Contacts of the helix formed by residues 203 - 208 (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 LYS 203 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C SER* 1.3 82.2 + - - +
204C ALA* 1.3 70.2 + - + +
205C ILE* 3.8 22.9 - - + +
206C HIS* 3.0 42.1 + - + +
207C LYS* 3.7 4.5 + - - +
270C GLU 5.7 2.9 - - - +
419C GLU* 5.3 6.0 + - - +
422C ARG* 5.3 3.4 - - - +
440C GLY* 3.2 36.2 + - - +
441C ASP* 4.2 10.1 + - - +
170D MET* 3.5 10.1 - - - +
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Residues in contact with ALA 204 (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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203C LYS* 1.3 75.4 - - - +
205C ILE* 1.3 64.3 + - - +
207C LYS* 2.9 13.7 + - - +
208C ILE* 2.9 17.0 + - - +
166D LEU* 3.8 36.8 - - + +
169D CYS* 3.7 14.7 - - - -
170D MET* 3.4 16.5 - - + +
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Residues in contact with ILE 205 (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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203C LYS* 3.8 21.2 - - + +
204C ALA* 1.3 78.1 - - - +
206C HIS* 1.3 79.6 + - + +
207C LYS 3.5 0.2 + - - -
208C ILE* 4.0 6.6 - - + +
161D PHE* 3.4 39.7 - - + -
166D LEU* 5.3 1.1 - - - +
346D ALA* 4.4 9.9 - - + -
347D PRO 4.1 8.3 - - - +
348D TYR* 4.4 10.3 - - + +
349D ARG* 3.6 42.0 + - + +
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Residues in contact with HIS 206 (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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189C PHE* 4.2 9.2 - + + -
192C ARG* 3.3 31.9 + - - +
197C LEU* 3.6 23.7 - - + +
200C THR* 5.1 1.8 - - + -
202C SER* 2.6 31.3 + - - +
203C LYS* 3.0 33.8 + - + +
204C ALA 3.0 0.2 + - - -
205C ILE* 1.3 91.0 - - + +
207C LYS* 1.3 60.5 + - + +
208C ILE 5.4 0.4 - - - -
210C ILE* 4.8 3.3 - - - +
270C GLU* 5.1 9.0 - - + -
500C ACT 5.1 0.9 - - - -
145D LYS* 4.8 5.0 + - - -
348D TYR* 3.3 31.4 + - + +
349D ARG* 4.9 3.5 - - - +
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Residues in contact with LYS 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C LEU* 2.7 46.3 + - + +
198C ALA* 3.7 2.6 + - - +
200C THR* 2.8 26.4 + - + +
201C HIS* 4.2 3.4 - - - +
203C LYS 3.9 11.7 - - - +
204C ALA 2.9 4.8 + - - +
206C HIS* 1.3 84.8 - - + +
208C ILE* 1.3 67.9 + - - +
209C ASP 3.6 0.2 + - - -
210C ILE* 3.3 24.3 + - - +
212C SER* 4.1 3.3 + - - -
169D CYS* 3.0 39.8 - - - +
170D MET* 4.3 10.5 - - - -
172D ASN* 2.7 28.7 + - - -
176D GLY 4.7 0.3 - - - +
177D CYS* 4.7 4.0 - - - -
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Residues in contact with ILE 208 (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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204C ALA 2.9 17.5 + - - +
205C ILE* 4.0 14.0 - - - +
206C HIS 3.8 0.7 - - - +
207C LYS* 1.3 80.9 - - - +
209C ASP* 1.3 75.5 + - - +
210C ILE* 3.3 9.9 + - - +
156D ARG* 4.6 0.4 - - - +
161D PHE* 3.2 57.0 - - + -
165D GLU* 3.9 24.9 - - + +
166D LEU* 3.8 13.5 - - + -
169D CYS* 3.8 10.8 - - - -
176D GLY 3.9 6.5 - - - +
349D ARG* 3.2 23.5 + - - +
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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