +
38B GLY* 1.3 74.3 + - - +
39B THR 3.0 0.4 + - - -
40B ALA* 2.8 35.7 + - + +
87B LEU* 4.6 8.3 - - + -
96B VAL* 3.4 10.6 - - - +
97B ARG 4.2 3.6 - - - -
98B ASP* 4.1 22.7 - - + +
100B THR* 3.6 20.6 - - + -
199B LEU* 3.9 22.2 - - + -
202B MET* 4.1 5.8 - - + -
203B LYS* 3.5 42.6 - - + -
206B VAL* 4.5 17.5 - - + -
207B ASP 5.2 3.4 - - - -
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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