Contacts of the strand formed by residues 313 - 318 (chain A) in PDB entry 7ODC
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 THR 313 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295A THR* 3.6 5.9 - - - +
296A VAL* 2.9 51.3 + - - +
312A GLN* 1.3 90.9 - - + +
314A PHE* 1.3 66.1 + - - +
315A MET* 5.7 0.9 - - - +
352A SER* 3.4 30.5 - - - +
369A ARG* 5.0 7.0 - - - +
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Residues in contact with PHE 314 (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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293A LYS* 3.7 26.7 - - + -
294A LYS 3.5 7.0 - - - -
295A THR* 3.3 28.7 - - + -
311A GLU* 3.5 36.3 - - + -
313A THR* 1.3 77.3 - - - +
315A MET* 1.3 65.5 + - - +
316A TYR* 3.5 30.5 - - + +
351A TYR* 3.7 34.8 - + + -
352A SER 3.1 7.1 + - - -
353A SER* 3.2 8.9 - - - +
354A SER* 3.1 24.1 + - - -
374A GLU* 3.5 26.7 - - + -
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Residues in contact with MET 315 (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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293A LYS* 3.3 5.9 - - - -
294A LYS* 2.9 52.1 + - + +
296A VAL* 4.0 27.8 - - + -
313A THR* 5.7 1.3 - - - +
314A PHE* 1.3 76.2 - - - +
316A TYR* 1.3 63.0 + - - +
317A TYR* 3.3 28.7 - - + +
354A SER* 3.5 17.3 - - - +
356A TRP* 3.5 32.5 - - + +
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Residues in contact with TYR 316 (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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290A ILE* 4.1 22.9 - - + -
292A ALA 3.8 2.2 - - - +
293A LYS* 4.0 19.5 - - + -
314A PHE* 3.5 30.7 - - + +
315A MET* 1.3 77.0 - - - +
317A TYR* 1.3 56.8 + - - +
318A VAL* 5.1 0.2 - - + -
353A SER* 3.8 19.5 + - - -
354A SER 2.9 16.8 + - - +
355A ILE* 3.3 5.9 - - + +
356A TRP* 2.8 33.8 + - - -
372A LEU* 4.3 9.6 - - + -
373A PRO 3.6 4.0 + - - -
374A GLU* 3.5 9.9 - - - -
375A MET* 2.9 49.0 + - + -
381A MET* 4.1 28.0 - - + -
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Residues in contact with TYR 317 (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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290A ILE* 3.5 4.9 - - - -
291A ILE* 2.8 39.3 + - + -
292A ALA* 3.0 40.4 + - + +
293A LYS 4.6 0.2 - - - -
294A LYS* 3.2 44.4 + - + -
315A MET* 3.3 40.6 - - + +
316A TYR* 1.3 75.3 - - - +
318A VAL* 1.3 54.9 + - - +
356A TRP* 3.4 28.7 - + + +
357A GLY 4.3 10.3 - - - +
358A PRO* 5.8 0.4 - - + -
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Residues in contact with VAL 318 (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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288A VAL* 3.7 28.5 - - + -
289A ASN 3.2 14.8 - - - +
290A ILE* 4.1 10.5 - - + -
291A ILE* 4.1 4.7 - - - +
316A TYR 5.0 0.4 - - - -
317A TYR* 1.3 79.9 - - - +
319A ASN* 1.3 58.5 + - - +
320A ASP 3.4 17.0 - - - +
326A PHE* 5.3 0.4 - - + -
355A ILE* 4.0 19.1 - - + -
356A TRP 2.8 18.1 + - - +
357A GLY 3.5 1.0 - - - -
358A PRO* 3.1 29.5 - - - +
366A ILE* 3.5 13.9 - - + -
381A MET* 4.2 12.3 - - + -
383A PHE* 5.6 0.9 - - + -
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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