Contacts of the strand formed by residues 257 - 262 (chain A) 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 MET 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A ARG* 4.4 6.3 - - - -
243A LEU* 3.6 35.4 - - + -
244A SER* 4.0 3.6 - - - +
247A SER* 3.0 17.5 + - - +
256A CYS* 1.3 76.4 - - - +
258A SER* 1.3 60.5 + - - +
259A TYR* 2.7 38.8 - - - +
260A ALA* 3.7 13.5 - - - -
269A PHE* 4.0 11.2 - - + -
270A ILE 3.3 8.3 - - - +
271A LEU* 4.0 13.7 - - + -
511A LEU* 4.1 13.5 - - + -
513A ILE* 3.7 28.1 - - + +
516A ARG* 3.4 14.4 - - - -
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Residues in contact with SER 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A TYR* 3.7 25.6 + - - -
256A CYS 4.3 0.9 + - - -
257A MET* 1.3 74.8 - - - +
259A TYR* 1.3 89.7 + - - +
270A ILE 2.9 7.5 + - - -
271A LEU* 5.8 0.9 - - - -
272A ASP* 5.4 0.7 + - - -
513A ILE* 3.1 32.0 + - - +
516A ARG* 3.5 34.2 + - - +
517A TRP 5.2 0.6 + - - -
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Residues in contact with TYR 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ILE* 4.7 4.7 - - + -
186A LEU* 3.2 33.0 - - + -
191A PHE* 4.8 0.4 - + - -
210A LYS* 3.1 31.6 + - + -
217A TYR* 4.1 7.0 - + - -
257A MET* 2.7 31.9 - - - +
258A SER* 1.3 100.7 - - - +
260A ALA* 1.3 62.0 + - - +
261A PHE* 4.8 0.2 - - + -
269A PHE* 3.9 0.5 - - - -
270A ILE* 3.3 36.0 + - + -
511A LEU 3.4 8.7 - - - +
512A THR* 3.7 24.0 - - + -
517A TRP* 3.3 25.5 - + + +
520A GLU* 2.8 26.6 + - - -
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Residues in contact with ALA 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A LEU* 5.6 0.7 - - - +
240A ARG* 4.4 8.3 - - - -
257A MET* 3.7 14.4 - - - -
259A TYR* 1.3 79.9 - - - +
261A PHE* 1.3 70.9 + - - +
268A SER 3.5 14.1 - - - +
269A PHE* 4.4 3.1 - - + -
509A PHE* 4.0 24.5 - - + +
510A PRO* 3.5 2.0 - - - +
511A LEU* 3.0 27.1 + - + +
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Residues in contact with PHE 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A LEU* 3.7 42.2 - - + +
187A THR* 3.2 31.4 - - - -
188A MET* 4.2 8.3 - - + -
191A PHE* 3.8 19.3 - + - -
219A MET* 4.0 12.6 - - + -
260A ALA* 1.3 82.7 - - - +
262A HIS* 1.3 70.5 + - - +
263A THR* 4.4 2.5 - - + -
267A LEU* 3.6 3.1 - - - -
268A SER* 2.9 59.9 + - - +
270A ILE* 3.9 10.8 - - + -
509A PHE* 4.0 6.6 - - - -
510A PRO* 4.2 14.4 - - + -
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Residues in contact with HIS 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A LEU 4.8 3.8 - - - +
187A THR* 5.8 1.9 - - - +
224A LYS* 3.8 11.4 + - - +
261A PHE* 1.3 81.3 - - - +
263A THR* 1.3 81.7 + - - +
264A PRO* 5.2 1.3 - - + +
266A LYS 3.5 4.5 - - - -
267A LEU* 3.8 21.1 - - + -
503A GLN* 5.7 5.8 - - - -
506A TYR* 4.8 10.2 + - + +
507A ARG* 6.3 0.6 - - - -
509A PHE* 4.7 4.9 - - + -
510A PRO* 3.9 27.6 - - + +
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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