Contacts of the helix formed by residues 186 - 197 (chain B) in PDB entry 2WV1
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 ASP 186 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ARG* 3.3 18.7 + - - -
185B GLY* 1.3 73.5 - - - -
187B LEU* 1.3 69.9 + - - +
188B VAL* 3.7 8.7 + - - +
189B SER* 3.2 30.6 + - - +
190B ARG* 3.0 27.2 + - - +
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Residues in contact with LEU 187 (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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91B THR* 4.5 24.2 - - + -
157B ILE* 4.0 24.9 - - + +
161B PRO* 4.2 22.4 - - + +
164B LYS* 4.2 18.4 - - + -
165B LYS* 6.1 4.9 - - + +
185B GLY 4.4 0.9 + - - +
186B ASP* 1.3 75.9 + - - +
188B VAL* 1.3 58.5 + - + +
190B ARG* 3.2 30.0 + - + +
191B ILE* 2.9 34.4 + - + +
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Residues in contact with VAL 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ARG* 3.5 43.3 - - - +
87B LEU* 3.7 35.9 - - + +
88B THR* 3.9 8.3 - - - +
91B THR* 3.8 24.9 - - + +
186B ASP* 3.2 6.9 + - - +
187B LEU* 1.3 76.0 - - + +
189B SER* 1.3 64.3 + - - +
191B ILE* 3.2 9.1 + - - +
192B ILE* 3.0 30.8 + - + +
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Residues in contact with SER 189 (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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84B ARG* 2.7 27.5 + - - +
186B ASP* 3.2 25.1 + - - +
188B VAL* 1.3 78.9 - - - +
190B ARG* 1.3 56.8 + - - +
192B ILE* 3.1 2.8 + - - +
193B SER* 2.9 34.7 + - - -
1199B NO3 3.5 7.1 + - - -
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Residues in contact with ARG 190 (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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145A PHE* 4.8 7.9 - - + -
148A ASN* 3.7 9.3 + - - -
153B TRP* 5.3 0.4 - - - -
157B ILE* 6.6 0.2 - - + -
164B LYS* 3.2 36.9 - - - +
168B ASP* 2.5 44.1 + - - -
185B GLY* 4.6 18.7 - - - +
186B ASP 3.0 24.9 + - - +
187B LEU* 3.6 17.9 - - - +
188B VAL 3.2 0.2 - - - -
189B SER* 1.3 74.7 - - - +
191B ILE* 1.3 63.6 + - + +
193B SER* 3.5 6.0 + - - -
194B ALA* 3.2 22.7 + - - +
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Residues in contact with ILE 191 (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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83B LEU* 4.5 0.7 - - + -
87B LEU* 3.6 40.6 - - + -
91B THR* 5.2 3.1 - - + -
153B TRP* 3.9 11.3 - - + -
154B ILE* 3.8 33.7 - - + +
157B ILE* 4.0 42.2 - - + -
158B VAL* 5.2 3.1 - - + -
187B LEU* 2.9 24.9 + - + +
188B VAL* 3.2 6.7 + - - +
190B ARG* 1.3 74.8 - - + +
192B ILE* 1.3 62.6 + - - +
194B ALA* 3.3 4.2 + - - +
195B LEU* 3.2 27.4 + - + +
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Residues in contact with ILE 192 (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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80B ILE* 4.1 17.3 - - + +
83B LEU* 4.1 20.2 - - + -
84B ARG* 3.7 40.2 - - + +
87B LEU* 4.7 1.6 - - + -
142B PHE* 5.2 1.6 - - + -
188B VAL* 3.0 24.6 + - + +
189B SER 3.8 3.4 - - - +
191B ILE* 1.3 78.5 - - - +
193B SER* 1.3 57.3 + - - +
195B LEU* 3.1 6.9 + - - +
196B THR* 2.9 46.2 + - + +
1199B NO3 3.6 36.8 - - - +
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Residues in contact with SER 193 (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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145A PHE* 3.4 32.8 - - - -
189B SER* 2.9 19.3 + - - -
190B ARG* 4.0 5.7 - - - -
191B ILE 3.4 0.4 - - - -
192B ILE* 1.3 76.4 - - - +
194B ALA* 1.3 62.7 + - - +
196B THR* 3.6 7.6 + - - -
197B ASP* 3.3 19.2 + - - +
1199B NO3 5.6 1.2 + - - -
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Residues in contact with ALA 194 (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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145A PHE* 3.9 24.5 - - + +
149A HIS* 3.8 22.7 - - + +
143B HIS 4.2 6.9 - - - +
153B TRP* 3.8 25.7 - - + -
190B ARG 3.2 15.0 + - - +
191B ILE 3.8 0.2 - - - +
192B ILE 3.3 0.4 - - - -
193B SER* 1.3 78.8 - - - +
195B LEU* 1.3 62.5 + - - +
197B ASP* 4.0 10.7 - - - +
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Residues in contact with LEU 195 (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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83B LEU* 3.3 34.8 - - + -
133B LEU* 3.8 13.7 - - + -
142B PHE* 3.2 19.3 - - + -
143B HIS* 2.7 33.1 + - - +
144B PHE* 4.0 24.0 - - + -
150B THR* 3.8 26.9 - - + -
153B TRP* 4.1 12.1 - - + -
154B ILE* 4.3 1.6 - - + -
191B ILE* 3.2 21.5 + - + +
192B ILE* 3.1 7.7 + - - +
194B ALA* 1.3 79.0 - - - +
196B THR* 1.3 57.6 + - - +
197B ASP 3.3 3.4 + - - -
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Residues in contact with THR 196 (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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80B ILE* 4.0 19.5 - - + -
141B VAL 3.5 22.0 - - - +
142B PHE* 4.2 7.0 - - + -
143B HIS* 4.2 3.5 + - - -
192B ILE* 2.9 33.6 + - + +
193B SER* 3.4 9.9 + - - -
195B LEU* 1.3 77.1 - - - +
197B ASP* 1.3 63.3 + - - +
198B LYS* 3.2 8.8 + - - +
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Residues in contact with ASP 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A PHE 4.5 3.6 - - - +
145A PHE* 3.8 38.9 + - + +
143B HIS* 3.6 19.5 - - - +
193B SER 3.3 16.2 + - - +
194B ALA 4.0 9.0 - - - +
195B LEU 3.3 1.5 - - - +
196B THR* 1.3 74.8 - - - +
198B LYS* 1.3 66.8 + - - +
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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