Contacts of the strand formed by residues 94 - 102 (chain A) 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 94 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A VAL* 3.6 12.3 - - + +
57A ILE* 3.4 36.3 - - + -
79A PHE* 3.7 19.1 - - + -
88A TRP* 4.1 5.8 - - + -
91A ASP* 3.6 29.0 - - + +
92A ALA 3.3 4.0 - - - +
93A GLN* 1.3 73.4 - - - +
95A VAL* 1.3 57.8 + - - +
96A ASP 3.2 4.7 - - - +
97A TYR* 3.7 28.3 - - + -
71B LEU* 3.1 25.0 + - + +
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Residues in contact with VAL 95 (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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54A PRO* 3.5 24.0 - - + -
55A VAL 3.0 18.0 + - - +
92A ALA 5.2 2.7 - - - +
93A GLN* 2.9 20.7 + - - +
94A VAL* 1.3 72.8 - - - +
96A ASP* 1.3 65.2 + - + +
117A MET* 4.8 13.2 - - - -
71B LEU* 3.7 7.2 - - - -
100B VAL* 4.4 0.9 - - - +
101B LYS* 2.9 38.3 + - + +
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Residues in contact with ASP 96 (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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56A LYS* 2.9 55.6 - - + +
57A ILE 2.9 2.8 + - - +
94A VAL* 3.2 4.4 + - - +
95A VAL* 1.3 89.5 - - + +
97A TYR* 1.3 66.0 + - - +
117A MET* 5.5 4.1 - - - +
71B LEU* 4.0 0.9 - - - +
98B ARG* 3.0 40.2 + - - -
99B VAL 3.5 8.1 - - - -
100B VAL* 3.3 17.2 - - + +
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Residues in contact with TYR 97 (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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57A ILE* 3.2 20.4 - - + +
59A ILE* 4.9 1.3 - - + -
75A GLN* 3.5 27.9 + - + -
79A PHE* 3.8 17.7 - + + -
94A VAL* 3.7 22.7 - - + -
96A ASP* 1.3 78.6 + - - +
98A ARG* 1.3 63.4 + - - +
99A VAL* 4.1 16.4 - - + -
71B LEU* 3.9 18.8 - - + -
72B ASP* 3.4 27.8 - - + +
75B GLN* 3.9 5.4 - - - +
97B TYR* 4.1 9.7 - + - -
98B ARG* 3.4 4.2 - - - +
99B VAL* 3.2 63.8 + - + +
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Residues in contact with ARG 98 (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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57A ILE 2.9 10.7 + - - +
58A ARG* 3.4 38.3 - - + +
59A ILE* 2.8 27.1 + - - +
97A TYR* 1.3 77.9 - - - +
99A VAL* 1.3 64.1 + - - +
100A VAL* 3.2 21.7 - - + +
56B LYS* 3.6 23.6 - - - +
96B ASP* 3.2 30.8 + - - +
97B TYR 3.4 12.6 - - - +
98B ARG* 3.6 31.0 - - + +
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Residues in contact with VAL 99 (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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59A ILE* 3.3 23.1 - - + +
61A CYS* 3.4 28.7 - - - -
71A LEU* 3.9 25.1 - - + +
75A GLN* 3.9 12.1 - - + +
97A TYR* 4.1 8.1 - - + -
98A ARG* 1.3 74.2 - - - +
100A VAL* 1.3 66.7 + - - +
101A LYS 4.4 0.2 - - - -
95B VAL 4.1 0.2 - - - +
96B ASP* 3.3 4.0 - - - -
97B TYR* 3.0 63.3 + - + +
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Residues in contact with VAL 100 (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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58A ARG* 4.3 14.8 - - + +
59A ILE 2.8 12.8 + - - +
60A GLU* 3.6 5.1 - - + -
61A CYS* 2.8 31.2 + - - -
71A LEU* 4.6 1.3 - - - -
98A ARG* 3.2 42.2 - - + +
99A VAL* 1.3 79.4 - - - +
101A LYS* 1.3 64.5 + - - +
102A MET* 3.4 29.3 + - + -
95B VAL 3.7 2.9 - - - -
96B ASP* 3.5 13.0 - - + +
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Residues in contact with LYS 101 (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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61A CYS* 3.9 5.8 - - - -
63A MET* 3.7 32.8 - - + -
71A LEU* 4.2 10.9 - - + +
100A VAL* 1.3 72.6 - - - +
102A MET* 1.3 72.7 + - - +
103A PRO* 4.8 0.5 - - - +
92B ALA 5.7 2.9 - - - +
94B VAL 5.8 0.2 - - - +
95B VAL* 2.8 46.5 + - + +
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Residues in contact with MET 102 (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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58A ARG* 5.6 1.6 - - - -
60A GLU* 3.9 20.9 - - + +
61A CYS 3.0 9.3 + - - +
62A HIS* 3.5 41.5 - - + +
63A MET* 3.3 18.2 + - - +
100A VAL* 3.4 26.9 + - + +
101A LYS* 1.3 81.9 - - - +
103A PRO* 1.3 91.3 - - + +
104A VAL 3.5 0.9 + - - -
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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