Contacts of the strand formed by residues 91 - 96 (chain A) in PDB entry 3C5H
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 MET 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A TYR* 3.2 15.9 - - + +
16A ILE* 4.5 5.2 - - + -
42A PHE* 3.7 20.2 - - + -
77A GLY 3.7 1.0 - - - +
78A GLU* 3.2 5.7 - - - +
79A VAL* 2.8 71.2 + - + +
80A SER* 5.7 1.6 - - - -
90A LYS* 1.3 79.0 - - - +
92A HIS* 1.3 62.7 + - - +
93A ILE* 4.2 14.1 + - + +
240A PHE* 4.8 3.8 - - - -
241A SER* 5.7 1.3 - - - -
244A VAL* 3.7 32.3 - - + -
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Residues in contact with HIS 92 (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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13A THR* 3.7 23.3 - - + +
14A TYR 2.9 6.9 + - - +
15A ASN* 3.4 24.6 - - - +
16A ILE 2.9 26.7 + - - +
75A TYR* 2.7 31.1 + - + -
77A GLY 3.5 1.8 - - - -
78A GLU* 3.6 32.2 + - + +
90A LYS* 4.6 4.2 - - + +
91A MET* 1.3 75.0 - - - +
93A ILE* 1.3 61.9 + - - +
94A VAL 4.1 0.2 + - - -
148A LYS* 4.4 1.6 - - - -
151A PRO* 3.5 29.5 - - + +
155A LEU* 4.0 12.5 - - + +
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Residues in contact with ILE 93 (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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16A ILE* 3.6 17.5 - - + +
18A VAL* 4.4 0.9 - - + -
39A CYS* 3.7 30.5 - - + -
42A PHE* 3.8 22.9 - - + -
43A VAL* 3.9 16.2 - - + -
75A TYR* 3.5 6.7 - - - -
76A TRP* 2.8 37.8 + - + -
77A GLY 3.0 12.4 + - - +
79A VAL* 4.7 1.6 - - + -
91A MET* 4.3 8.5 - - + +
92A HIS* 1.3 82.3 - - - +
94A VAL* 1.3 61.8 + - - +
240A PHE* 3.6 35.7 - - + -
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Residues in contact with VAL 94 (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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16A ILE 2.9 11.9 + - - +
17A SER* 3.5 5.0 - - - +
18A VAL* 2.8 36.6 + - - +
73A PHE* 3.4 46.0 - - + -
74A LEU 3.2 11.0 - - - +
75A TYR* 4.0 9.9 - - + -
76A TRP* 4.5 2.0 - - - -
92A HIS 4.1 0.4 + - - -
93A ILE* 1.3 78.9 - - - +
95A GLU* 1.3 59.2 + - - +
96A GLN* 4.3 5.8 - - + +
125A LEU* 3.9 17.0 - - + -
150A MET* 4.6 0.2 - - - -
155A LEU* 3.8 26.9 - - + -
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Residues in contact with GLU 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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18A VAL* 3.5 4.7 - - - -
35A LYS* 3.5 30.7 - - + -
36A SER* 2.5 22.1 + - - -
39A CYS* 4.2 6.7 - - - -
73A PHE* 3.0 6.1 - - - +
74A LEU* 2.9 38.3 + - + +
76A TRP* 2.9 31.0 + - + +
94A VAL* 1.3 74.9 - - - +
96A GLN* 1.3 62.1 + - - +
97A THR* 3.6 9.4 + - - +
301A GNP 3.0 10.6 + - - -
302A MG 2.2 25.2 - - - -
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Residues in contact with GLN 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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17A SER* 3.5 20.3 + - - +
18A VAL 2.8 8.9 + - - +
19A VAL* 3.8 9.0 - - + -
35A LYS* 3.2 14.7 - - - +
72A HIS 3.7 7.6 - - - +
73A PHE* 3.4 21.8 - - + +
94A VAL* 4.1 1.5 - - + -
95A GLU* 1.3 70.6 - - - +
97A THR* 1.3 59.8 + - - +
116A TYR* 2.6 34.2 + - + +
119A ARG* 3.7 23.1 + - - +
120A ALA* 3.9 25.4 + - + +
122A ALA* 4.6 1.8 + - - +
125A LEU* 3.6 36.0 - - - +
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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