Contacts of the strand formed by residues 314 - 320 (chain F) in PDB entry 4OMC
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 314 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274F PHE* 3.6 34.5 - - + -
289F PHE* 3.2 10.5 - - + -
291F TRP* 3.9 20.4 - - + +
308F TYR 2.7 27.5 + - - +
309F THR* 3.5 2.8 + - - -
311F SER* 3.4 6.9 + - - +
312F ILE 3.3 0.9 - - - +
313F TYR* 1.3 81.1 - - - +
315F LEU* 1.3 61.6 + - - +
316F SER 3.5 0.7 + - - -
337F LEU* 5.9 0.2 - - - +
394F GLN* 4.0 9.2 + - - +
486F HIS* 5.7 0.2 + - - -
534F MET* 5.5 0.5 - - - +
608F NA 2.3 45.7 - - - -
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Residues in contact with LEU 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288F ILE* 3.6 27.8 - - + -
289F PHE 2.8 23.5 + - - +
290F VAL* 3.7 3.4 - - + -
291F TRP 2.9 22.4 + - - +
313F TYR 5.2 1.1 - - - +
314F THR* 1.3 70.6 - - - +
316F SER* 1.3 63.8 + - - +
317F ILE* 3.6 15.6 + - + +
337F LEU* 4.0 15.0 - - + -
378F ILE* 3.9 23.1 - - + -
390F TRP 5.6 0.7 - - - +
393F MET* 4.5 6.3 - - + -
394F GLN* 3.9 34.5 - - + +
397F VAL* 4.0 22.7 - - + -
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Residues in contact with SER 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291F TRP* 3.5 7.4 - - - -
293F SER* 3.4 14.7 - - - -
309F THR* 3.3 49.0 - - - +
314F THR 3.5 4.6 + - - -
315F LEU* 1.3 72.8 - - - +
317F ILE* 1.3 59.4 + - - +
335F SER* 4.2 2.8 + - - -
336F THR* 3.7 19.5 + - - +
337F LEU* 3.0 29.1 + - - +
338F ALA 3.6 5.4 + - - -
608F NA 3.8 1.7 - - - -
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Residues in contact with ILE 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290F VAL* 4.0 7.4 - - + -
291F TRP 2.8 17.0 + - - +
292F ALA* 3.9 2.9 - - - -
293F SER* 3.0 23.4 + - - -
315F LEU* 3.6 24.2 - - + +
316F SER* 1.3 81.2 + - - +
318F SER* 1.3 74.7 + - - +
337F LEU* 5.4 1.3 - - + -
338F ALA* 3.4 24.2 - - + +
339F THR* 4.1 0.2 - - - -
340F THR* 3.9 28.3 - - + +
367F THR* 4.3 2.8 + - - -
370F SER* 4.1 10.1 - - - +
371F ALA* 4.4 5.8 - - - -
374F ALA* 3.7 22.7 - - + -
378F ILE* 6.1 0.9 - - + -
397F VAL* 5.9 1.1 - - + -
429F LEU* 4.9 4.7 - - + -
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Residues in contact with SER 318 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293F SER* 2.7 21.3 + - - -
317F ILE* 1.3 76.9 - - - +
319F SER* 1.3 65.0 + - - +
330F SER* 4.8 3.7 + - - -
331F GLU 4.1 8.1 + - - -
336F THR* 3.4 21.6 + - - +
338F ALA 2.9 8.7 + - - -
339F THR* 3.3 8.2 - - - +
340F THR 3.1 24.1 + - - +
367F THR* 5.5 0.4 - - - -
370F SER* 3.5 2.2 + - - -
422F HIS 5.3 0.2 + - - -
423F SER 3.3 26.0 + - - -
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Residues in contact with SER 319 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318F SER* 1.3 78.1 - - - +
320F ALA* 1.3 60.8 + - - +
326F VAL* 5.4 0.2 - - - +
327F PRO* 3.2 18.1 - - - +
329F TYR* 3.5 39.6 - - - -
330F SER* 4.8 5.0 + - - -
339F THR* 3.5 4.4 - - - +
340F THR 3.3 4.3 - - - -
342F SER* 3.8 4.0 - - - -
367F THR* 3.7 11.6 - - - -
370F SER* 2.8 22.0 + - - -
423F SER 4.6 1.0 - - - +
424F TYR* 3.6 14.2 - - - -
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Residues in contact with ALA 320 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319F SER* 1.3 75.1 - - - +
321F THR* 1.3 69.7 + - - +
324F GLY* 5.1 0.7 - - - -
325F ASN 3.6 7.6 - - - +
327F PRO* 4.0 2.7 - - - -
339F THR* 3.8 15.0 - - + -
340F THR 3.3 4.8 + - - +
341F TYR* 3.4 12.8 - - + -
342F SER 3.0 23.4 + - - +
406F LEU* 4.0 25.6 - - + -
424F TYR* 4.0 7.2 - - + -
428F LEU* 4.4 2.2 - - + -
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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