Contacts of the strand formed by residues 88 - 93 (chain A) in PDB entry 4WNO
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 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A LYS 3.8 0.5 - - - +
47A CYS* 3.8 2.3 - - - -
48A ILE* 3.7 34.8 + - + +
57A GLN* 3.9 33.9 - - + +
60A LEU* 3.8 21.6 - - + +
64A ILE* 3.6 30.3 - - + -
82A GLN 3.3 7.0 - - - +
83A GLU* 4.0 20.0 - - + +
87A SER* 1.3 82.6 - - - +
89A TYR* 1.3 74.5 + - - +
90A LEU* 3.9 2.2 - - + -
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Residues in contact with TYR 89 (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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9A GLU* 4.4 10.5 + - + -
11A VAL* 4.1 24.0 - - + -
16A PHE* 3.9 19.1 - + - -
45A VAL* 4.3 5.8 - - + -
46A LYS 3.3 4.5 - - - +
47A CYS* 3.7 36.1 - - + -
48A ILE 5.4 0.7 - - - -
64A ILE* 4.3 0.7 - - - +
81A PHE* 3.2 7.0 - - - +
82A GLN* 2.8 63.7 + - + +
87A SER* 4.0 26.1 - - - -
88A VAL* 1.3 79.2 - - - +
90A LEU* 1.3 64.7 + - - +
91A VAL* 4.2 0.7 - - - -
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Residues in contact with LEU 90 (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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44A ALA 3.4 2.1 - - - +
45A VAL* 3.2 6.0 - - - -
46A LYS* 2.9 43.5 + - + +
60A LEU* 3.9 21.1 - - + +
63A GLU* 3.7 40.4 - - + +
64A ILE* 3.7 36.8 - - + +
67A LEU* 4.7 1.6 - - + -
78A LEU* 3.8 17.7 - - + -
80A ASP 4.0 3.1 - - - -
81A PHE* 4.7 0.2 - - + -
88A VAL* 3.9 10.5 - - + -
89A TYR* 1.3 79.6 - - - +
91A VAL* 1.3 62.8 + - - +
92A MET* 3.8 13.9 - - + +
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Residues in contact with VAL 91 (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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11A VAL* 3.7 34.5 - - + -
14A PHE* 3.5 47.1 - - + -
43A VAL* 3.8 20.2 - - + -
44A ALA 3.9 2.2 - - - -
45A VAL* 4.5 12.3 - - + +
78A LEU* 3.7 1.9 - - - +
79A TYR* 2.8 33.6 + - + -
80A ASP* 2.9 25.2 + - + +
81A PHE* 5.1 0.4 - - - -
90A LEU* 1.3 73.0 - - - +
92A MET* 1.3 55.7 + - - +
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Residues in contact with MET 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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43A VAL* 3.3 9.5 - - - +
44A ALA 2.8 34.4 + - - +
46A LYS* 3.5 29.8 - - + -
63A GLU* 4.8 3.4 - - - +
67A LEU* 3.4 30.7 - - + -
76A VAL* 3.9 18.8 - - + +
77A ALA 3.2 17.9 - - - +
78A LEU* 4.5 4.3 - - + +
79A TYR* 4.1 4.7 - - - -
90A LEU* 3.8 19.5 - - + +
91A VAL* 1.3 79.0 - - - +
93A GLU* 1.3 64.9 + - - +
164A ALA* 6.5 0.4 - - - -
165A ASP 6.2 1.3 - - - +
401A 3RF 3.8 24.5 - - + -
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Residues in contact with GLU 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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72A HIS 5.5 0.2 - - - +
73A GLU 4.9 0.2 - - - +
75A ILE 3.9 2.3 - - - +
76A VAL* 3.5 12.7 - - + +
77A ALA* 2.9 46.1 + - + +
79A TYR* 3.6 29.6 - - + +
92A MET* 1.3 71.6 - - - +
94A TYR* 1.3 72.4 + - - +
95A CYS* 4.5 2.8 - - - -
147A SER* 5.2 1.6 + - - -
162A LYS* 2.8 41.3 + - - -
401A 3RF 2.8 22.5 + - - -
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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