Contacts of the helix formed by residues 193 - 200 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A SER* 3.8 16.7 + - - +
141A GLU* 2.4 36.8 + - + +
191A GLY 3.8 0.2 - - - -
192A ARG* 1.3 78.5 - - - +
194A MET* 1.3 57.6 + - - +
195A GLY 3.0 1.0 + - - -
196A CYS* 3.2 9.2 + - - -
197A LEU* 2.6 30.3 + - - +
800A FES 4.6 6.7 - - - -
138B CYS* 4.5 17.0 - - + -
141B GLU* 3.9 33.0 - - + -
142B ASN* 4.8 6.1 - - - +
145B LYS* 5.3 0.9 - - - +
193B THR* 5.1 1.1 - - + +
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Residues in contact with MET 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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193A THR* 1.3 71.0 - - - +
195A GLY* 1.3 61.7 + - - +
197A LEU* 3.9 7.9 - - - +
198A ALA* 3.5 16.3 + - - +
210A ILE* 4.4 12.8 - - + -
211A PRO* 4.7 13.0 - - - +
212A SER* 5.5 0.7 - - - -
213A PHE* 4.3 8.9 - - - -
141B GLU* 2.9 18.1 + - - +
144B PHE* 3.4 30.3 - - + -
145B LYS* 4.4 17.9 - - + -
148B PHE* 3.8 24.7 - - - -
195B GLY* 3.2 30.7 - - - -
213B PHE* 4.6 11.3 - - + -
215B TRP* 3.7 19.5 - - + -
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Residues in contact with GLY 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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141A GLU* 2.8 13.3 + - - -
144A PHE* 3.8 12.7 - - - -
194A MET* 1.3 76.3 - - - +
196A CYS* 1.3 64.4 + - - +
198A ALA* 3.1 19.4 + - - +
199A THR 3.7 2.1 + - - -
213A PHE* 4.6 3.1 - - - -
215A TRP* 4.1 3.3 - - - -
141B GLU* 4.7 0.2 + - - -
194B MET* 3.3 33.0 - - - +
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Residues in contact with CYS 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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137A SER* 3.2 32.3 - - - -
140A ASN* 3.6 13.5 - - - -
141A GLU* 3.0 12.7 + - - -
144A PHE* 3.8 4.6 - - - -
190A HIS 3.2 27.6 - - - +
191A GLY 3.5 14.1 - - - -
193A THR* 3.5 15.9 - - - +
195A GLY* 1.3 73.6 - - - +
197A LEU* 1.3 63.6 + - - +
199A THR* 2.7 27.2 + - - -
200A THR* 3.1 9.5 + - - -
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Residues in contact with LEU 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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191A GLY 3.6 6.7 - - - +
192A ARG* 3.8 31.6 - - + +
193A THR 2.6 23.4 + - - +
194A MET* 4.0 4.9 - - - +
195A GLY 3.1 0.2 - - - -
196A CYS* 1.3 73.2 - - - +
198A ALA* 1.3 55.7 + - - +
200A THR* 2.9 18.9 + - + +
206A HIS* 3.5 27.6 - - + +
207A LYS* 2.7 45.7 + - + +
210A ILE* 3.7 38.8 - - + -
211A PRO 5.4 1.3 - - - +
212A SER* 5.2 0.2 - - - -
145B LYS* 4.2 3.6 - - + -
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Residues in contact with ALA 198 (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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184A SER* 4.0 1.2 + - - -
194A MET 3.5 5.9 + - - +
195A GLY 3.1 12.5 + - - +
197A LEU* 1.3 79.4 - - - +
199A THR* 1.3 57.1 + - - +
201A HIS* 3.2 12.6 + - - -
207A LYS* 3.7 0.7 - - - +
212A SER* 3.7 24.6 + - - +
213A PHE* 3.9 29.2 - - + +
215A TRP* 4.0 9.9 - - + +
172B ASN* 2.9 25.2 + - - +
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Residues in contact with THR 199 (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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144A PHE* 3.5 27.8 - - + -
182A ILE* 4.1 13.5 - - + +
184A SER* 3.4 21.8 - - - +
188A ALA* 3.5 3.1 - - - +
190A HIS* 3.2 36.1 - - - +
196A CYS 2.7 20.1 + - - -
198A ALA* 1.3 75.0 - - - +
200A THR* 1.3 58.8 + - - +
201A HIS* 3.2 15.3 - - - -
215A TRP* 3.8 25.6 - - + -
263A ILE* 3.9 2.2 - - + -
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Residues in contact with THR 200 (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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188A ALA 3.6 9.6 - - - +
189A PHE* 3.6 15.5 - - + +
190A HIS 3.0 16.8 + - - -
191A GLY 2.8 24.1 + - - +
196A CYS 3.1 3.7 + - - -
197A LEU* 2.9 22.0 + - + -
199A THR* 1.3 75.3 - - - +
201A HIS* 1.3 68.7 + - - +
202A SER* 3.3 24.2 - - - +
206A HIS* 5.0 1.6 - - + +
207A LYS* 2.8 33.0 + - + -
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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