Contacts of the strand formed by residues 97 - 108 (chain B) in PDB entry 1WUR
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 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A GLU* 3.7 37.7 - - + +
192A THR* 4.4 15.3 - - + -
193A VAL 3.5 8.5 - - - +
194A THR* 4.4 5.2 - - + -
95B GLU 4.1 9.0 - - - +
96B MET* 1.3 76.6 - - - +
98B VAL* 1.3 63.6 - - - +
99B VAL* 4.3 10.5 + - + -
121B ILE 3.8 0.5 - - - +
122B GLY* 3.3 2.4 - - - -
123B TYR* 2.9 64.7 + - + +
125B PRO* 4.7 7.0 - - + -
132B LEU* 4.5 2.9 - - + -
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Residues in contact with VAL 98 (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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191A ARG 3.9 0.2 - - - +
192A THR* 3.3 3.9 - - - +
193A VAL* 2.7 51.0 + - + +
96B MET* 3.8 27.8 - - + -
97B VAL* 1.3 78.3 - - - +
99B VAL* 1.3 66.6 + - - +
100B LYS* 3.9 14.7 + - + -
121B ILE 3.2 8.7 - - - +
211B PHE* 4.1 20.9 - - + -
214B HIS* 4.1 20.4 - - + -
215B LEU* 4.2 17.5 - - + -
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Residues in contact with VAL 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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180A MET* 5.5 4.3 - - + -
190A SER* 3.6 21.3 - - - +
191A ARG 3.7 2.9 - - - -
192A THR* 3.9 9.0 - - - +
97B VAL* 4.4 7.0 - - + -
98B VAL* 1.3 74.5 - - - +
100B LYS* 1.3 58.6 + - - +
102B VAL* 3.8 15.2 - - + +
119B VAL 4.1 1.9 - - - +
120B HIS* 3.6 1.4 - - - -
121B ILE* 2.7 44.2 + - + +
123B TYR* 5.7 0.7 - - + -
132B LEU* 3.8 33.2 - - + +
135B PHE* 3.9 29.6 - - + -
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Residues in contact with LYS 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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174A GLU* 2.9 30.4 + - - -
190A SER* 2.9 20.8 + - - -
191A ARG* 2.9 53.6 + - + +
193A VAL* 3.6 18.4 - - - +
98B VAL* 3.8 10.5 - - + +
99B VAL* 1.3 73.9 - - - +
101B GLY* 1.3 62.2 + - - +
102B VAL 3.4 2.7 - - - -
120B HIS* 3.4 18.8 - - + +
214B HIS* 3.0 30.8 + - - +
215B LEU* 4.1 19.1 - - + -
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Residues in contact with GLY 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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189A HIS* 3.0 36.0 - - - +
190A SER* 3.2 1.1 + - - -
100B LYS* 1.3 73.1 - - - +
102B VAL* 1.3 60.3 + - - +
103B GLU 3.0 8.0 + - - -
118B LYS* 4.0 15.5 - - - -
119B VAL 3.6 0.2 + - - -
120B HIS* 3.0 27.2 + - - -
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Residues in contact with VAL 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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187A LYS* 4.0 9.6 - - + -
190A SER* 3.8 21.5 - - - +
99B VAL* 3.8 21.1 - - + +
100B LYS 4.4 0.4 - - - +
101B GLY* 1.3 74.6 - - - +
103B GLU* 1.3 72.2 + - - +
104B PHE 3.5 0.2 + - - -
119B VAL* 2.8 46.4 + - + +
121B ILE* 5.2 5.4 - - + -
135B PHE* 5.4 0.2 - - + -
136B ALA* 3.9 37.2 - - + +
139B VAL* 4.1 16.2 - - + -
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Residues in contact with GLU 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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186A GLU 4.3 1.4 - - - +
187A LYS* 2.8 47.5 + - + +
188A GLN* 2.7 33.2 + - - +
189A HIS* 3.0 46.1 + - + +
101B GLY 3.0 4.6 + - - +
102B VAL* 1.3 77.5 - - - +
104B PHE* 1.3 60.2 + - - +
105B TYR* 4.5 20.6 - - + +
117B GLY 3.2 13.0 - - - +
118B LYS* 4.2 3.6 - - + +
139B VAL* 4.5 0.2 - - - +
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Residues in contact with PHE 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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187A LYS* 4.5 3.4 - - - +
103B GLU* 1.3 76.5 - - - +
105B TYR* 1.3 79.6 + - - +
106B SER* 4.1 2.2 - - - -
115B PHE* 3.7 41.7 - + - -
116B PHE* 3.2 26.2 - - - +
117B GLY* 2.9 38.9 + - - +
118B LYS 3.4 11.9 - - - -
119B VAL* 3.6 17.0 - - + -
139B VAL* 3.8 23.6 - - + -
140B ASP* 5.1 1.6 - - - -
143B ALA* 4.4 5.8 - - + -
152B LEU* 3.7 14.6 - - + -
173B VAL* 3.5 28.0 - - + -
174B GLU 3.8 3.6 - - - -
175B GLY* 4.5 3.4 - - - -
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Residues in contact with TYR 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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187A LYS* 5.7 3.1 - - - -
72B LEU* 6.2 4.0 - - + -
103B GLU* 4.5 22.0 - - + +
104B PHE* 1.3 82.9 - - - +
106B SER* 1.3 61.5 + - - +
114B PRO* 6.0 3.8 - - + -
115B PHE 3.8 3.8 - - - -
116B PHE* 3.5 36.6 - + + -
140B ASP* 5.6 1.0 + - - -
143B ALA* 3.4 20.0 - - - +
144B ARG* 4.4 6.9 + - - +
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Residues in contact with SER 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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104B PHE* 4.3 5.8 - - - -
105B TYR* 1.3 73.8 - - - +
107B MET* 1.3 69.3 + - - +
114B PRO* 3.1 9.7 - - - +
115B PHE* 2.9 50.5 + - - +
143B ALA* 2.7 29.2 + - - -
145B ARG 3.4 6.4 + - - -
147B GLN* 3.6 17.3 - - - +
152B LEU* 4.7 1.6 - - - -
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Residues in contact with MET 107 (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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69B TRP* 3.7 30.3 - - + +
72B LEU* 3.6 37.0 - - + +
73B THR* 6.6 0.2 - - + -
106B SER* 1.3 78.6 + - - +
108B CYS* 1.3 63.4 + - - +
112B LEU 3.7 13.2 - - - +
113B LEU 3.6 5.2 - - - -
114B PRO* 3.5 37.0 - - + -
115B PHE* 3.7 3.7 - - - -
145B ARG 3.7 7.7 + - - +
146B LEU* 3.4 20.7 - - + -
147B GLN 2.8 26.0 + - - +
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Residues in contact with CYS 108 (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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107B MET* 1.3 70.6 - - - +
109B GLU* 1.3 61.4 + - - +
110B HIS 3.1 0.4 - - - +
111B HIS* 3.3 20.0 - - - -
112B LEU* 2.8 31.8 + - - +
113B LEU 2.9 24.6 + - - +
115B PHE* 3.5 15.4 - - + -
147B GLN 3.3 7.0 - - - +
177B HIS* 4.9 1.1 - - - +
179B CYS* 3.9 5.4 - - - -
1002B ZN 2.3 37.7 - - - -
822C 8DG 3.7 16.8 - - + +
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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