Contacts of the helix formed by residues 191 - 199 (chain C) in PDB entry 2WPA
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 CYS 191 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167C TRP 4.2 10.1 - - - +
168C TYR* 3.8 20.4 - - + -
187C TRP* 3.0 46.7 + - - -
188C SER 3.6 8.3 - - - +
189C LEU 3.3 0.4 - - - -
190C GLY* 1.3 75.0 - - - +
192C ILE* 1.3 57.2 + - - +
194C ALA* 3.6 3.1 + - - +
195C GLU* 3.0 29.3 + - - +
202C LEU* 4.3 17.7 + - + +
203C PHE* 4.2 19.5 - - - +
267C LEU* 4.3 5.1 - - - +
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Residues in contact with ILE 192 (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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87C LEU* 3.9 26.0 - - + -
91C MET* 5.1 1.1 - - - +
111C LEU* 4.8 7.2 - - + -
128C LEU 3.7 10.1 - - - +
129C LYS* 3.7 30.7 - - - +
130C PRO* 4.1 7.9 - - + -
133C LEU* 3.9 18.8 - - + -
168C TYR* 4.0 17.7 - - + -
188C SER 3.1 13.2 + - - +
189C LEU* 3.6 17.5 - - + +
190C GLY 3.1 0.2 - - - -
191C CYS* 1.3 73.6 - - - +
193C PHE* 1.3 63.8 - - - +
195C GLU* 3.8 7.5 - - - +
196C MET* 3.1 29.8 + - + +
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Residues in contact with PHE 193 (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 ILE* 3.7 28.0 - - + -
108C LEU* 3.8 36.1 - - + -
189C LEU 2.9 12.7 + - - +
190C GLY* 2.9 11.2 + - - +
192C ILE* 1.3 74.1 - - - +
194C ALA* 1.3 65.3 + - - +
196C MET* 3.0 21.6 + - + +
197C VAL* 3.2 18.8 + - + +
255C LEU* 4.1 16.4 - - + -
259C GLY 3.9 18.2 - - - -
262C LEU* 4.3 8.5 - - + -
263C LEU* 3.7 24.9 - - + -
266C MET* 4.6 5.4 - - + -
285C PHE* 3.9 22.9 - + - -
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Residues in contact with ALA 194 (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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190C GLY 3.0 7.4 + - - +
191C CYS 3.8 3.8 - - - +
193C PHE* 1.3 80.0 - - - +
195C GLU* 1.3 58.9 + - - +
197C VAL* 3.0 5.8 + - - +
198C THR* 2.9 35.2 + - + +
200C ARG 4.7 0.4 - - - -
202C LEU* 3.5 34.5 - - + -
251C VAL* 6.0 0.2 - - + -
252C VAL* 4.3 23.1 - - + -
255C LEU* 6.5 0.2 - - - -
263C LEU* 4.3 10.5 - - + +
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Residues in contact with GLU 195 (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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91C MET* 3.3 32.9 - - + +
130C PRO* 4.3 2.3 - - - +
167C TRP* 5.5 2.1 - - - -
168C TYR* 2.8 39.8 + - - -
191C CYS 3.0 17.2 + - - +
192C ILE* 3.8 6.3 - - - +
193C PHE 3.2 0.2 - - - -
194C ALA* 1.3 76.4 - - - +
196C MET* 1.3 61.1 + - - +
199C ARG* 3.1 23.5 + - - +
200C ARG* 3.4 21.5 - - - +
201C ALA* 3.7 25.2 + - - +
202C LEU* 4.7 1.3 + - - +
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Residues in contact with MET 196 (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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87C LEU* 4.0 28.0 - - + -
91C MET* 3.9 21.5 - - - -
99C ILE* 4.4 22.4 + - + +
104C ILE* 3.5 52.5 - - + +
107C TYR* 4.4 19.3 - - + -
108C LEU* 4.9 8.5 - - + +
111C LEU* 5.8 2.9 - - + -
192C ILE* 3.1 23.7 + - + +
193C PHE* 3.0 16.8 + - + +
195C GLU* 1.3 78.6 - - - +
197C VAL* 1.3 63.8 + - - +
199C ARG* 4.0 10.6 + - - +
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Residues in contact with VAL 197 (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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101C LEU* 5.3 3.6 - - + -
104C ILE* 3.7 20.9 - - + -
193C PHE* 3.2 28.5 + - + +
194C ALA* 3.0 10.4 + - - +
196C MET* 1.3 79.2 - - - +
198C THR* 1.3 68.4 + - + +
199C ARG* 3.7 12.1 + - - -
252C VAL* 4.5 9.9 - - + -
254C PRO* 3.8 45.6 - - + +
255C LEU* 4.3 17.5 - - + +
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Residues in contact with THR 198 (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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194C ALA* 2.9 18.9 + - + +
197C VAL* 1.3 79.9 - - + +
199C ARG* 1.3 73.7 + - - +
200C ARG* 2.9 50.0 + - - +
202C LEU* 5.8 3.8 - - + +
251C VAL 3.8 13.0 - - - +
252C VAL* 3.7 27.6 - - + -
253C PRO* 4.9 4.7 - - + -
254C PRO* 5.1 2.7 - - + -
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Residues in contact with ARG 199 (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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91C MET* 5.4 5.4 - - - +
94C SER 4.3 3.8 - - - +
95C ALA* 3.6 25.3 + - + +
96C LEU 3.4 20.2 + - - -
97C THR 3.4 10.9 + - - -
98C GLY* 3.1 28.6 - - - +
99C ILE 5.3 0.4 - - - +
195C GLU* 3.1 18.3 + - - +
196C MET 4.0 7.4 + - - +
197C VAL 3.4 13.2 + - - -
198C THR* 1.3 85.8 + - - +
200C ARG* 1.3 61.3 + - + +
201C ALA 4.3 0.3 + - - -
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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