Contacts of the strand formed by residues 98 - 106 (chain B) in PDB entry 4WB7
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 PHE 98 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ALA* 3.8 26.0 - - + -
94B HIS 3.6 21.3 - - - -
95B LEU* 3.2 14.8 + - + +
96B ASP* 3.1 2.3 - - - -
97B GLN* 1.3 82.1 - - + +
99B GLU* 1.3 60.6 + - - +
100B ARG* 3.7 12.0 + - + +
115B VAL* 3.8 34.1 - - + -
116B LYS 3.4 2.5 - - - +
117B HIS* 3.6 37.7 - + - -
118B LYS* 3.9 10.2 + - - -
124B TYR* 4.2 15.3 - + - -
126B MET* 4.8 8.7 - - + -
163B PHE* 4.0 14.6 - + - -
165B PHE* 4.0 15.0 - + - -
174B VAL* 4.2 12.1 - - + -
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Residues in contact with GLU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B PHE* 1.3 71.2 - - - +
100B ARG* 1.3 65.7 + - - +
101B ILE* 3.6 24.3 + - + +
115B VAL* 3.2 5.2 - - - -
116B LYS* 2.8 56.5 + - + +
118B LYS* 3.9 19.3 - - + +
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Residues in contact with ARG 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LEU* 3.6 34.6 + - + +
96B ASP* 5.8 1.2 - - - +
98B PHE* 3.7 12.1 + - + +
99B GLU* 1.3 80.6 - - - +
101B ILE* 1.3 61.6 + - - +
113B MET* 4.1 21.7 - - + +
115B VAL* 4.0 17.9 - - + -
126B MET* 4.0 19.1 - - + -
390B ILE* 3.7 41.0 + - - +
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Residues in contact with ILE 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLU* 3.7 40.8 - - + +
100B ARG* 1.3 76.4 - - - +
102B LYS* 1.3 67.4 + - + +
113B MET* 4.6 2.0 - - - +
114B LEU* 2.9 47.7 + - + +
115B VAL* 4.1 3.4 - - - -
116B LYS* 4.3 14.1 - - + +
123B HIS* 4.9 4.5 - - + +
377B GLY 5.5 1.8 - - - +
379B THR* 5.9 0.7 - - + -
387B GLU* 5.5 1.0 - - - -
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Residues in contact with LYS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ARG 3.9 0.2 - - - -
101B ILE* 1.3 91.2 - - + +
103B THR* 1.3 74.2 + - - +
104B LEU* 3.5 0.6 + - + +
113B MET* 3.4 12.2 - - - +
114B LEU* 2.8 31.0 + - + +
379B THR* 3.5 31.0 + - + +
382B PHE 5.5 0.8 + - - -
383B ASP 4.4 2.6 + - - -
384B ASP* 2.6 43.9 + - - +
385B TYR 4.5 2.6 + - - +
387B GLU* 3.6 14.4 + - - +
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Residues in contact with THR 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LYS* 1.3 87.6 + - - +
104B LEU* 1.3 62.6 + - - +
105B GLY 3.5 20.9 - - - +
106B THR* 3.9 5.6 - - + -
111B ARG* 3.1 36.1 + - + +
112B VAL 3.6 9.2 - - - +
113B MET* 3.8 5.4 - - - +
382B PHE* 5.5 0.5 - - - +
383B ASP 4.4 1.9 - - - +
385B TYR* 3.8 30.4 - - + +
387B GLU* 2.8 35.9 + - - +
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LYS* 4.9 0.9 - - + +
103B THR* 1.3 74.0 - - - +
105B GLY* 1.3 59.6 + - - +
112B VAL* 2.8 11.1 + - + +
113B MET 4.0 3.8 - - - -
114B LEU* 3.6 30.1 - - + +
125B ALA* 4.1 7.9 - - + -
177B TYR* 3.7 30.3 - - + -
182B GLU* 5.1 0.3 - - - +
379B THR* 3.9 25.8 - - + -
382B PHE* 3.4 54.4 - - + +
385B TYR* 3.3 14.0 + - - -
501B ATP 3.9 23.8 + - + +
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Residues in contact with GLY 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B THR* 3.5 3.4 - - - +
104B LEU* 1.3 81.7 - - - +
106B THR* 1.3 68.1 + - - +
112B VAL* 2.8 28.6 + - - +
385B TYR* 3.6 16.4 - - - -
501B ATP 3.6 21.4 + - - +
18J ARG* 4.6 0.4 - - - -
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Residues in contact with THR 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B THR* 3.9 16.2 - - + -
105B GLY* 1.3 80.4 - - - +
107B GLY* 1.3 63.4 + - - +
110B GLY 3.5 9.6 - - - -
111B ARG* 4.3 24.5 - - + +
385B TYR* 3.9 25.0 - - + -
501B ATP 3.8 6.4 - - - +
18J ARG* 2.9 32.9 + - - +
20J ASN* 4.7 2.5 + - - -
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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