Contacts of the helix formed by residues 193 - 200 (chain C) in PDB entry 1OHV
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 THR 193 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C SER* 3.8 15.9 + - - +
141C GLU* 2.4 36.4 + - + +
191C GLY 3.8 0.2 - - - -
192C ARG* 1.3 78.8 - - - +
194C MET* 1.3 56.5 + - - +
195C GLY 3.0 0.7 + - - -
196C CYS* 3.1 10.6 + - - -
197C LEU* 2.7 30.5 + - - +
800C FES 4.6 7.0 - - - -
138D CYS* 4.5 17.0 - - + -
141D GLU* 3.9 33.0 - - + -
142D ASN* 5.0 4.7 - - - +
145D LYS* 5.4 0.4 - - - +
193D THR* 4.9 1.6 - - + +
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Residues in contact with MET 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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141C GLU* 3.7 0.2 + - - -
193C THR* 1.3 70.9 - - - +
195C GLY* 1.3 62.1 + - - +
197C LEU* 3.9 8.8 - - - +
198C ALA* 3.5 16.1 + - - +
210C ILE* 4.4 19.1 - - + -
211C PRO* 4.7 12.0 - - - +
212C SER* 5.5 0.9 - - - -
213C PHE* 4.4 8.3 - - - -
141D GLU* 3.0 18.7 + - - +
144D PHE* 3.5 28.3 - - + -
145D LYS* 4.5 11.4 - - + -
148D PHE* 3.9 23.3 - - - -
195D GLY* 3.1 37.5 - - - +
213D PHE* 4.5 13.4 - - + -
215D TRP* 3.6 19.7 - - + -
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Residues in contact with GLY 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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141C GLU* 2.9 12.8 + - - -
144C PHE* 3.8 12.1 - - - -
194C MET* 1.3 76.1 - - - +
196C CYS* 1.3 63.9 + - - -
198C ALA* 3.1 19.4 + - - +
199C THR 3.7 2.4 + - - -
213C PHE* 4.6 4.0 - - - -
215C TRP* 4.1 3.3 - - - -
194D MET* 3.1 34.2 - - - +
195D GLY 4.9 0.2 - - - +
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Residues in contact with CYS 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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137C SER* 3.2 32.5 - - - -
140C ASN* 3.8 10.5 - - - -
141C GLU* 3.0 13.5 + - - -
144C PHE* 3.8 5.3 - - - -
190C HIS* 3.4 26.6 - - - +
191C GLY 3.4 14.8 - - - +
193C THR* 3.3 17.5 - - - +
195C GLY* 1.3 73.8 - - - +
197C LEU* 1.3 58.4 - - - +
199C THR* 2.7 32.5 + - - -
200C THR* 3.1 9.7 + - - -
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Residues in contact with LEU 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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191C GLY 3.6 7.0 - - - +
192C ARG* 3.9 30.7 - - + +
193C THR 2.7 22.9 + - - +
194C MET* 4.0 6.1 - - - +
196C CYS* 1.3 73.2 - - - +
198C ALA* 1.3 53.3 + - - +
200C THR* 2.9 20.8 + - + +
206C HIS* 3.6 27.1 - - + +
207C LYS* 2.7 45.9 + - + +
210C ILE* 3.7 39.7 - - + +
211C PRO 5.4 1.6 - - - +
212C SER* 5.2 0.2 - - - -
145D LYS* 4.3 3.1 - - + -
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Residues in contact with ALA 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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184C SER* 4.0 1.6 + - - -
194C MET 3.5 5.2 + - - +
195C GLY 3.1 12.9 + - - +
197C LEU* 1.3 79.5 - - - +
199C THR* 1.3 57.3 + - - +
200C THR 3.4 0.2 - - - -
201C HIS* 3.1 11.6 + - - -
207C LYS* 3.7 1.1 - - - +
212C SER* 3.7 23.3 - - - +
213C PHE* 3.9 29.8 - - + +
215C TRP* 4.0 11.0 - - + +
172D ASN* 2.9 24.1 + - - +
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Residues in contact with THR 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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144C PHE* 3.5 27.5 - - + -
182C ILE* 4.0 13.0 - - + +
184C SER* 3.3 21.7 - - - +
188C ALA* 3.6 2.6 - - - +
190C HIS* 3.2 36.1 - - - +
195C GLY 4.1 0.2 - - - +
196C CYS 2.7 19.9 + - - -
198C ALA* 1.3 77.0 - - - +
200C THR* 1.3 59.3 + - - +
201C HIS* 3.1 16.9 - - - -
215C TRP* 3.8 23.8 - - + -
263C ILE* 3.9 2.0 - - + -
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Residues in contact with THR 200 (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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188C ALA 3.5 7.0 - - - +
189C PHE* 3.6 19.1 - - + +
190C HIS 3.0 16.3 + - - -
191C GLY 2.8 23.7 + - - +
196C CYS 3.1 3.4 + - - -
197C LEU* 2.9 22.7 + - + -
199C THR* 1.3 75.5 - - - +
201C HIS* 1.3 78.8 + - - +
202C SER* 3.3 24.9 - - - +
206C HIS* 5.0 1.6 - - + +
207C LYS* 2.8 23.6 + - + -
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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