Contacts of the helix formed by residues 193 - 200 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138C CYS* 4.6 16.6 - - + -
141C GLU* 3.9 33.7 - - + -
142C ASN* 5.0 5.4 - - - +
145C LYS* 5.4 0.2 - - - +
193C THR* 4.9 1.6 - - - +
800C FES 4.6 7.0 - - - -
137D SER* 3.8 16.3 + - - -
141D GLU* 2.4 36.3 + - + +
191D GLY 3.8 0.2 - - - -
192D ARG* 1.3 78.7 - - - +
194D MET* 1.3 56.6 + - - +
195D GLY 3.0 0.9 + - - -
196D CYS* 3.2 10.2 + - - -
197D LEU* 2.7 30.1 + - - +
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Residues in contact with MET 194 (chain D).
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* 3.0 17.4 + - + +
144C PHE* 3.5 27.1 - - + -
145C LYS* 4.5 11.2 - - + -
148C PHE* 3.9 24.7 - - - -
195C GLY* 3.1 38.4 - - - +
213C PHE* 4.5 13.6 - - + -
215C TRP* 3.6 18.2 - - + -
141D GLU* 3.7 0.2 + - - -
193D THR* 1.3 70.5 - - - +
195D GLY* 1.3 60.4 + - - +
197D LEU* 4.0 8.4 - - - +
198D ALA* 3.5 16.5 + - - +
210D ILE* 4.4 19.1 - - + -
211D PRO* 4.8 12.0 - - - +
212D SER* 5.5 0.7 - - - -
213D PHE* 4.3 8.0 - - - -
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Residues in contact with GLY 195 (chain D).
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* 4.8 0.2 + - - -
194C MET* 3.1 35.7 - - - +
141D GLU* 2.9 12.6 + - - -
144D PHE* 3.7 11.6 - - - -
194D MET* 1.3 74.6 - - - +
196D CYS* 1.3 65.0 + - - +
197D LEU 3.1 1.1 - - - -
198D ALA* 3.1 19.4 + - - +
199D THR 3.7 2.3 + - - -
213D PHE* 4.6 3.6 - - - -
215D TRP* 4.0 3.3 - - - -
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Residues in contact with CYS 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D SER* 3.2 32.5 - - - -
140D ASN* 3.7 11.2 - - - -
141D GLU* 3.1 12.8 + - - -
144D PHE* 3.9 4.9 - - - -
190D HIS 3.3 26.7 - - - +
191D GLY 3.4 14.4 - - - +
193D THR* 3.4 16.6 - - - +
195D GLY* 1.3 73.8 - - - +
197D LEU* 1.3 58.5 - - - +
199D THR* 2.7 32.1 + - - -
200D THR* 3.0 10.2 + - - -
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Residues in contact with LEU 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C LYS* 4.4 3.6 - - + +
191D GLY 3.5 6.0 + - - +
192D ARG* 3.9 32.5 - - + +
193D THR 2.7 22.4 + - - +
194D MET* 4.0 6.1 - - - +
195D GLY 3.1 0.2 - - - -
196D CYS* 1.3 74.6 - - - +
198D ALA* 1.3 52.8 + - - +
200D THR* 3.0 18.2 + - + +
206D HIS* 3.6 27.1 - - + +
207D LYS* 2.7 44.6 + - + +
210D ILE* 3.7 39.0 - - + +
211D PRO 5.4 1.8 - - - +
212D SER* 5.1 0.4 - - - -
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Residues in contact with ALA 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C ASN* 2.9 23.9 + - - +
184D SER* 4.0 1.4 + - - -
194D MET 3.5 5.2 + - - +
195D GLY 3.1 13.2 + - - +
197D LEU* 1.3 78.7 - - - +
199D THR* 1.3 58.3 + - - +
201D HIS* 3.0 13.2 + - - -
207D LYS* 3.7 0.7 - - - +
212D SER* 3.7 23.6 - - - +
213D PHE* 3.9 30.1 - - + +
215D TRP* 4.0 10.7 - - + +
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Residues in contact with THR 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D PHE* 3.5 27.8 - - + -
182D ILE* 4.1 13.5 - - + +
184D SER* 3.3 21.8 - - - -
188D ALA* 3.6 2.8 - - - +
190D HIS* 3.2 34.2 - - - +
195D GLY 4.1 0.2 - - - +
196D CYS 2.7 21.0 + - - -
198D ALA* 1.3 74.8 - - - +
200D THR* 1.3 59.9 + - - +
201D HIS* 3.1 16.9 - - - -
215D TRP* 3.8 25.8 - - + -
263D ILE* 4.0 2.7 - - + -
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Residues in contact with THR 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D ALA 3.5 10.3 - - - +
189D PHE* 3.6 15.9 - - + +
190D HIS 3.0 15.8 + - - -
191D GLY 2.8 24.6 + - - +
196D CYS 3.0 2.9 + - - -
197D LEU* 3.0 20.6 + - + -
199D THR* 1.3 75.1 - - - +
201D HIS* 1.3 77.3 + - - +
202D SER* 3.3 24.2 - - - +
206D HIS* 5.0 1.6 - - + +
207D LYS* 2.8 24.7 + - + -
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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