Contacts of the strand formed by residues 27 - 36 (chain A) in PDB entry 2WHR
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 GLY 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A LYS* 3.4 18.5 - - - +
24A ALA* 2.8 35.3 + - - +
25A PRO 3.5 0.8 + - - -
26A GLY* 1.3 79.8 - - - +
28A PRO* 1.3 72.6 - - - +
140A GLN* 3.5 6.6 - - - +
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Residues in contact with PRO 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 ARG* 3.5 47.8 - - + +
22A LEU 3.1 12.1 - - - +
23A LYS* 4.3 5.4 - - - +
24A ALA 4.6 0.2 - - - +
27A GLY* 1.3 86.9 - - - +
29A VAL* 1.3 65.4 + - - +
104A PRO* 5.0 0.3 - - - +
105A TYR* 3.4 36.3 + - + +
140A GLN* 4.1 5.6 + - - +
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Residues in contact with VAL 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 ARG* 3.5 4.9 - - - -
22A LEU* 2.8 56.2 + - + +
24A ALA* 4.4 4.5 - - + -
28A PRO* 1.3 76.6 - - - +
30A SER* 1.3 61.7 + - - +
102A TRP* 4.5 7.6 - - + -
103A THR 3.6 9.0 - - - +
104A PRO* 5.0 1.1 - - + -
105A TYR* 3.6 8.9 - - - +
136A ARG* 3.4 43.1 - - + +
139A ALA* 4.1 7.4 - - + -
140A GLN* 3.4 28.5 - - + +
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Residues in contact with SER 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 GLN 5.0 0.7 + - - -
8A LEU* 4.2 10.5 - - - +
20A ILE 3.7 4.0 - - - -
29A VAL* 1.3 73.6 - - - +
31A ALA* 1.3 59.7 + - - +
32A PHE* 4.1 18.0 - - - -
101A VAL 3.7 0.5 - - - +
102A TRP* 3.2 7.3 - - - +
103A THR* 2.8 47.0 + - - -
104A PRO 2.9 16.8 + - - -
105A TYR* 3.3 19.0 - - - -
107A ARG* 4.1 8.7 + - - +
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Residues in contact with ALA 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 GLY* 3.2 2.8 - - - -
20A ILE* 2.8 53.2 + - + +
22A LEU* 3.6 32.5 - - + -
29A VAL 3.8 0.2 + - - -
30A SER* 1.3 74.3 - - - +
32A PHE* 1.3 63.5 + - - +
33A LEU* 3.9 12.8 - - + -
62A ALA 3.6 0.5 - - - +
101A VAL 3.4 3.6 - - - -
102A TRP* 4.0 11.4 - - + +
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Residues in contact with PHE 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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7A GLN 4.8 0.2 - - - -
8A LEU* 3.3 23.3 - - + -
10A VAL* 3.7 28.5 - - + -
17A LEU* 4.3 13.7 - - + -
18A ARG 4.3 1.6 - - - -
19A GLY* 3.3 32.8 - - - -
30A SER* 4.1 22.2 - - - -
31A ALA* 1.3 73.5 - - - +
33A LEU* 1.3 60.2 + - - +
35A ILE* 3.7 23.1 - - + +
62A ALA* 3.6 6.3 - - + -
100A ASN* 3.3 4.2 - - - -
101A VAL* 2.7 46.7 + - + +
103A THR* 4.9 1.1 - - - -
107A ARG* 4.5 8.1 - - - -
190A PHE* 3.5 30.5 - + + -
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Residues in contact with LEU 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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20A ILE* 4.9 2.5 - - + -
22A LEU* 5.1 7.6 - - + -
31A ALA* 4.1 22.4 - - + -
32A PHE* 1.3 79.0 - - - +
34A GLY* 1.3 62.2 + - - +
35A ILE 3.5 2.5 - - - -
61A ASP 4.4 0.7 - - - +
62A ALA* 2.8 37.3 + - - +
63A THR 4.1 15.7 - - - +
64A THR* 3.3 23.8 - - - +
65A PHE* 3.8 36.6 - - + +
100A ASN* 3.5 24.2 - - + +
101A VAL 4.6 1.3 - - - +
102A TRP* 4.1 13.7 - - + -
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Residues in contact with GLY 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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33A LEU* 1.3 74.8 - - - +
35A ILE* 1.3 62.9 + - - +
36A PRO* 3.6 5.0 - - - +
60A LEU* 4.1 9.7 - - - +
61A ASP 4.9 1.0 - - - +
64A THR 3.8 3.3 + - - -
66A GLN* 3.5 33.6 + - - +
98A TYR* 3.4 18.6 - - - -
99A LEU 3.4 2.4 + - - -
100A ASN* 3.0 14.9 + - - -
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Residues in contact with ILE 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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12A VAL* 5.0 0.2 - - + -
17A LEU* 3.6 35.0 - - + -
32A PHE* 3.7 33.4 - - + +
34A GLY* 1.3 76.8 - - - +
36A PRO* 1.3 79.1 - - + +
37A PHE 3.6 0.5 + - - -
56A TRP* 4.8 4.7 - - + -
60A LEU* 4.8 1.3 - - - -
62A ALA* 4.3 7.9 - - + -
98A TYR* 3.1 2.1 - - - -
99A LEU* 2.7 55.9 + - + +
101A VAL* 4.2 9.2 - - + -
182A TRP* 3.7 27.6 - - + +
190A PHE* 4.4 1.3 - - + -
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Residues in contact with PRO 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 GLY 3.6 3.4 - - - +
35A ILE* 1.3 95.4 - - + +
37A PHE* 1.3 59.7 + - - +
38A ALA 3.6 3.1 - - - +
53A LYS* 3.9 40.3 - - + +
56A TRP* 4.3 10.3 - - + -
60A LEU* 3.5 33.4 - - + -
97A LEU 3.7 3.4 - - - +
98A TYR* 3.5 28.9 - - + -
182A TRP* 4.3 5.4 + - - -
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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