Contacts of the strand formed by residues 16 - 23 (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 THR 16 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B VAL* 3.0 19.6 + - - +
13B MET 3.4 12.6 + - - +
14B GLY 4.5 0.9 - - - +
15B ASN* 1.3 76.8 - - - +
17B LYS* 1.3 63.6 + - - +
32B CYS* 4.2 13.9 - - + -
33B ALA 3.3 11.0 - - - +
34B THR* 3.8 15.5 + - - +
58B ASP* 5.0 0.2 - - - +
118B VAL* 3.9 21.6 + - - +
119B VAL 4.3 3.6 - - - -
120B ASN* 2.8 48.7 + - + +
126B ARG* 3.7 4.2 + - - -
165B GLY* 5.2 0.2 - - - -
166B ALA* 4.8 0.2 - - - +
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Residues in contact with LYS 17 (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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14B GLY 5.1 3.6 - - - +
15B ASN* 3.5 13.2 - - - +
16B THR* 1.3 79.0 - - - +
18B PRO* 1.3 65.1 - - - +
32B CYS* 3.6 2.3 - - - +
33B ALA* 2.8 38.5 + - - +
41B TYR* 3.8 28.5 - - + +
57B LEU* 4.2 13.0 - - + -
58B ASP* 3.2 39.9 - - + +
96B VAL* 5.6 2.7 - - + -
120B ASN 3.6 3.8 - - - -
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Residues in contact with PRO 18 (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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17B LYS* 1.3 83.5 - - - +
19B VAL* 1.3 60.8 + - - +
20B GLU* 5.1 4.3 - - + +
31B CYS 3.9 2.9 - - - +
56B MET 3.5 1.7 - - - +
57B LEU* 3.8 1.2 - - - -
58B ASP* 2.9 51.3 + - - +
59B GLY 4.8 0.8 + - - +
120B ASN* 3.1 35.0 - - - +
121B ASN* 3.6 19.1 - - - -
122B ALA* 4.2 4.9 - - + +
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Residues in contact with VAL 19 (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* 1.3 72.2 - - - +
20B GLU* 1.3 77.6 - - - +
21B LEU* 5.2 0.2 - - + -
29B ALA 6.4 0.2 - - - -
30B ILE* 3.6 5.2 - - - +
31B CYS* 2.8 49.9 + - - +
32B CYS 3.9 8.3 - - - +
33B ALA* 3.5 33.0 - - + -
43B VAL* 4.9 5.4 - - + -
47B LEU* 4.3 16.2 - - + -
55B ILE* 4.3 17.3 - - + -
56B MET 3.3 6.3 - - - +
57B LEU* 3.6 13.7 - - + -
88B MET* 5.3 2.9 - - + -
122B ALA 5.6 0.2 + - - -
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Residues in contact with GLU 20 (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* 5.1 4.3 - - + +
19B VAL* 1.3 88.0 - - - +
21B LEU* 1.3 62.1 + - - +
22B ILE* 3.1 7.8 - - + +
27B THR* 4.3 15.0 - - + +
29B ALA 3.3 9.6 - - - +
30B ILE* 4.5 11.9 - - + -
55B ILE* 3.6 2.1 - - - +
56B MET* 2.8 50.3 + - + +
122B ALA* 4.6 14.1 - - + -
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Residues in contact with LEU 21 (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* 5.2 0.4 - - + -
20B GLU* 1.3 74.5 - - - +
22B ILE* 1.3 60.5 + - - +
27B THR* 3.5 5.4 - - - +
28B VAL* 2.9 33.9 + - + -
29B ALA* 3.1 28.3 + - + +
47B LEU* 3.5 46.7 - - + +
48B PHE* 6.0 0.2 - - + -
50B GLU* 3.7 22.2 - - + -
51B LYS 5.0 0.7 - - - +
52B TYR* 3.9 22.9 - - + -
54B LYS 3.8 1.1 - - - -
55B ILE* 3.5 35.9 - - + -
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Residues in contact with ILE 22 (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* 3.1 25.1 - - + +
21B LEU* 1.3 75.6 - - - +
23B LEU* 1.3 58.2 + - - +
25B GLY* 3.7 28.9 - - - +
26B LYS 3.6 11.4 - - - +
27B THR* 4.9 9.6 - - - +
52B TYR* 3.5 2.7 - - - +
53B ASP* 2.7 35.3 + - + +
54B LYS* 3.0 30.3 + - + +
56B MET* 3.6 33.9 - - + +
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Residues in contact with LEU 23 (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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22B ILE* 1.3 74.0 - - - +
24B ASP* 1.3 78.5 + - + +
25B GLY 3.3 0.2 - - - -
26B LYS* 3.0 21.8 + - - +
28B VAL* 4.0 19.1 - - + +
51B LYS* 3.7 39.0 - - + +
52B TYR* 3.7 15.3 - - - +
53B ASP* 3.1 27.4 - - - +
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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