Contacts of the strand formed by residues 265 - 270 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B TRP* 3.6 25.6 - - + +
147B TYR* 3.7 8.3 - - - +
158B SER* 5.7 0.2 - - - -
192B LEU 4.0 0.6 - - - +
194B THR* 4.5 0.4 - - - -
219B TRP* 3.6 48.0 - - + +
220B THR 3.7 29.8 - - - +
221B VAL* 4.2 8.3 - - + -
249B PHE* 3.2 9.5 - - - -
250B GLY 2.8 43.3 + - - +
251B GLN 4.0 9.9 - - - +
264B PRO* 1.3 76.6 - - - +
266B THR* 1.3 65.1 + - - +
267B VAL* 4.1 12.6 - - + -
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Residues in contact with THR 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B TYR* 5.0 2.5 + - - -
158B SER* 5.3 1.0 + - - -
185B TYR* 3.4 25.1 - - - +
192B LEU 3.3 11.3 + - - -
194B THR* 3.2 38.8 + - - -
196B THR 4.8 0.2 - - - +
197B ALA* 3.6 14.3 - - + -
198B MET* 3.0 27.3 + - - +
247B ILE* 4.1 11.0 - - + -
248B PHE 3.6 2.0 - - - -
249B PHE* 3.4 17.8 - - + -
265B ILE* 1.3 73.2 - - - +
267B VAL* 1.3 65.3 + - - +
268B LYS* 4.7 1.8 - - + -
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Residues in contact with VAL 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B MET* 3.4 23.6 - - + +
200B VAL* 4.3 9.9 - - + -
219B TRP* 4.0 21.1 - - + -
221B VAL* 3.9 26.0 - - + -
224B PHE* 3.7 29.8 - - + -
240B PHE* 4.5 0.2 - - + -
247B ILE* 3.6 3.3 - - - +
248B PHE* 2.9 38.6 + - + +
265B ILE* 4.1 2.7 - - + -
266B THR* 1.3 77.0 - - - +
268B LYS* 1.3 65.6 + - - +
269B VAL* 4.2 10.1 - - + -
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Residues in contact with LYS 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 4.2 19.7 - - + +
183B ALA 4.5 11.3 + - - -
185B TYR* 3.6 24.7 + - - -
197B ALA* 3.9 20.6 - - + +
198B MET 2.9 8.6 + - - +
199B VAL* 3.4 16.5 - - + +
200B VAL* 3.0 27.2 + - - +
246B GLY 3.5 3.6 - - - -
247B ILE* 4.1 21.9 - - + +
266B THR* 4.2 2.2 - - + -
267B VAL* 1.3 74.3 - - - +
269B VAL* 1.3 62.2 + - - +
270B VAL* 4.0 5.4 - - + -
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Residues in contact with VAL 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 3.6 2.6 - - - +
200B VAL* 3.5 15.3 - - + +
201B PRO 4.1 2.0 - - - +
202B VAL* 3.5 31.6 - - + +
224B PHE* 3.8 9.4 - - + -
242B ALA* 3.6 24.5 - - + -
244B ARG 3.6 20.9 - - - +
245B GLU* 3.3 5.7 - - - +
246B GLY 2.9 28.5 + - - +
248B PHE* 3.4 27.6 - - + -
267B VAL* 4.2 1.3 - - + -
268B LYS* 1.3 74.0 - - - +
270B VAL* 1.3 63.9 - - - +
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 3.8 23.8 - - + -
199B VAL* 3.8 19.5 - - + -
200B VAL 2.9 18.8 + - - +
201B PRO* 3.2 2.4 - - - +
202B VAL 2.7 27.4 + - - -
245B GLU* 3.9 13.2 - - - +
268B LYS* 4.5 4.9 - - + -
269B VAL* 1.3 79.9 - - - +
271B SER* 1.3 70.1 + - - +
274B ALA* 3.8 13.0 - - + -
275B TYR* 3.5 22.7 - - + +
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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