Contacts of the strand formed by residues 168 - 177 (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 GLY 168 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B TYR* 3.3 5.9 - - - +
124B ILE 3.1 22.5 + - - -
161B GLN* 5.0 1.6 - - - -
166B PRO* 3.0 9.8 - - - +
167B GLN* 1.3 82.9 - - - +
169B VAL* 1.3 62.2 + - - +
198B LEU 3.2 13.9 - - - -
199B GLY* 4.1 1.3 - - - -
200B VAL* 3.6 12.9 - - - +
201B PHE* 3.4 7.0 - - - -
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Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ILE* 4.4 1.6 - - + -
122B GLY 3.2 13.2 - - - +
123B TYR* 4.0 5.6 - - + -
157B ALA* 3.8 21.5 - - + +
160B ILE* 3.8 33.4 - - + -
161B GLN* 3.9 14.8 - - + +
166B PRO* 4.3 6.3 - - + -
168B GLY* 1.3 76.1 - - - +
170B GLY* 1.3 67.5 + - - +
171B VAL* 4.4 4.7 - - + -
196B ALA 4.0 0.9 - - - +
197B MET* 3.7 0.7 - - - -
198B LEU* 2.8 50.3 + - + +
201B PHE* 3.3 7.6 - - - +
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Residues in contact with GLY 170 (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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121B ILE* 3.5 0.5 - - - +
122B GLY 2.7 37.5 + - - +
169B VAL* 1.3 74.1 - - - +
171B VAL* 1.3 67.9 + - - +
196B ALA 3.3 8.3 - - - -
197B MET* 3.7 8.3 - - - -
201B PHE* 3.5 18.6 - - - -
211B PHE* 3.5 8.0 - - - -
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Residues in contact with VAL 171 (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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119B VAL* 3.8 26.7 - - + -
120B HIS 3.4 3.6 - - - +
121B ILE* 4.3 4.7 - - + -
153B ALA* 3.8 29.4 - - - +
156B ILE* 3.9 13.9 - - + -
157B ALA* 3.7 31.9 - - + +
160B ILE* 4.3 9.6 - - + -
169B VAL* 4.4 1.8 - - + -
170B GLY* 1.3 80.0 - - - +
172B VAL* 1.3 65.5 + - - +
173B VAL* 4.1 3.4 - - + -
195B SER* 3.0 8.8 - - - -
196B ALA 2.9 32.1 + - - +
197B MET* 4.7 0.4 - - - -
211B PHE* 4.1 0.8 - - - -
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B VAL* 3.4 2.9 - - - +
120B HIS* 2.8 51.1 + - + +
171B VAL* 1.3 78.3 - - - +
173B VAL* 1.3 67.4 + - - +
174B GLU* 4.9 2.9 - - + +
193B VAL* 3.9 24.5 - - + -
194B THR 3.5 2.9 - - - +
195B SER* 4.1 9.9 - - - -
197B MET* 4.4 0.9 - - + -
211B PHE* 3.8 22.2 - - + -
212B LEU* 3.8 20.0 - - + -
215B LEU* 3.9 14.1 - - + -
214C HIS* 4.9 5.6 - - + -
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Residues in contact with VAL 173 (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* 3.5 33.7 - - + -
118B LYS 3.6 3.1 - - - +
119B VAL* 4.1 15.3 - - + -
149B GLN* 2.8 31.9 + - + +
152B LEU* 4.3 9.0 - - + -
153B ALA* 3.7 33.7 - - + +
156B ILE* 4.8 0.7 - - + -
171B VAL* 4.1 6.5 - - + -
172B VAL* 1.3 78.6 - - - +
174B GLU* 1.3 62.5 + - - +
193B VAL* 3.3 3.5 - - - +
194B THR* 2.8 30.0 + - - +
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Residues in contact with GLU 174 (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* 3.8 2.8 - - - -
117B GLY* 3.2 2.4 - - - -
118B LYS* 2.9 37.8 + - + +
120B HIS* 4.6 17.3 + - + +
149B GLN* 4.2 0.4 - - - -
172B VAL* 4.2 2.9 - - + -
173B VAL* 1.3 75.8 - - - +
175B GLY* 1.3 61.1 + - - +
191B ARG* 3.0 36.2 + - + -
192B THR 3.2 2.5 - - - +
193B VAL* 3.5 16.1 - - + +
100C LYS* 2.9 38.3 + - - -
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Residues in contact with GLY 175 (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* 4.5 4.3 - - - -
115B PHE* 5.6 0.2 - - - -
116B PHE* 3.1 14.6 - - - -
117B GLY* 4.1 0.9 - - - -
149B GLN* 3.8 8.1 - - - +
174B GLU* 1.3 76.4 - - - +
176B VAL* 1.3 65.7 + - - -
177B HIS* 4.0 9.1 - - - -
191B ARG* 3.6 5.6 - - - -
192B THR* 2.9 34.6 + - - +
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Residues in contact with VAL 176 (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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115B PHE* 3.1 4.0 - - - +
116B PHE* 2.8 69.5 + - + +
175B GLY* 1.3 77.9 - - - +
177B HIS* 1.3 61.7 + - - +
178B LEU 4.1 0.6 + - - -
181B MET* 3.8 23.3 - - + -
190B SER 3.8 21.3 - - - +
191B ARG* 4.3 12.8 - - + -
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Residues in contact with HIS 177 (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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108B CYS* 4.9 0.6 - - - +
115B PHE* 3.4 32.7 - + + +
149B GLN* 2.9 27.0 + - + -
175B GLY 4.0 7.4 - - - -
176B VAL* 1.3 79.8 - - - +
178B LEU* 1.3 61.4 + - - +
179B CYS* 4.1 16.4 - - - -
180B MET* 3.0 31.3 + - + +
181B MET* 3.2 18.9 + - - +
190B SER 5.5 0.4 + - - -
192B THR* 4.3 4.5 - - - -
132C LEU* 3.4 25.9 - - + +
822C 8DG 3.3 36.8 + - - -
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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