Contacts of the strand formed by residues 5 - 11 (chain B) in PDB entry 1JXH
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 ASN 5 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A LEU* 6.1 0.2 - - - +
251A GLU* 2.9 31.7 + - - +
252A VAL* 4.1 4.0 - - - +
3B ARG* 5.1 2.6 - - - +
4B ILE* 1.3 77.7 + - - +
6B ALA* 1.3 61.0 + - - +
33B TYR* 3.4 30.9 - - + +
35B CYS* 5.3 0.4 - - - -
71B VAL* 3.9 16.5 - - + +
72B ARG* 2.9 41.7 + - - +
73B ILE* 3.9 5.6 - - + -
74B ASP* 2.9 33.8 + - - +
75B THR 3.4 5.4 + - - -
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Residues in contact with ALA 6 (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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4B ILE* 4.1 0.6 + - + -
5B ASN* 1.3 75.6 - - - +
7B LEU* 1.3 60.7 + - - +
27B PHE* 3.7 35.3 - - + -
32B ALA* 4.1 12.8 - - + -
33B TYR 2.8 13.0 + - - +
34B GLY* 3.4 1.7 - - - -
35B CYS* 2.8 28.1 + - - +
73B ILE* 4.8 0.9 - - - -
75B THR* 3.4 20.2 - - - +
220B ALA* 5.8 0.2 - - + -
221B ALA* 5.0 2.7 - - - -
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Residues in contact with LEU 7 (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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6B ALA* 1.3 75.2 - - - +
8B THR* 1.3 80.0 + - - +
9B ILE* 3.9 19.1 - - + -
27B PHE* 3.7 5.6 - - - -
35B CYS* 3.5 22.9 - - + -
36B SER* 3.7 5.4 - - - +
37B VAL* 3.9 13.2 - - + +
64B LEU* 4.8 2.9 - - + -
67B VAL* 4.4 8.3 - - + -
68B PHE* 3.6 37.0 - - + -
73B ILE* 3.7 23.8 - - + +
75B THR 2.9 7.7 + - - -
76B THR* 3.2 8.4 - - + +
77B LYS 2.8 26.0 + - - +
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Residues in contact with THR 8 (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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7B LEU* 1.3 77.2 - - - +
9B ILE* 1.3 57.9 + - - +
10B ALA* 3.8 6.1 - - - +
20B ILE* 4.0 8.5 - - + +
23B ASP* 2.6 46.9 + - + -
24B LEU* 4.1 5.8 - - + -
27B PHE* 3.8 11.2 - - + -
35B CYS 3.0 16.2 + - - +
36B SER* 3.2 16.1 - - - -
37B VAL 2.8 32.1 + - - +
77B LYS* 3.3 9.6 - - - +
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Residues in contact with ILE 9 (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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7B LEU* 3.9 22.2 - - + -
8B THR* 1.3 75.9 + - - +
10B ALA* 1.3 59.4 + - - +
37B VAL* 3.3 16.2 - - + +
39B THR* 3.6 23.6 - - + -
64B LEU* 3.8 23.1 - - + -
76B THR* 4.1 13.5 - - + -
77B LYS 2.9 10.5 + - - +
78B ILE* 3.4 12.1 - - + +
79B GLY 2.8 25.3 + - - -
80B MET 4.3 0.7 - - - +
81B LEU* 4.9 0.2 - - + -
90B VAL* 4.0 35.2 - - + -
94B LEU* 4.4 9.0 - - + -
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Residues in contact with ALA 10 (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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8B THR* 3.8 3.5 - - - +
9B ILE* 1.3 77.8 - - - +
11B GLY* 1.3 66.7 + - - +
19B GLY* 4.9 2.5 - - - -
20B ILE* 3.7 10.7 - - + +
23B ASP* 3.8 22.0 - - - +
37B VAL 3.1 6.5 + - - +
38B ILE* 3.4 8.8 - - - -
39B THR* 2.9 32.0 + - - +
77B LYS* 4.6 0.2 - - - -
79B GLY* 3.8 17.7 - - - +
80B MET 3.8 5.8 - - - +
213B CYS* 6.5 0.2 - - - -
2004B SO4 5.8 0.9 - - - +
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Residues in contact with GLY 11 (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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10B ALA* 1.3 78.7 - - - +
12B THR* 1.3 62.3 + - - -
19B GLY* 3.1 4.9 - - - -
20B ILE* 2.8 26.0 + - - +
39B THR* 3.6 5.6 + - - -
40B ALA 3.3 14.4 - - - -
80B MET* 3.8 17.1 - - - +
2004B SO4 3.8 15.1 + - - -
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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