Contacts of the strand formed by residues 168 - 177 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D TYR* 3.3 6.2 - - - +
124D ILE 3.2 23.4 + - - +
161D GLN* 4.9 1.3 - - - -
166D PRO* 3.1 5.0 - - - +
167D GLN* 1.3 83.3 - - - +
169D VAL* 1.3 66.6 + - - +
198D LEU 3.1 14.1 - - - -
199D GLY* 3.9 1.3 - - - -
200D VAL* 3.6 13.1 - - - +
201D PHE* 3.5 7.0 - - - -
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Residues in contact with VAL 169 (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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121D ILE* 4.6 1.3 - - + -
122D GLY 3.4 10.3 - - - +
123D TYR* 4.3 3.6 - - + -
157D ALA* 4.4 8.3 - - + +
160D ILE* 3.8 41.3 - - + -
161D GLN* 4.1 21.1 - - + +
166D PRO* 3.4 25.1 - - + -
168D GLY* 1.3 78.6 - - - +
170D GLY* 1.3 66.2 + - - +
171D VAL* 4.4 5.8 - - + -
196D ALA 3.9 0.7 - - - +
197D MET* 3.6 1.0 - - - -
198D LEU* 2.8 39.5 + - + +
201D PHE* 3.5 6.6 - - - +
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Residues in contact with GLY 170 (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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121D ILE* 3.4 3.8 - - - +
122D GLY 2.7 37.8 + - - +
169D VAL* 1.3 74.1 - - - +
171D VAL* 1.3 65.0 + - - +
196D ALA 3.5 5.8 - - - -
197D MET* 3.8 8.1 - - - -
201D PHE* 3.5 18.7 - - - -
211D PHE* 3.5 8.7 - - - -
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Residues in contact with VAL 171 (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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119D VAL* 3.8 26.5 - - + -
120D HIS 3.3 2.9 - - - -
121D ILE* 4.1 9.2 - - + -
153D ALA* 3.9 20.2 - - - +
156D ILE* 3.9 16.2 - - + -
157D ALA* 3.7 31.6 - - + +
160D ILE* 4.2 6.7 - - + -
169D VAL* 4.4 1.6 - - + -
170D GLY* 1.3 79.3 - - - +
172D VAL* 1.3 64.6 + - - +
173D VAL* 4.2 10.8 - - + -
195D SER* 3.0 7.6 - - - -
196D ALA 3.0 31.4 + - - +
197D MET* 4.6 0.6 - - - +
211D PHE* 4.1 0.8 - - - -
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Residues in contact with VAL 172 (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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119D VAL* 3.4 3.1 - - - +
120D HIS* 2.8 52.5 + - + +
171D VAL* 1.3 76.8 - - - +
173D VAL* 1.3 68.0 + - - +
174D GLU* 4.9 3.1 - - + +
193D VAL* 4.0 24.9 - - + -
194D THR 3.5 3.4 - - - +
195D SER* 4.1 10.3 - - - -
197D MET* 4.3 1.3 - - + -
211D PHE* 3.8 22.0 - - + -
212D LEU* 3.8 20.4 - - + -
215D LEU* 4.0 15.3 - - + -
214E HIS* 5.0 6.5 - - + -
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Residues in contact with VAL 173 (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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104D PHE* 3.4 36.6 - - + -
118D LYS 3.6 2.9 - - - +
119D VAL* 4.2 13.9 - - + -
149D GLN* 2.9 31.2 + - + +
152D LEU* 4.3 10.8 - - + -
153D ALA* 3.8 31.9 - - + +
156D ILE* 4.7 0.7 - - + -
171D VAL* 4.2 7.2 - - + -
172D VAL* 1.3 77.9 - - - +
174D GLU* 1.3 62.3 + - - +
193D VAL* 3.3 3.6 - - - +
194D THR* 2.8 31.3 + - - +
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Residues in contact with GLU 174 (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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104D PHE* 3.8 2.8 - - - -
117D GLY* 3.3 2.3 - - - -
118D LYS* 2.9 36.6 + - + +
120D HIS* 4.7 16.2 + - - +
149D GLN* 4.3 0.2 - - - -
172D VAL* 4.2 4.5 + - + +
173D VAL* 1.3 76.0 - - - +
175D GLY* 1.3 61.6 + - - +
191D ARG* 2.7 40.5 + - + +
192D THR 3.2 4.9 - - - +
193D VAL* 3.8 15.5 - - + -
100E LYS* 2.9 23.8 + - - -
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Residues in contact with GLY 175 (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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104D PHE* 4.5 3.6 - - - -
115D PHE* 5.6 0.4 - - - -
116D PHE 3.1 15.5 - - - -
117D GLY* 4.1 0.9 - - - -
149D GLN* 3.8 9.4 + - - -
174D GLU* 1.3 77.3 - - - +
176D VAL* 1.3 66.8 + - - -
177D HIS* 3.8 9.2 - - - -
191D ARG* 3.4 3.3 - - - -
192D THR 2.8 34.5 + - - +
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Residues in contact with VAL 176 (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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115D PHE* 3.1 4.0 - - - +
116D PHE* 2.8 72.0 + - + +
175D GLY* 1.3 78.5 - - - +
177D HIS* 1.3 61.7 + - - +
178D LEU 4.1 0.3 + - - -
181D MET* 3.8 24.2 - - + -
190D SER 3.8 19.5 - - - +
191D ARG* 4.0 11.2 - - + +
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Residues in contact with HIS 177 (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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108D CYS* 5.1 0.6 - - - +
115D PHE* 3.5 30.9 - + + +
149D GLN* 2.8 28.1 + - + -
175D GLY 3.8 10.8 - - - -
176D VAL* 1.3 80.4 - - - +
178D LEU* 1.3 65.4 + - - +
179D CYS* 4.2 16.0 - - - -
180D MET* 3.0 25.3 + - + +
181D MET* 3.2 18.9 + - - +
190D SER 5.3 0.8 + - - -
191D ARG* 6.0 0.2 - - - -
192D THR* 4.2 4.2 - - - -
824D 8DG 3.5 28.5 + - - -
132E LEU* 3.4 33.5 - - + +
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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