Contacts of the strand formed by residues 168 - 177 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123E TYR* 3.2 6.2 - - - +
124E ILE 3.2 22.7 + - - +
161E GLN* 4.9 1.6 - - - -
166E PRO* 3.1 5.1 - - - +
167E GLN* 1.3 83.8 - - - +
169E VAL* 1.3 66.7 + - - +
198E LEU 3.2 13.9 - - - -
199E GLY* 4.0 1.6 - - - -
200E VAL* 3.7 12.9 - - - +
201E PHE* 3.4 7.4 - - - -
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Residues in contact with VAL 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E ILE* 4.7 1.1 - - + -
122E GLY 3.3 11.7 - - - +
123E TYR* 4.2 3.1 - - + -
157E ALA* 4.2 9.0 - - - +
160E ILE* 3.9 35.7 - - + -
161E GLN* 3.6 17.7 - - - +
166E PRO* 3.2 31.2 - - + -
168E GLY* 1.3 72.0 - - - +
170E GLY* 1.3 63.4 + - - +
171E VAL* 4.2 17.3 - - + -
196E ALA 4.0 0.5 - - - +
197E MET* 3.6 0.3 - - - -
198E LEU* 2.8 38.3 + - + +
201E PHE* 3.4 8.1 - - - +
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Residues in contact with GLY 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E ILE* 3.5 2.6 - - - +
122E GLY 2.7 34.6 + - - +
169E VAL* 1.3 75.5 - - - +
171E VAL* 1.3 64.6 + - - +
196E ALA 3.4 7.6 - - - -
197E MET* 3.8 7.9 - - - -
201E PHE* 3.6 17.3 - - - -
211E PHE* 3.5 9.5 - - - -
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Residues in contact with VAL 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E VAL* 3.7 27.6 - - + -
120E HIS 3.4 3.8 - - - +
121E ILE* 4.3 8.3 - - + -
153E ALA* 3.8 18.6 - - - +
156E ILE* 4.0 15.9 - - + -
157E ALA* 3.6 33.9 - - + +
160E ILE* 4.3 0.9 - - + -
169E VAL* 4.2 7.2 - - + -
170E GLY* 1.3 78.4 - - - +
172E VAL* 1.3 64.0 + - - +
173E VAL* 4.3 10.3 - - + -
195E SER* 3.0 7.4 - - - -
196E ALA 2.9 31.4 + - - +
197E MET* 4.4 0.6 - - - +
211E PHE* 4.2 0.4 - - - -
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Residues in contact with VAL 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A HIS* 5.0 5.2 - - + -
118E LYS 3.9 0.7 - - - +
119E VAL* 3.3 4.3 - - - +
120E HIS* 2.8 48.4 + - + +
171E VAL* 1.3 78.3 - - - +
173E VAL* 1.3 67.3 + - - +
174E GLU* 5.3 2.2 - - + -
193E VAL* 3.8 26.2 - - + -
194E THR 3.4 3.6 - - - +
195E SER* 4.0 10.8 - - - -
197E MET* 4.2 1.6 - - + -
211E PHE* 3.8 13.5 - - + -
212E LEU* 3.8 28.0 - - + -
215E LEU* 4.0 13.5 - - + -
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Residues in contact with VAL 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E PHE* 3.5 35.0 - - + -
118E LYS 3.6 3.1 - - - +
119E VAL* 4.2 12.6 - - + -
149E GLN* 2.9 31.2 + - + +
152E LEU* 4.3 10.5 - - + -
153E ALA* 3.8 32.1 - - + +
156E ILE* 4.8 0.7 - - + -
171E VAL* 4.3 6.5 - - + -
172E VAL* 1.3 78.4 - - - +
174E GLU* 1.3 63.5 + - - +
193E VAL* 3.2 3.8 - - - +
194E THR* 2.8 31.5 + - - +
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Residues in contact with GLU 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LYS* 2.9 23.2 + - - -
104E PHE* 3.8 2.9 - - - -
117E GLY* 3.3 2.9 - - - -
118E LYS* 3.0 37.0 + - + +
120E HIS* 4.7 16.9 + - + +
149E GLN* 4.2 0.2 - - - -
172E VAL* 4.2 2.4 - - + -
173E VAL* 1.3 75.8 - - - +
175E GLY* 1.3 61.1 + - - +
191E ARG* 2.8 42.6 + - + +
192E THR 3.1 9.4 - - - +
193E VAL* 3.4 11.9 - - + +
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Residues in contact with GLY 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E PHE* 4.5 3.8 - - - -
115E PHE* 5.5 0.7 - - - -
116E PHE 3.1 13.9 - - - -
117E GLY* 4.1 0.9 - - - -
149E GLN* 3.7 10.3 + - - -
174E GLU* 1.3 77.3 - - - +
176E VAL* 1.3 65.5 + - - -
177E HIS* 3.6 9.7 - - - -
191E ARG* 3.4 4.7 - - - -
192E THR 2.8 33.6 + - - +
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Residues in contact with VAL 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E PHE* 3.1 4.7 - - - +
116E PHE* 2.8 73.0 + - + +
117E GLY* 6.3 0.2 - - - -
175E GLY* 1.3 77.4 - - - +
177E HIS* 1.3 60.7 + - - +
178E LEU 4.1 0.5 + - - -
181E MET* 3.9 23.8 - - + -
190E SER 3.9 18.8 - - - +
191E ARG* 4.0 11.2 - - + +
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Residues in contact with HIS 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LEU* 3.4 32.3 - - + +
825A 8DG 3.7 25.0 + - - -
108E CYS* 5.3 0.2 - - - +
114E PRO 5.1 0.2 - - - +
115E PHE* 3.4 31.6 - + + +
149E GLN* 2.8 30.0 + - + -
175E GLY 3.6 10.0 + - - -
176E VAL* 1.3 79.8 - - - +
178E LEU* 1.3 61.8 + - - +
179E CYS* 3.1 16.3 - - - -
180E MET* 2.9 33.5 + - + +
181E MET* 3.2 17.5 + - - +
190E SER 5.3 0.8 + - - -
191E ARG* 5.8 0.4 - - - -
192E THR* 4.1 5.3 - - - -
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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