Contacts of the strand formed by residues 55 - 62 (chain B) in PDB entry 2H8C
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 VAL 55 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B LEU* 5.2 13.2 - - + +
53B MET 3.1 17.0 - - - +
54B PRO* 1.3 74.1 - - - +
56B LYS* 1.3 60.8 + - - +
57B ILE* 4.0 16.6 - - + -
88B TRP* 4.2 15.7 - - + -
93B GLN* 3.0 14.2 + - + +
94B VAL* 3.6 30.8 - - + +
95B VAL* 3.2 25.3 + - - +
96B ASP 3.7 1.9 + - - +
114B ILE* 3.9 22.0 - - + -
115B THR 3.6 4.9 - - - +
116B GLU* 6.0 1.1 - - - -
117B MET* 4.3 2.9 - - - -
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Residues in contact with LYS 56 (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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98A ARG* 3.6 21.3 - - - +
55B VAL* 1.3 74.3 - - - +
57B ILE* 1.3 68.2 + - - +
96B ASP* 3.0 29.2 - - + +
113B THR 3.4 3.5 - - - +
114B ILE* 3.4 1.7 - - - -
115B THR* 2.8 58.2 + - + +
117B MET* 3.8 32.1 - - + +
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Residues in contact with ILE 57 (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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55B VAL* 4.0 5.6 - - + -
56B LYS* 1.3 83.7 - - - +
58B ARG* 1.3 74.3 + - - +
59B ILE* 4.4 9.0 - - + -
79B PHE* 3.5 32.5 - - + -
82B LEU* 5.6 0.9 - - + -
88B TRP* 3.7 28.0 - - + -
94B VAL* 3.7 19.1 - - + -
96B ASP* 2.9 5.1 + - - +
97B TYR* 3.3 10.0 - - + -
98B ARG* 2.9 23.0 + - - +
112B LEU* 4.6 8.5 - - + -
113B THR 3.3 9.4 - - - +
114B ILE* 3.9 18.8 - - + -
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Residues in contact with ARG 58 (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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57B ILE* 1.3 75.0 - - - +
59B ILE* 1.3 61.1 + - - +
60B GLU* 2.9 44.1 + - + +
98B ARG* 3.2 42.6 - - + +
100B VAL* 4.5 17.6 - - - +
102B MET* 5.0 3.2 - - - -
111B GLU 3.3 4.5 - - - +
112B LEU* 3.5 3.6 - - - +
113B THR* 3.1 52.3 + - + +
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Residues in contact with ILE 59 (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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57B ILE* 4.4 10.5 - - + -
58B ARG* 1.3 75.2 - - - +
60B GLU* 1.3 61.6 + - - +
61B CYS* 3.5 13.7 + - - -
74B LEU 5.3 2.2 - - - +
75B GLN* 4.0 16.6 - - + +
78B ALA* 4.8 10.8 - - + -
79B PHE* 3.7 29.8 - - + -
97B TYR* 4.7 2.0 - - + -
98B ARG 2.6 17.0 + - - +
99B VAL* 3.3 24.4 - - + +
100B VAL* 2.9 26.7 + - - -
110B LEU* 4.7 14.4 - - + -
111B GLU 3.6 1.8 - - - -
112B LEU* 3.4 23.8 - - + -
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Residues in contact with GLU 60 (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 ARG* 2.9 48.0 + - + +
59B ILE* 1.3 69.9 - - - +
61B CYS* 1.3 61.8 + - - +
62B HIS* 3.3 23.0 + - + -
100B VAL* 3.7 6.5 - - + +
102B MET* 3.8 24.7 - - + +
109B ARG 3.7 0.3 - - - +
110B LEU* 3.2 8.6 - - - -
111B GLU* 2.8 57.0 + - + +
113B THR* 6.1 0.2 - - - -
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Residues in contact with CYS 61 (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 TRP* 4.6 1.6 - - - -
59B ILE* 4.2 7.6 - - - -
60B GLU* 1.3 71.0 - - - +
62B HIS* 1.3 58.7 + - - +
63B MET* 3.4 9.7 + - - +
71B LEU* 3.6 11.4 - - + -
74B LEU* 3.1 44.0 - - + -
99B VAL* 3.3 33.2 - - - -
100B VAL 2.8 13.8 + - - +
101B LYS 3.7 0.2 - - - -
102B MET 2.7 30.9 + - - +
109B ARG 4.2 2.2 - - - -
110B LEU* 4.8 3.4 - - - -
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Residues in contact with HIS 62 (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 TRP* 3.7 4.2 - - - -
60B GLU* 3.3 22.7 + - + -
61B CYS* 1.3 68.7 - - - +
63B MET* 1.3 69.8 - - - +
102B MET* 3.1 38.6 - - + +
103B PRO* 3.9 19.9 - - + +
105B THR* 4.3 8.4 - - + +
108B GLY* 3.3 19.2 - - - -
109B ARG* 2.9 59.8 + - + +
111B GLU* 3.3 25.6 - - + +
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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