Contacts of the strand formed by residues 77 - 83 (chain B) in PDB entry 3JCA
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 TYR 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B VAL* 4.3 1.6 - - + -
67B THR 3.4 7.2 - - - -
68B HIS* 3.7 29.8 - + - -
73B GLY 5.6 0.2 - - - -
74B LYS* 3.9 8.1 - - - -
75B LEU 3.1 1.2 + - - -
76B LYS* 1.3 103.2 + - + +
78B VAL* 1.3 62.7 + - - +
79B HIS* 3.3 11.0 - - + -
94B ARG 2.8 28.2 + - - +
95B THR 3.4 26.5 - - - -
96B GLY* 3.4 24.0 - - - +
97B GLU* 3.7 22.7 - - + -
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Residues in contact with VAL 78 (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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66B VAL* 3.3 2.8 - - - -
67B THR* 3.0 35.4 + - + -
69B VAL* 3.6 21.3 - - + -
72B PHE* 4.4 5.2 - - + -
75B LEU 3.8 11.9 - - - +
76B LYS 2.7 17.6 + - - +
77B TYR* 1.3 70.1 - - - +
79B HIS* 1.3 72.1 + - - +
80B VAL* 3.7 11.0 + - + +
91B ALA* 3.8 20.4 - - + -
92B THR 3.4 9.4 - - - +
93B ALA* 3.9 12.3 - - + +
164B ILE* 5.5 4.7 - - + -
184B LEU* 4.5 9.0 - - + -
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Residues in contact with HIS 79 (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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64B MET* 3.8 6.0 - - + +
65B ASP 3.6 3.8 - - - -
66B VAL* 3.7 24.0 - - + +
77B TYR 3.3 15.3 - - - -
78B VAL* 1.3 73.3 - - - +
80B VAL* 1.3 60.4 + - - +
91B ALA* 3.1 3.3 - - - +
92B THR 2.8 33.6 + - - +
94B ARG* 3.6 8.2 - - + +
96B GLY 2.9 21.3 + - - -
97B GLU* 4.1 3.5 - - - -
101B ASP* 3.6 17.0 + - + -
102B VAL* 3.5 48.2 - - + +
105B HIS* 3.1 28.5 - - + +
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Residues in contact with VAL 80 (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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63B GLN 3.5 1.3 - - - +
64B MET* 3.2 9.8 - - - +
65B ASP* 2.7 41.2 + - + +
67B THR* 5.2 0.7 - - + -
78B VAL* 3.8 23.1 - - + +
79B HIS* 1.3 81.0 - - - +
81B THR* 1.3 65.7 + - - +
82B VAL* 3.7 24.5 - - + -
89B THR* 3.9 11.2 - - + -
90B PHE 3.4 8.3 - - - +
91B ALA* 4.0 5.8 - - + -
105B HIS* 3.6 1.1 + - - -
157B VAL* 6.4 0.9 - - + -
160B THR* 3.9 8.7 - - + -
161B HIS* 4.0 22.2 - - + +
164B ILE* 4.2 7.9 - - + -
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Residues in contact with THR 81 (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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62B TRP* 3.5 43.1 - - + -
63B GLN 3.5 4.5 - - - +
64B MET* 3.7 8.7 - - - -
80B VAL* 1.3 71.3 - - - +
82B VAL* 1.3 65.5 + - - +
88B PHE 3.6 1.7 - - - +
90B PHE* 2.8 38.9 + - - -
105B HIS* 2.7 29.6 + - - -
106B LEU* 5.4 3.7 - - + +
109B SER* 4.2 9.4 + - - +
113B MET* 3.8 17.0 - - - +
119B ILE* 5.8 3.6 - - + -
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Residues in contact with VAL 82 (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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62B TRP* 3.3 3.5 - - - -
63B GLN* 2.8 42.0 + - + +
80B VAL* 3.7 18.6 - - + -
81B THR* 1.3 79.8 - - - +
83B ASP* 1.3 75.9 + - - +
84B THR* 3.2 1.8 + - - -
87B HIS* 3.9 15.9 - - + +
88B PHE 3.2 9.0 - - - +
89B THR* 3.7 12.3 - - - +
113B MET* 4.2 2.2 - - - -
156B ILE* 4.1 24.9 - - + -
157B VAL* 5.9 2.9 - - + -
160B THR* 3.6 22.4 - - + +
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Residues in contact with ASP 83 (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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58B PRO* 3.9 3.6 - - - +
59B ARG* 2.8 20.3 + - - -
60B VAL 4.2 1.0 + - - -
61B LEU 4.7 0.3 - - - +
62B TRP* 2.8 32.3 + - - +
82B VAL* 1.3 71.3 - - - +
84B THR* 1.3 61.1 + - - +
85B TYR* 3.1 10.3 - - - +
86B SER* 2.8 40.1 + - - +
87B HIS* 2.7 32.2 + - - -
88B PHE* 3.0 10.6 + - + -
113B MET* 3.6 7.2 - - + +
207B HIS* 3.4 20.7 + - - +
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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