Contacts of the strand formed by residues 168 - 177 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123C TYR* 3.4 6.1 - - - +
124C ILE 3.2 23.3 + - - -
161C GLN* 4.6 2.2 - - - -
166C PRO* 3.0 6.1 - - - +
167C GLN* 1.3 81.4 - - - +
169C VAL* 1.3 64.2 + - - +
198C LEU 3.2 15.9 - - - -
199C GLY* 3.9 2.0 - - - -
200C VAL* 3.6 11.5 - - - +
201C PHE* 3.4 7.6 - - - -
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Residues in contact with VAL 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ILE* 4.5 1.3 - - + -
122C GLY 3.4 11.9 - - - +
123C TYR* 4.2 3.4 - - + -
157C ALA* 4.5 7.6 - - + +
160C ILE* 3.7 43.5 - - + -
161C GLN* 4.0 20.4 - - + +
166C PRO* 3.3 22.9 - - + -
168C GLY* 1.3 77.7 - - - +
170C GLY* 1.3 66.5 + - - +
171C VAL* 4.3 6.5 - - + -
196C ALA 3.9 1.7 - - - +
197C MET* 3.6 0.9 - - - -
198C LEU* 2.8 38.8 + - + +
201C PHE* 3.4 6.7 - - - +
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Residues in contact with GLY 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C ILE* 3.5 2.8 - - - +
122C GLY 2.7 37.7 + - - +
169C VAL* 1.3 74.5 - - - +
171C VAL* 1.3 63.9 + - - +
196C ALA 3.4 6.1 - - - -
197C MET* 3.7 7.9 - - - -
201C PHE* 3.5 18.9 - - - -
211C PHE* 3.4 9.7 - - - -
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Residues in contact with VAL 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C VAL* 3.8 25.6 - - + -
120C HIS 3.5 2.5 - - - +
121C ILE* 4.3 3.4 - - + -
153C ALA* 3.8 28.0 - - - +
156C ILE* 4.0 14.6 - - + -
157C ALA* 3.6 31.6 - - + +
160C ILE* 4.3 10.8 - - + -
169C VAL* 4.3 2.0 - - + -
170C GLY* 1.3 80.0 - - - +
172C VAL* 1.3 65.4 + - - +
173C VAL* 4.2 3.6 - - + -
195C SER* 3.0 8.0 - - - -
196C ALA* 2.9 34.6 + - + +
197C MET* 4.6 0.2 - - - +
211C PHE* 4.1 0.6 - - - -
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Residues in contact with VAL 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C VAL* 3.4 4.2 - - - +
120C HIS* 2.8 50.8 + - + +
171C VAL* 1.3 78.8 - - - +
173C VAL* 1.3 65.4 + - - +
174C GLU* 4.9 3.8 - - + +
193C VAL* 3.9 24.7 - - + -
194C THR 3.5 2.9 - - - +
195C SER* 4.1 10.5 - - - -
197C MET* 4.3 0.9 - - + -
211C PHE* 3.9 11.9 - - + -
212C LEU* 3.8 28.9 - - + -
215C LEU* 4.0 15.3 - - + -
214D HIS* 4.8 7.0 - - + -
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Residues in contact with VAL 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C PHE* 3.6 33.2 - - + -
118C LYS 3.6 3.1 - - - +
119C VAL* 4.1 14.8 - - + -
149C GLN* 2.9 31.7 + - + +
152C LEU* 4.2 7.0 - - + -
153C ALA* 3.7 31.4 - - + +
156C ILE* 4.6 4.5 - - + -
171C VAL* 4.2 6.5 - - + -
172C VAL* 1.3 77.5 - - - +
174C GLU* 1.3 63.2 + - - +
193C VAL* 3.2 3.5 - - - +
194C THR* 2.8 33.3 + - - +
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Residues in contact with GLU 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C PHE* 3.8 2.7 - - - -
117C GLY* 3.3 2.6 - - - -
118C LYS* 2.9 38.1 + - + +
120C HIS* 4.6 17.0 + - + +
149C GLN* 4.3 0.2 - - - -
172C VAL* 4.2 2.4 - - + +
173C VAL* 1.3 75.1 - - - +
175C GLY* 1.3 60.5 + - - +
191C ARG* 2.9 39.2 + - + +
192C THR 3.2 4.7 - - - +
193C VAL* 3.7 20.5 - - + +
100D LYS* 3.0 23.0 + - - -
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Residues in contact with GLY 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C PHE* 4.5 4.3 - - - -
115C PHE* 5.6 0.4 - - - -
116C PHE 3.1 14.8 - - - -
117C GLY* 4.1 0.9 - - - -
149C GLN* 3.8 9.2 + - - -
174C GLU* 1.3 76.5 - - - +
176C VAL* 1.3 64.2 + - - -
177C HIS* 3.8 9.6 - - - -
191C ARG* 3.6 4.6 - - - -
192C THR 2.9 33.5 + - - +
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Residues in contact with VAL 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C PHE* 3.2 3.1 - - - +
116C PHE* 2.8 70.9 + - + +
175C GLY* 1.3 76.6 - - - -
177C HIS* 1.3 62.9 + - - +
178C LEU 4.0 0.5 + - - -
181C MET* 3.8 23.8 - - + -
190C SER 3.8 20.0 - - - +
191C ARG* 3.9 18.4 - - + -
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Residues in contact with HIS 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C CYS* 5.2 0.4 - - - +
115C PHE* 3.4 31.1 - + + +
149C GLN* 2.7 29.1 + - + -
175C GLY 3.8 10.3 - - - -
176C VAL* 1.3 78.3 - - - +
178C LEU* 1.3 67.2 + - - +
179C CYS* 4.0 13.1 - - - -
180C MET* 3.1 28.8 + - + +
181C MET* 3.2 18.1 - - - +
190C SER 5.4 1.0 + - - -
192C THR* 4.0 6.4 - - - -
132D LEU* 3.3 33.2 - - + +
823D 8DG 3.6 26.6 + - - -
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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