Contacts of the helix formed by residues 186 - 197 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A ARG* 3.7 11.7 + - - -
185A GLY* 1.3 73.6 - - - -
187A LEU* 1.3 65.0 + - - +
188A VAL* 3.0 13.2 + - - +
189A SER* 2.5 49.2 + - - +
190A ARG* 3.0 25.0 + - - +
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Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A THR* 4.4 19.7 - - + -
157A ILE* 3.6 36.1 - - + +
161A PRO* 5.5 8.5 - - + -
164A LYS* 4.4 16.2 - - + -
185A GLY 3.7 3.4 + - - -
186A ASP* 1.3 71.0 - - - +
188A VAL* 1.3 66.0 + - + +
190A ARG* 3.1 31.1 + - + +
191A ILE* 3.0 36.0 + - + +
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Residues in contact with VAL 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ARG* 3.6 43.7 - - + +
87A LEU* 3.7 28.0 - - + +
88A THR* 4.2 16.8 - - - +
91A THR* 4.7 8.7 - - + +
186A ASP* 3.0 10.5 + - - +
187A LEU* 1.3 78.8 - - + +
189A SER* 1.3 57.3 + - - +
191A ILE* 3.1 10.2 + - + +
192A ILE* 2.8 40.7 + - + +
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Residues in contact with SER 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ARG* 3.0 19.4 + - - +
186A ASP* 2.5 36.5 + - - +
188A VAL* 1.3 70.5 - - - +
190A ARG* 1.3 55.0 + - - +
192A ILE* 3.3 4.4 + - - +
193A SER* 2.7 42.0 + - - -
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Residues in contact with ARG 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LYS* 3.6 22.8 - - - +
168A ASP* 2.6 32.3 + - - -
184A SER 5.2 7.0 + - - -
185A GLY* 5.1 9.6 + - - -
186A ASP 3.0 23.8 + - - +
187A LEU* 3.1 24.3 + - + +
189A SER* 1.3 74.2 - - - +
191A ILE* 1.3 65.1 + - + +
193A SER* 3.9 5.9 - - - -
194A ALA* 3.2 23.0 + - - +
145B PHE* 4.0 14.7 - - + -
148B ASN* 3.4 26.1 + - - +
149B HIS* 5.6 0.9 + - - -
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Residues in contact with ILE 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LEU* 3.5 39.5 - - + -
91A THR* 5.8 2.5 - - + -
153A TRP* 3.9 22.9 - - + -
154A ILE* 4.0 16.4 - - + -
157A ILE* 4.0 43.3 - - + -
158A VAL* 5.5 2.0 - - + -
187A LEU* 3.0 22.8 + - + +
188A VAL* 3.6 7.0 - - + +
190A ARG* 1.3 75.5 - - + +
192A ILE* 1.3 63.8 + - - +
194A ALA* 3.1 13.2 + - - +
195A LEU* 3.2 23.0 + - + +
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Residues in contact with ILE 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ILE* 4.3 27.4 - - + +
83A LEU* 4.4 17.9 - - + -
84A ARG* 3.8 41.5 - - + +
87A LEU* 4.8 1.8 - - + -
142A PHE* 5.3 2.2 - - + -
188A VAL* 2.8 29.4 + - + +
189A SER* 3.8 4.7 - - - +
191A ILE* 1.3 76.2 - - - +
193A SER* 1.3 63.6 + - - +
195A LEU* 3.0 8.7 + - - +
196A THR* 2.9 39.7 + - + +
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Residues in contact with SER 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A SER* 2.7 29.8 + - - -
190A ARG* 3.9 2.8 - - - -
192A ILE* 1.3 74.1 - - - +
194A ALA* 1.3 60.2 + - - +
196A THR* 3.6 9.1 + - - -
197A ASP* 3.2 24.9 + - - +
145B PHE* 3.6 27.9 - - - -
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Residues in contact with ALA 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A HIS 4.3 5.9 - - - +
153A TRP* 3.8 19.8 - - + -
190A ARG 3.2 12.7 + - - +
191A ILE 3.1 10.7 + - - +
193A SER* 1.3 76.6 - - - +
195A LEU* 1.3 61.6 + - - +
196A THR 3.5 0.2 - - - -
197A ASP* 3.9 10.7 + - - +
145B PHE* 3.7 32.2 - - + +
149B HIS* 3.9 14.1 - - + +
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Residues in contact with LEU 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LEU* 3.2 35.7 - - + -
133A LEU* 3.8 14.8 - - + -
142A PHE* 3.3 18.7 - - + -
143A HIS* 2.7 34.7 + - - +
144A PHE* 4.3 16.4 - - + -
150A THR* 3.7 28.9 - - + -
153A TRP* 4.0 13.0 - - + -
154A ILE* 4.3 1.8 - - + -
191A ILE* 3.2 20.8 + - + +
192A ILE* 3.0 7.3 + - - +
194A ALA* 1.3 80.0 - - - +
196A THR* 1.3 59.6 + - - +
197A ASP 3.3 1.2 + - - -
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Residues in contact with THR 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ILE* 4.3 13.9 - - + -
141A VAL 3.4 22.0 - - - +
142A PHE* 4.2 8.7 - - + -
143A HIS* 3.9 9.3 + - - -
192A ILE* 2.9 35.1 + - + +
193A SER* 3.6 10.6 + - - -
195A LEU* 1.3 76.7 - - - +
197A ASP* 1.3 65.4 + - - +
198A LYS* 3.2 12.8 + - - +
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Residues in contact with ASP 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A HIS* 4.0 17.8 - - - +
193A SER 3.2 17.6 + - - +
194A ALA 3.9 11.3 - - - +
195A LEU 3.3 1.7 - - - +
196A THR* 1.3 75.7 - - - +
198A LYS* 1.3 70.4 + - - +
144B PHE 4.4 3.3 - - - +
145B PHE* 3.6 35.9 + - + +
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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