Contacts of the strand formed by residues 101 - 105 (chain A) in PDB entry 4O91
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 CYS 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A TYR* 4.6 5.4 - - + -
36A ILE* 4.5 8.3 - - - -
62A ILE* 3.6 40.8 - - - -
63A LYS 3.2 13.9 - - - +
64A GLN* 4.2 13.0 - - + -
74A PHE* 5.1 0.2 - - - -
95A ALA* 3.3 7.3 - - - +
96A CYS* 3.1 46.9 + - - -
99A PRO 3.9 1.6 - - - +
100A VAL* 1.3 78.6 - - - +
102A LEU* 1.3 66.4 + - - +
103A VAL* 3.8 1.4 + - - +
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Residues in contact with LEU 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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61A ALA 3.6 1.4 - - - +
62A ILE* 3.1 7.8 - - - +
63A LYS* 2.9 46.8 + - + +
74A PHE* 4.1 22.2 - - + -
77A GLU* 3.7 39.3 - - + +
78A LEU* 3.6 43.3 - - + +
81A LEU* 4.2 9.6 - - + -
92A LEU* 4.5 9.9 - - + -
94A GLY 4.0 2.2 - - - -
95A ALA* 4.5 3.6 - - + -
100A VAL* 5.4 3.4 - - + -
101A CYS* 1.3 74.3 - - - +
103A VAL* 1.3 61.4 + - - +
104A MET* 4.0 6.6 - - - +
601A NG2 4.4 2.5 - - + -
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Residues in contact with VAL 103 (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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31A ILE* 3.7 30.5 - - + -
36A ILE* 3.8 25.4 - - + -
55A TRP* 4.6 5.2 - - + -
60A VAL* 3.8 36.3 - - + -
61A ALA 3.8 1.6 - - - -
62A ILE* 4.1 5.8 - - + -
92A LEU* 3.6 2.3 - - - +
93A TYR* 2.8 30.1 + - + +
94A GLY 2.9 20.6 + - - +
95A ALA* 4.8 1.1 - - - -
96A CYS 5.3 0.4 - - - +
101A CYS* 4.2 7.6 - - - +
102A LEU* 1.3 77.8 - - - +
104A MET* 1.3 61.4 + - - +
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Residues in contact with MET 104 (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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60A VAL* 3.3 11.6 - - - +
61A ALA 2.8 31.1 + - - +
81A LEU* 3.9 22.4 - - + -
90A VAL* 3.5 32.1 - - + +
91A LYS 3.3 23.6 - - - +
92A LEU* 3.6 29.2 - - + +
93A TYR* 3.9 4.3 - - - -
102A LEU* 4.5 4.3 - - - +
103A VAL* 1.3 76.0 - - - +
105A GLU* 1.3 59.4 + - - +
601A NG2 3.5 53.8 - - + -
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Residues in contact with GLU 105 (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 ASP 5.4 0.2 - - - +
90A VAL* 4.4 3.6 - - - +
91A LYS* 2.8 55.1 + - + +
93A TYR* 3.6 32.6 + - + +
104A MET* 1.3 68.5 - - - +
106A TYR* 1.3 73.2 + - - +
107A ALA* 3.2 4.5 + - - +
172A LYS* 3.9 24.4 + - - -
601A NG2 3.2 16.0 - - - -
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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