Contacts of the strand formed by residues 31 - 38 (chain A) in PDB entry 2H7Z
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 SER 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A THR* 4.8 4.3 - - - -
10A CYS* 4.0 5.8 - - - -
27A CYS* 4.0 1.6 - - - -
30A GLY* 1.3 75.4 - - - -
32A CYS* 1.3 68.2 + - - +
33A TYR* 5.1 0.2 - - - +
51A CYS* 3.4 2.4 - - - -
52A ALA* 2.9 33.4 + - - +
53A GLU 4.8 0.5 + - - -
55A CYS* 5.0 7.8 + - - +
66A CYS* 4.2 13.2 - - - +
67A CYS 3.6 12.6 - - - -
68A ARG* 3.5 30.2 + - - -
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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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8A THR* 4.2 7.4 - - - -
9A LEU 3.3 14.4 - - - -
10A CYS* 2.0 48.2 - - - -
31A SER* 1.3 75.4 + - - +
33A TYR* 1.3 62.8 + - - +
50A GLY 3.4 2.2 - - - -
66A CYS* 3.2 7.3 - - - +
67A CYS* 2.8 40.1 + - - +
69A SER 4.2 1.8 - - - -
72A CYS* 3.8 16.6 - - - -
73A ASN* 3.7 19.1 - - + -
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Residues in contact with TYR 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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31A SER* 5.1 0.4 - - - +
32A CYS* 1.3 78.8 - - - +
34A THR* 1.3 74.2 + - - +
35A LEU* 3.9 15.5 - - + -
48A VAL* 3.6 31.0 - - + +
49A LYS* 3.4 1.0 - - - -
50A GLY* 2.9 50.3 + - - -
51A CYS 3.8 11.7 - - - -
52A ALA* 3.9 17.7 - - + -
56A PRO* 3.9 25.8 - - + -
64A VAL* 4.4 3.6 - - + -
65A LYS 3.2 7.2 - - - +
66A CYS* 3.5 22.4 - - - -
67A CYS* 5.5 0.2 - - - -
73A ASN* 3.1 19.8 + - - -
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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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33A TYR* 1.3 75.0 + - - +
35A LEU* 1.3 60.5 + - - +
36A TYR* 3.4 38.0 + - + +
46A TRP* 3.6 27.6 - - + -
48A VAL 3.4 7.4 - - - +
49A LYS* 4.0 12.3 - - + +
64A VAL* 3.3 4.7 - - - +
65A LYS* 2.9 33.9 + - - -
73A ASN* 3.3 28.4 + - - +
75A ASP* 4.6 1.9 - - + +
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Residues in contact with LEU 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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33A TYR* 3.9 15.1 - - + -
34A THR* 1.3 72.6 - - - +
36A TYR* 1.3 69.2 + - - +
37A ARG* 3.6 38.1 - - + +
46A TRP* 3.7 1.4 - - - -
47A ALA* 2.8 33.1 + - + -
48A VAL* 2.8 25.2 + - + +
56A PRO* 5.9 2.9 - - + -
57A THR 5.8 1.3 - - - +
58A ALA* 5.8 0.7 - - - -
62A GLU* 3.8 24.9 - - + +
63A ARG 3.4 4.0 - - - +
64A VAL* 4.1 20.6 - - + -
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Residues in contact with TYR 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* 3.4 37.8 + - + -
35A LEU* 1.3 79.0 - - - +
37A ARG* 1.3 64.1 + - - +
44A LEU* 4.0 26.7 - - + -
45A LYS* 3.4 12.3 - - - +
46A TRP* 3.6 18.4 - - - -
62A GLU* 3.3 6.9 - - - -
63A ARG* 2.6 53.0 + - + +
64A VAL 4.7 0.4 - - - -
65A LYS* 3.9 22.6 - - + +
75A ASP* 2.6 39.1 + - + +
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Residues in contact with ARG 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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14A ASN* 6.1 0.6 - - - +
16A MET* 6.2 1.8 - - - +
35A LEU* 3.6 23.2 - - + +
36A TYR* 1.3 80.4 - - - +
38A PRO* 1.4 77.1 - - + +
39A ASP 3.5 0.7 + - - -
44A LEU* 4.0 4.5 - - - -
45A LYS* 3.0 28.6 + - - +
47A ALA* 3.7 22.3 - - + +
48A VAL* 4.6 12.5 - - - +
61A ASN 4.4 0.7 - - - +
62A GLU* 2.9 33.2 + - + -
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Residues in contact with PRO 38 (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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37A ARG* 1.4 89.3 - - + +
39A ASP* 1.3 63.8 + - - +
42A CYS* 3.9 8.1 - - - -
43A GLU 3.5 9.0 - - - +
44A LEU* 3.9 3.5 - - + -
61A ASN* 3.1 27.8 - - + +
18B CYS* 3.7 29.6 - - - +
22B PHE* 3.8 23.3 - - + -
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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