Contacts of the strand formed by residues 177 - 184 (chain E) in PDB entry 2WP9
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 177 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169E LEU* 4.4 27.1 - - + -
170E VAL 3.3 5.8 - - - +
171E LYS* 4.4 20.2 - - + +
175E GLY 3.8 1.1 + - - +
176E ALA* 1.3 74.2 - - - +
178E VAL* 1.3 65.9 + - - +
179E GLY 3.9 11.8 + - - +
195E ALA 4.6 2.6 - - - +
196E ARG 4.9 6.8 - - - +
198E THR* 3.7 30.6 + - - +
231E VAL* 5.4 7.2 - - + -
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Residues in contact with VAL 178 (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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170E VAL* 2.7 29.3 + - + +
171E LYS 4.2 0.7 - - - -
172E ASN* 4.0 36.1 - - + +
176E ALA* 4.2 9.0 - - + +
177E VAL* 1.3 79.1 - - - +
179E GLY* 1.3 55.4 + - - +
192E TYR* 2.8 28.5 + - - +
194E LYS* 4.1 2.4 - - + +
195E ALA 3.2 29.8 + - - +
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Residues in contact with GLY 179 (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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11E VAL* 5.6 0.9 - - - -
169E LEU* 3.6 4.3 - - - +
170E VAL* 2.9 22.4 + - - +
177E VAL* 3.9 6.2 - - - +
178E VAL* 1.3 79.0 - - - +
180E CYS* 1.3 63.5 + - - +
192E TYR* 4.2 0.4 - - - -
193E PHE 3.1 13.2 - - - -
195E ALA* 4.1 4.7 - - - -
198E THR* 3.1 24.1 + - - -
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Residues in contact with CYS 180 (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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11E VAL* 4.7 4.5 - - - -
13E ILE* 3.6 29.4 - - + -
36E LEU* 4.5 11.7 - - - -
166E ALA* 4.4 6.3 - - - -
168E ASP 3.2 21.3 - - - +
169E LEU* 4.0 4.0 - - + -
170E VAL* 3.7 10.8 - - - +
179E GLY* 1.3 76.3 - - - +
181E THR* 1.3 68.4 + - - +
192E TYR* 3.5 2.1 - - - -
193E PHE* 2.8 36.1 + - - +
198E THR* 4.9 0.9 - - + -
225E MET* 4.2 7.2 - - + -
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Residues in contact with THR 181 (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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3E LEU* 4.3 19.1 - - + -
166E ALA* 3.5 3.1 - - - -
167E LEU* 2.8 45.8 + - - +
168E ASP* 3.2 15.6 + - - +
170E VAL* 4.2 13.9 - - + +
180E CYS* 1.3 80.7 - - - +
182E ALA* 1.3 62.4 + - - +
190E VAL* 4.9 3.4 - - + -
191E VAL 3.2 10.5 - - - +
192E TYR* 4.4 5.6 - - + -
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Residues in contact with ALA 182 (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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36E LEU* 4.0 11.4 - - + -
164E TRP* 4.1 9.0 - - + -
165E TYR 3.1 19.7 - - - +
166E ALA* 4.0 3.8 - - - -
167E LEU* 4.1 5.4 - - - -
180E CYS* 5.2 0.2 - - - -
181E THR* 1.3 77.5 - - - +
183E LEU* 1.3 61.2 + - - +
184E CYS 4.0 0.2 + - - -
189E GLU 3.8 0.7 - - - +
190E VAL* 3.4 4.9 - - - +
191E VAL* 2.9 31.9 + - - -
193E PHE* 3.8 27.4 - - + -
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Residues in contact with LEU 183 (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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164E TRP* 3.4 1.7 - - - -
165E TYR* 2.7 55.1 + - + +
167E LEU* 4.2 19.9 - - + +
182E ALA* 1.3 73.7 - - - +
184E CYS* 1.3 67.3 + - - +
185E ILE* 3.2 11.1 + - + -
188E GLY* 3.4 35.7 - - - +
189E GLU 3.6 1.3 - - - -
190E VAL* 3.9 11.9 - - + +
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Residues in contact with CYS 184 (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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163E GLU 4.1 1.1 - - - -
164E TRP* 3.5 52.2 - - + -
183E LEU* 1.3 71.7 - - - +
185E ILE* 1.3 60.8 + - - +
186E GLU* 3.3 9.8 + - - -
187E THR* 3.4 35.2 - - - +
188E GLY* 2.8 31.9 + - - -
189E GLU* 2.8 17.8 + - + +
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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