Contacts of the strand formed by residues 78 - 87 (chain J) in PDB entry 3SHD
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 PRO 78 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2J PHE* 3.9 33.7 - - + -
3J LYS 5.3 2.0 - - - +
4J PRO* 4.4 9.6 - - + -
5J HIS* 2.9 38.1 + - + +
71J TRP 3.7 4.0 - - - +
72J ILE* 3.7 18.8 - - + -
76J LYS 3.8 6.1 - - - +
77J THR* 1.3 91.1 - - + +
79J PHE* 1.3 59.7 + - - +
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Residues in contact with PHE 79 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J PRO* 4.8 2.0 - - - +
5J HIS* 3.4 27.6 - - + -
7J THR* 3.8 33.7 - - + +
37J HIS* 4.0 12.1 - + - -
70J GLN* 3.5 5.0 - - - +
71J TRP* 2.7 74.5 + + + +
72J ILE* 4.7 0.2 - - - +
73J ALA* 4.0 11.0 - - + -
77J THR* 3.5 38.8 - - + -
78J PRO* 1.3 73.9 - - - +
80J LEU* 1.3 65.6 + - - +
81J ARG* 4.1 3.4 - - + +
158J SO4 4.5 13.2 - - - -
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Residues in contact with LEU 80 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J PRO* 3.5 30.3 - - + -
5J HIS 2.9 10.8 + - - +
6J VAL* 3.5 16.6 - - + +
7J THR* 2.9 28.5 + - - +
68J MET* 3.7 24.7 - - + -
69J HIS 3.3 2.7 - - - -
70J GLN* 3.6 36.1 - - + +
79J PHE* 1.3 81.9 - - - +
81J ARG* 1.3 60.5 + - - +
82J PHE* 3.9 7.4 + - + -
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Residues in contact with ARG 81 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J THR* 3.3 17.9 - - - +
9J ALA* 3.4 27.9 - - + +
32J ASN* 3.3 16.4 + - - -
33J GLN* 2.8 26.3 + - - -
67J ARG 4.1 0.3 - - - +
68J MET* 3.1 6.4 - - - +
69J HIS* 2.8 48.1 + - + +
71J TRP* 6.0 0.7 - - + -
79J PHE* 4.1 4.9 - - + -
80J LEU* 1.3 73.7 - - - +
82J PHE* 1.3 62.0 + - - +
83J LEU* 3.8 15.3 + - - +
120J SER* 5.7 0.2 + - - -
122J LEU* 3.7 39.3 - - + +
123J VAL* 4.9 2.8 - - - +
126J SER* 3.0 22.0 + - - -
158J SO4 3.0 23.9 + - - +
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Residues in contact with PHE 82 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J VAL* 3.8 17.5 - - + -
7J THR 2.7 21.7 + - - +
8J VAL* 3.1 4.7 - - + -
9J ALA 2.8 28.5 + - - +
44J LEU* 3.6 36.3 - - + -
65J PHE* 3.7 18.4 - + + -
67J ARG 4.1 2.0 - - - -
68J MET* 3.7 30.5 - - + -
80J LEU* 4.0 13.2 - - + -
81J ARG* 1.3 73.6 - - - +
83J LEU* 1.3 59.9 + - - +
84J PHE* 3.6 20.0 - - + -
141J ILE* 4.1 17.7 - - + -
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Residues in contact with LEU 83 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J ALA* 3.5 26.9 - - + +
10J CYS 4.4 0.4 - - - +
11J VAL* 4.0 18.4 - - + -
33J GLN* 5.0 0.9 - - + -
65J PHE* 3.6 6.7 - - - -
66J ILE* 2.9 45.6 + - + -
67J ARG 2.9 22.9 + - - +
69J HIS* 4.5 14.1 - - + +
81J ARG* 3.9 16.4 - - - +
82J PHE* 1.3 73.3 - - - +
84J PHE* 1.3 67.2 - - - +
126J SER* 3.7 34.8 - - - +
129J CYS* 4.7 1.3 - - + -
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Residues in contact with PHE 84 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J VAL* 4.3 7.6 - - + -
9J ALA 3.0 18.6 + - - +
10J CYS* 3.5 8.0 - - - -
11J VAL* 2.8 25.8 + - - +
44J LEU* 4.3 12.8 - - + -
45J VAL* 4.7 4.0 - - + -
48J ALA* 3.9 18.8 - - + -
62J PRO* 3.8 21.8 - - + -
64J HIS 3.1 16.4 - - - +
65J PHE* 4.1 15.9 - + + -
66J ILE* 3.9 6.7 - - - +
82J PHE* 3.6 30.5 - - + -
83J LEU* 1.3 76.8 - - - +
85J ALA* 1.3 62.0 + - - +
138J LEU* 3.7 26.7 - - + -
141J ILE* 4.0 23.3 - - + -
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Residues in contact with ALA 85 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J VAL 3.5 7.4 - - - +
62J PRO 3.9 0.2 - - - -
63J GLN* 2.8 29.9 + - - +
64J HIS* 2.8 26.3 + - + +
66J ILE* 3.6 24.4 - - + +
84J PHE* 1.3 75.7 - - - +
86J ILE* 1.3 64.3 + - - +
87J GLU* 5.3 2.0 - - + +
130J TYR* 4.7 9.6 - - + -
135J ARG* 4.6 12.8 - - - +
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Residues in contact with ILE 86 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J CYS* 3.9 28.9 - - + -
11J VAL 3.1 8.9 + - - +
12J VAL* 4.4 8.7 - - + -
13J HIS 3.0 23.4 + - - -
52J LEU* 3.9 23.3 - - + -
60J ALA* 3.9 6.5 - - + +
61J GLN 3.1 27.8 - - - +
62J PRO* 3.4 11.9 - - + -
63J GLN* 3.4 13.0 - - - +
85J ALA* 1.3 79.8 - - - +
87J GLU* 1.3 67.9 + - - +
88J LEU* 3.6 31.0 - - + -
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Residues in contact with GLU 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J HIS* 2.8 31.4 + - - +
63J GLN* 2.9 34.1 - - - +
85J ALA* 5.3 2.5 - - + +
86J ILE* 1.3 78.7 - - - +
88J LEU* 1.3 64.9 + - - +
89J GLU* 4.2 1.2 + - - +
130J TYR* 2.3 41.5 + - - -
135J ARG* 5.0 4.1 + - - -
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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