Contacts of the strand formed by residues 32 - 37 (chain A) in PDB entry 1X7H
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 ARG 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A SER* 2.7 48.2 + - - +
7A GLU 2.9 8.2 + - - +
8A VAL* 3.2 11.4 - - - +
9A ALA* 2.8 26.3 + - - +
30A GLY 4.0 0.2 + - - -
31A LEU* 1.3 72.0 - - - +
33A VAL* 1.3 60.4 + - - +
56A GLU* 3.4 29.6 - - + +
81A TYR* 3.1 66.8 + - + +
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Residues in contact with VAL 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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9A ALA* 3.5 8.7 - - + +
11A VAL* 5.5 3.4 - - + -
23A ALA* 4.0 12.8 - - + +
26A LEU* 4.0 13.7 - - + -
27A GLY* 3.8 23.1 - - - +
31A LEU* 3.6 14.8 - - + +
32A ARG* 1.3 79.6 - - - +
34A PHE* 1.3 60.3 + - - +
35A VAL* 4.5 9.0 - - + -
50A LEU* 4.3 14.1 - - + -
55A VAL* 4.9 3.8 - - + -
56A GLU 3.0 7.8 + - - +
57A ALA* 3.1 39.5 - - + +
58A ASP 3.1 5.2 + - - +
81A TYR* 3.9 3.2 - - - -
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Residues in contact with PHE 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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9A ALA 2.8 9.1 + - - +
10A LEU* 3.4 10.3 - - + +
11A VAL* 2.9 26.2 + - - +
32A ARG 4.2 0.2 + - - -
33A VAL* 1.3 74.5 - - - +
35A VAL* 1.3 66.1 + - - +
58A ASP* 3.2 36.8 - - + -
59A GLY 3.7 27.6 - - - -
60A ARG* 3.8 3.8 - - + -
73A LEU* 3.7 22.2 - - + -
76A ALA* 4.0 31.4 - - + -
77A VAL* 3.4 41.1 - - + -
80A ARG* 4.2 4.0 - - + -
81A TYR* 4.1 13.7 - + + -
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Residues in contact with VAL 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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10A LEU* 5.1 0.9 - - - -
11A VAL* 3.4 8.7 - - + +
14A ALA* 3.7 29.8 - - + +
15A THR* 5.3 1.1 - - + -
23A ALA* 4.0 18.2 - - + -
33A VAL* 4.5 10.5 - - + -
34A PHE* 1.3 83.9 - - - +
36A CYS* 1.3 64.3 + - - +
43A LEU* 3.6 21.7 - - + +
46A THR* 4.6 11.4 - - + -
47A LEU* 4.2 10.8 - - + -
50A LEU* 4.7 5.2 - - + -
58A ASP 3.0 11.7 + - - +
59A GLY* 3.1 3.9 - - - -
60A ARG 3.1 23.2 + - - -
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Residues in contact with CYS 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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10A LEU* 5.4 0.7 - - + -
11A VAL 3.3 6.2 + - - +
12A THR* 3.7 27.4 - - - -
13A GLY 2.9 22.1 + - - -
14A ALA* 3.2 7.8 + - - -
15A THR* 4.4 3.4 - - - +
35A VAL* 1.3 76.5 - - - +
37A ALA* 1.3 66.8 + - - +
43A LEU* 4.5 3.1 - - - -
60A ARG 3.2 18.8 - - - +
62A CYS* 4.0 16.2 - - + -
64A VAL* 6.1 1.3 - - - -
73A LEU* 3.7 33.4 - - + -
301A NDP 4.8 4.0 - - - -
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Residues in contact with ALA 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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15A THR* 3.5 35.7 - - + +
36A CYS* 1.3 80.0 - - - +
38A ARG* 1.3 58.6 + - - +
39A GLY 3.6 5.6 - - - +
43A LEU* 5.1 2.3 - - + +
60A ARG 3.9 1.2 + - - -
61A THR* 3.0 10.3 - - - +
62A CYS 2.7 27.5 + - - -
301A NDP 3.7 29.4 - - - +
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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