Contacts of the strand formed by residues 26 - 37 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ILE* 3.3 4.6 - - - +
23A LEU 2.7 39.6 + - - +
24A ASP 3.2 2.7 - - - +
25A GLY* 1.3 80.9 - - - +
27A THR* 1.3 72.8 + - - +
28A VAL* 3.1 20.8 + - + +
10C PHE* 3.3 31.4 + - - -
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Residues in contact with THR 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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20A GLU* 4.6 10.2 - - + +
21A LEU 3.2 9.4 - - - +
22A ILE* 3.4 17.5 - - - +
25A GLY 4.3 0.6 + - - -
26A LYS* 1.3 75.3 - - - +
28A VAL* 1.3 60.8 + - - +
29A ALA 4.0 5.6 - - - +
30A ILE* 4.0 30.7 - - + -
10C PHE* 3.4 28.8 - - + +
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Residues in contact with VAL 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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21A LEU* 2.8 37.8 + - + +
22A ILE 4.4 0.2 - - - +
23A LEU* 3.5 31.9 - - + +
26A LYS* 3.1 27.1 + - + +
27A THR* 1.3 73.7 - - - +
29A ALA* 1.3 62.2 + - + +
50A GLU* 4.6 6.9 - - + +
51A LYS 3.7 19.5 - - - +
52A TYR* 4.5 0.7 - - + -
9C ASN* 3.9 5.7 + - - -
10C PHE* 2.9 33.9 + - - -
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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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19A VAL 4.0 0.2 - - - +
20A GLU* 3.4 4.7 - - - -
21A LEU* 2.8 55.7 + - + +
27A THR* 3.5 3.4 - - - +
28A VAL* 1.3 83.3 - - - +
30A ILE* 1.3 66.1 + - - +
47A LEU* 4.9 1.3 - - + -
50A GLU* 4.5 3.6 - - + -
7C LEU* 4.3 12.6 - - + -
8C LEU 3.1 13.0 - - - +
9C ASN* 4.2 10.5 - - - +
10C PHE* 3.9 2.4 - - - -
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Residues in contact with ILE 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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19A VAL 3.5 7.4 - - - +
20A GLU* 4.3 9.0 - - + -
27A THR* 4.0 12.1 - - + -
29A ALA* 1.3 79.8 - - - +
31A CYS* 1.3 68.8 + - - +
121A ASN* 3.7 32.3 - - + +
122A ALA* 3.8 24.7 - - + +
123A ASP* 4.3 15.0 - - + +
161A GLY* 3.7 2.3 - - - -
7C LEU* 3.9 1.7 - - - +
8C LEU* 2.8 49.0 + - + +
10C PHE* 3.7 25.1 - - + -
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Residues in contact with CYS 31 (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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19A VAL* 2.9 41.4 + - - +
30A ILE* 1.3 78.9 - - - +
32A CYS* 1.3 76.0 + - - +
43A VAL* 5.8 0.2 - - - -
44A PRO* 4.0 12.1 - - - -
47A LEU* 3.8 16.6 - - - -
121A ASN* 3.7 7.7 - - - +
161A GLY 3.5 13.2 - - - +
163A ALA 3.3 12.1 - - - +
7C LEU* 3.3 28.9 - - + -
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Residues in contact with CYS 32 (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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16A THR* 4.1 10.1 - - + -
17A LYS 3.6 6.3 - - - +
19A VAL* 3.7 3.3 - - - +
31A CYS* 1.3 89.4 - - - +
33A ALA* 1.3 62.4 + - - +
43A VAL* 4.4 0.2 - - - +
44A PRO* 3.7 5.7 - - - +
119A VAL* 3.5 19.1 - - - -
120A ASN 3.3 39.9 - - - +
121A ASN* 3.7 4.3 - - - -
161A GLY 3.8 6.3 - - - -
162A TYR 4.5 1.1 - - - -
163A ALA 3.0 7.7 + - - +
164A GLY* 3.3 30.5 - - - +
165A GLY 4.0 3.8 - - - +
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Residues in contact with ALA 33 (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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15A ASN 3.6 1.6 - - - +
16A THR* 3.4 4.3 - - - +
17A LYS* 2.9 35.3 + - + +
19A VAL* 3.6 15.5 - - + -
32A CYS* 1.3 76.0 - - - +
34A THR* 1.3 63.3 + - - +
35A GLY 4.0 0.4 - - - -
41A TYR* 4.3 16.8 - - + -
42A LEU 3.4 6.1 - - - +
43A VAL* 3.4 23.1 - - + -
57A LEU* 6.1 2.5 - - + -
88A MET* 5.8 3.4 - - + -
164A GLY 4.1 1.3 - - - -
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Residues in contact with THR 34 (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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12A VAL* 4.7 2.9 - - + -
15A ASN* 3.8 4.3 - - + +
16A THR* 4.4 11.1 + - - +
33A ALA* 1.3 71.8 + - - +
35A GLY* 1.3 73.4 + - - +
36A VAL* 3.5 8.1 + - + +
41A TYR* 3.4 1.7 - - - -
42A LEU* 2.9 37.4 + - + -
99A ILE* 4.5 12.6 - - + -
103A PHE* 5.7 3.1 - - + -
164A GLY 2.8 23.7 + - - -
165A GLY* 4.4 0.3 - - - -
166A ALA* 3.5 31.9 + - + +
177A ILE* 6.0 0.4 - - + -
180A THR* 3.8 11.4 - - + +
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Residues in contact with GLY 35 (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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15A ASN* 2.8 41.8 + - - +
34A THR* 1.3 73.4 - - - +
36A VAL* 1.3 60.1 + - - +
37A PHE 3.9 0.4 - - - -
40A ALA 3.4 9.9 - - - -
41A TYR* 3.6 17.7 - - - -
96A VAL* 4.0 8.5 - - - -
99A ILE* 3.4 13.3 - - - +
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Residues in contact with VAL 36 (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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34A THR* 3.7 12.1 - - + +
35A GLY* 1.3 78.5 - - - +
37A PHE* 1.3 89.0 + - + +
40A ALA* 2.9 16.8 + - + +
42A LEU* 3.7 25.4 - - + -
87A LEU* 3.8 21.1 - - + -
97A ARG 4.0 3.6 - - - -
99A ILE* 2.8 33.9 + - + -
100A THR* 3.8 12.7 + - + +
103A PHE* 4.0 17.5 - - + -
199A LEU* 4.4 6.7 - - + -
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Residues in contact with PHE 37 (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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36A VAL* 1.3 100.3 - - + +
38A GLY* 1.3 75.7 + - - +
39A THR 2.9 0.8 + - - -
40A ALA* 2.7 40.3 + - + +
87A LEU* 4.3 12.6 - - + -
89A VAL* 5.6 1.6 - - + -
96A VAL* 3.6 7.8 - - - +
98A ASP* 3.9 28.5 - - + +
100A THR* 4.0 13.7 - - + -
199A LEU* 4.0 11.2 - - + -
202A MET 4.0 5.8 - - - -
203A LYS* 3.4 52.3 - - + -
206A VAL* 5.1 5.8 - - + -
207A ASP* 4.2 17.7 - - + -
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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