Contacts of the strand formed by residues 181 - 185 (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 SER 181 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148D PHE* 4.0 1.3 - - - -
180D TYR* 1.3 74.7 - - - +
182D ILE* 1.3 67.3 + - - +
214D ASP 4.7 0.4 - - - -
215D TRP* 3.3 24.7 - - - +
216D PRO* 3.5 14.7 - - - +
252D TYR* 4.7 2.0 - - - -
257D LYS* 2.9 25.2 + - - -
258D THR 2.8 11.1 + - - -
259D VAL* 3.3 17.7 - - - +
260D ALA* 2.9 27.0 + - - +
261D GLY 3.7 1.7 + - - -
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Residues in contact with ILE 182 (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* 3.9 32.5 - - + -
147D ILE* 4.2 14.1 - - + -
148D PHE* 3.5 29.8 - - + -
181D SER* 1.3 81.1 - - - +
183D LEU* 1.3 71.4 + - - +
184D SER* 3.7 2.3 + - - -
199D THR* 4.1 5.2 - - + +
215D TRP* 3.4 42.0 - - + +
216D PRO* 4.1 2.6 - - - +
261D GLY* 3.4 26.5 - - - +
262D ILE 4.7 0.4 - - - -
263D ILE* 3.9 22.7 - - + +
296D LEU* 5.5 0.7 - - + -
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Residues in contact with LEU 183 (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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182D ILE* 1.3 73.8 - - - +
184D SER* 1.3 73.8 - - - +
185D PHE* 4.1 16.6 - - + -
216D PRO* 3.5 23.1 - - + +
218D ALA* 4.1 13.7 - - + -
245D VAL* 3.8 29.6 - - + +
248D LEU* 4.0 16.8 - - + -
249D ILE* 3.8 18.6 - - + +
259D VAL* 3.6 16.6 - - + +
261D GLY 2.9 9.3 + - - +
262D ILE* 3.5 12.8 - - + -
263D ILE* 3.0 28.8 + - - +
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Residues in contact with SER 184 (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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182D ILE 3.7 1.4 + - - -
183D LEU* 1.3 78.8 - - - +
185D PHE* 1.3 66.2 + - - +
190D HIS* 4.8 0.9 - - - -
198D ALA 4.0 1.0 + - - -
199D THR* 3.3 39.3 - - - +
201D HIS* 2.6 26.5 + - - -
215D TRP* 5.8 1.4 - - - +
216D PRO 3.2 9.3 + - - -
217D ILE* 3.3 5.5 - - - +
218D ALA 2.8 23.4 + - - -
263D ILE* 3.9 11.2 - - - -
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Residues in contact with PHE 185 (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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183D LEU* 4.1 6.1 - - + -
184D SER* 1.3 79.0 - - - +
186D MET* 1.3 66.5 + - - +
188D ALA* 2.9 25.1 + - + +
201D HIS* 3.1 11.0 - - - -
217D ILE* 4.2 0.2 - - - -
218D ALA* 3.1 9.4 - - + +
219D PRO 3.5 26.0 - - - -
220D PHE* 3.8 11.2 - + + -
245D VAL* 3.7 31.2 - - + -
262D ILE* 4.1 11.0 - - + -
263D ILE 3.6 20.6 + - - -
264D VAL* 3.9 14.6 - - + -
268D GLN* 3.8 17.7 - - - +
280D PHE* 4.2 13.9 - + - -
284D LEU* 3.6 33.4 - - + -
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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