Contacts of the strand formed by residues 293 - 298 (chain B) in PDB entry 1OMW
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 ASN 293 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B TYR* 3.2 28.6 + - + +
291B ASP* 3.0 27.2 + - - +
292B PHE* 1.3 84.3 - - - +
294B CYS* 1.3 63.6 + - - +
295B ASN* 4.2 7.0 - - - +
307B VAL* 4.1 18.6 - - + +
308B LEU 3.6 0.8 - - - +
309B ALA* 3.3 31.3 - - - +
315B VAL* 3.6 4.1 - - - +
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Residues in contact with CYS 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 4.8 4.5 - - - -
287B ALA 3.5 19.1 - - - +
288B GLY* 4.5 4.0 - - - -
293B ASN* 1.3 78.2 - - - +
295B ASN* 1.3 64.1 + - - +
296B VAL* 5.3 0.2 - - - -
307B VAL* 3.4 1.8 - - - -
308B LEU* 2.6 68.0 + - + +
315B VAL* 4.6 11.7 - - + -
318B LEU* 3.7 25.6 - - - -
329B THR* 4.9 6.5 - - + -
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Residues in contact with ASN 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B ILE* 3.6 21.4 - - - +
285B LEU 3.7 2.4 - - - +
286B LEU* 3.7 1.4 - - - -
287B ALA* 3.0 30.7 + - - +
289B TYR* 3.4 37.1 - - + -
291B ASP* 5.7 0.4 + - - -
293B ASN* 5.2 5.7 - - - +
294B CYS* 1.3 73.3 - - - +
296B VAL* 1.3 62.2 + - - +
297B TRP* 3.9 15.4 - - + +
304B ARG* 3.4 25.9 + - - -
306B GLY 3.4 2.2 - - - +
307B VAL* 3.5 17.7 - - - +
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Residues in contact with VAL 296 (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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43B ILE* 4.4 14.1 - - + -
45B MET* 4.0 25.1 - - + -
284B LEU* 3.8 25.4 - - + -
285B LEU 3.7 2.7 - - - -
286B LEU* 3.9 24.0 - - + -
294B CYS* 5.2 0.4 - - - -
295B ASN* 1.3 77.0 - - - +
297B TRP* 1.3 61.2 + - - +
304B ARG* 3.7 4.2 - - - +
305B ALA* 2.9 23.8 + - + -
306B GLY* 2.5 31.2 + - - +
308B LEU* 4.1 15.0 - - + -
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Residues in contact with TRP 297 (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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250B CYS* 5.0 2.4 - - - -
264B TYR* 3.8 29.4 - - + +
265B SER* 3.4 43.1 - - - -
266B HIS* 5.6 0.2 - - + -
269B ILE* 4.1 17.3 - - + -
284B LEU* 3.3 13.1 - - - +
285B LEU* 2.9 54.6 + - + +
287B ALA* 4.2 10.3 - - + +
289B TYR* 3.6 25.5 + - - -
295B ASN* 3.9 18.2 - - + +
296B VAL* 1.3 78.3 - - - +
298B ASP* 1.3 59.9 + - - +
299B ALA 3.2 2.3 + - - -
302B ALA 3.6 19.1 - - - -
303B ASP 3.5 5.6 - - - -
304B ARG* 3.6 39.5 - - + -
305B ALA* 4.5 0.7 - - - -
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Residues in contact with ASP 298 (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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39B PRO* 4.4 0.2 - - - +
40B VAL* 3.6 21.5 + - + +
264B TYR* 3.6 1.2 - - - -
283B ARG* 2.7 49.2 + - - -
284B LEU* 4.6 3.8 - - - -
296B VAL 4.3 0.2 + - - -
297B TRP* 1.3 69.1 - - - +
299B ALA* 1.3 61.0 + - - +
300B LEU* 3.3 10.4 + - - +
301B LYS* 3.3 22.9 + - + +
302B ALA* 2.7 32.9 + - - -
303B ASP* 2.7 28.0 + - + +
305B ALA* 4.4 5.1 - - + +
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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