Contacts of the strand formed by residues 265 - 270 (chain D) in PDB entry 3OMA
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 ILE 265 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D TRP* 3.6 23.3 - - + +
147D TYR* 3.6 9.4 - - - +
158D SER* 6.4 0.2 - - - -
192D LEU 4.0 0.8 - - - +
219D TRP* 3.6 49.1 - - + +
220D THR 3.5 33.0 - - - +
221D VAL* 4.2 9.9 - - + -
249D PHE* 3.2 10.9 - - - -
250D GLY* 2.8 42.0 + - - +
251D GLN 4.3 7.6 - - - +
264D PRO* 1.3 78.8 - - - +
266D THR* 1.3 65.3 + - - +
267D VAL* 4.2 12.1 - - + +
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Residues in contact with THR 266 (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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147D TYR* 4.8 3.1 + - - -
158D SER* 6.2 0.6 - - - -
185D TYR* 3.5 22.2 - - - +
192D LEU 3.4 3.8 + - - -
194D THR* 2.8 40.5 + - - +
196D THR 4.8 0.2 - - - +
197D ALA* 3.5 14.1 - - + -
198D MET* 2.9 27.0 + - - +
247D ILE* 3.9 13.5 - - + -
248D PHE 3.7 2.5 - - - -
249D PHE* 3.4 24.2 - - + -
265D ILE* 1.3 71.3 - - - +
267D VAL* 1.3 65.7 + - - +
268D LYS* 4.6 1.3 - - + -
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Residues in contact with VAL 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D MET* 3.3 35.2 - - + +
200D VAL* 4.0 20.2 - - + -
219D TRP* 4.1 17.3 - - + -
221D VAL* 4.1 16.2 - - + -
224D PHE* 3.6 31.0 - - + -
247D ILE* 3.6 4.9 - - - +
248D PHE* 2.9 38.3 + - - +
265D ILE* 4.2 2.7 - - + -
266D THR* 1.3 76.8 - - - +
268D LYS* 1.3 63.1 + - - +
269D VAL* 4.1 2.2 - - + -
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Residues in contact with LYS 268 (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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30D LEU* 4.1 20.9 - - + -
183D ALA 4.6 11.1 + - - -
185D TYR* 3.5 26.7 + - - -
197D ALA* 3.7 21.3 - - + +
198D MET 2.8 11.5 + - - +
199D VAL* 3.4 17.8 - - + +
200D VAL* 3.0 27.4 + - - +
246D GLY 3.5 3.6 - - - -
247D ILE* 4.2 20.0 - - + -
266D THR* 4.2 1.8 - - + -
267D VAL* 1.3 74.4 - - - +
269D VAL* 1.3 62.3 + - - +
270D VAL* 3.8 4.9 + - + -
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Residues in contact with VAL 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D LEU* 3.7 3.3 - - - +
200D VAL* 3.4 15.5 - - + +
201D PRO 4.1 1.1 - - - +
202D VAL* 3.3 42.8 - - + +
224D PHE* 3.7 13.0 - - + -
242D ALA* 3.6 23.6 - - + -
244D ARG 3.4 13.7 - - - +
245D GLU* 3.2 6.4 - - - +
246D GLY 2.9 29.5 + - - +
248D PHE* 3.5 23.3 - - + -
267D VAL* 4.1 1.1 - - + -
268D LYS* 1.3 74.5 - - - +
270D VAL* 1.3 62.9 + - - +
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Residues in contact with VAL 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D LEU* 3.9 25.1 - - + -
199D VAL* 3.7 20.6 - - + -
200D VAL 3.0 16.6 + - - +
201D PRO* 3.3 2.1 - - - +
202D VAL* 2.7 27.4 + - - +
245D GLU* 3.9 11.9 - - - +
268D LYS* 4.5 4.7 - - + +
269D VAL* 1.3 78.8 - - - +
271D SER* 1.3 61.5 + - - +
274D ALA* 3.8 13.2 - - + -
275D TYR* 3.5 33.2 - - + +
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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