Contacts of the strand formed by residues 88 - 93 (chain D) in PDB entry 4WNP
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46D LYS 3.8 0.6 - - - +
47D CYS* 3.8 4.2 - - - -
48D ILE* 3.7 28.4 + - + +
57D GLN* 3.5 37.2 - - + +
60D LEU* 4.0 24.5 - - + +
61D GLY 4.5 0.9 - - - +
64D ILE* 3.6 29.6 - - + -
82D GLN 3.4 7.0 - - - +
83D GLU* 4.2 18.8 - - + +
87D SER* 1.3 83.2 - - - +
89D TYR* 1.3 71.5 + - - +
90D LEU* 4.0 1.6 - - + -
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Residues in contact with TYR 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D GLU* 4.1 7.9 + - - -
11D VAL* 3.9 30.5 - - + -
16D PHE* 4.2 7.9 - + - -
18D ARG* 3.6 20.9 + - - -
45D VAL* 4.2 10.3 - - + -
46D LYS 3.4 3.4 - - - +
47D CYS* 3.4 35.9 - - + -
64D ILE* 4.4 0.7 - - - +
81D PHE* 3.2 7.2 - - - +
82D GLN* 2.9 56.5 + - - +
87D SER* 3.8 28.9 - - - -
88D VAL* 1.3 79.1 - - - +
90D LEU* 1.3 65.7 + - - +
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Residues in contact with LEU 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D ALA 3.4 2.4 - - - +
45D VAL* 3.3 5.2 - - - -
46D LYS* 2.8 46.0 + - + +
60D LEU* 3.9 27.6 - - + +
63D GLU* 3.7 39.7 - - + +
64D ILE* 3.6 37.2 - - + +
67D LEU* 4.7 1.3 - - + -
78D LEU* 3.9 16.8 - - + -
80D ASP 3.9 3.1 - - - -
81D PHE* 4.4 0.2 - - - -
88D VAL* 4.0 2.0 - - + -
89D TYR* 1.3 78.7 - - - +
91D VAL* 1.3 60.9 - - - +
92D MET* 3.7 13.5 + - - +
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Residues in contact with VAL 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D VAL* 3.8 31.6 - - + -
14D PHE* 3.6 41.5 - - + -
43D VAL* 3.7 26.5 - - + -
44D ALA 3.8 2.2 - - - -
45D VAL* 4.4 10.1 - - + +
78D LEU* 3.7 2.1 - - - +
79D TYR* 2.7 35.6 + - + +
80D ASP* 2.9 28.6 + - + +
81D PHE* 4.9 0.4 - - - +
90D LEU* 1.3 72.2 - - - +
92D MET* 1.3 57.1 + - - +
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Residues in contact with MET 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D VAL* 3.2 10.4 - - - +
44D ALA 2.7 42.7 + - - +
46D LYS* 4.3 8.3 - - + -
63D GLU* 5.0 4.0 - - - +
67D LEU* 3.6 26.5 - - + -
76D VAL* 3.6 32.5 - - + +
77D ALA 3.3 8.1 - - - +
78D LEU* 3.8 24.9 - - - -
79D TYR* 4.0 3.8 - - - -
90D LEU* 4.1 17.7 - - - +
91D VAL* 1.3 74.8 - - - +
93D GLU* 1.3 66.5 + - - +
164D ALA* 6.0 1.6 - - + -
165D ASP 6.1 0.9 - - - +
401D 3RJ 3.9 28.7 - - + -
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Residues in contact with GLU 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D HIS 5.4 0.3 - - - +
75D ILE 3.9 2.4 - - - +
76D VAL* 3.5 12.9 - - + +
77D ALA* 2.9 44.4 + - + +
79D TYR* 3.6 31.7 - - + +
92D MET* 1.3 73.4 - - - +
94D TYR* 1.3 64.9 + - - +
95D CYS* 4.5 2.9 - - - -
147D SER* 5.2 1.6 + - - -
162D LYS* 2.9 40.9 + - - -
401D 3RJ 2.7 28.8 + - - -
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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