Contacts of the strand formed by residues 371 - 380 (chain B) in PDB entry 2OHI
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 PHE 371 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305B ILE* 3.9 23.8 - - + -
311B ILE* 4.0 26.9 - - + -
333B LEU* 4.0 24.0 - - + -
338B PHE* 4.1 21.8 - + + -
343B THR* 4.4 2.5 - - - -
344B ARG* 3.6 40.6 - - + +
345B LYS 4.3 0.7 - - - -
346B ALA* 4.2 8.5 - - + -
366B LEU* 2.9 35.8 + - + +
367B ALA* 3.6 19.4 + - - +
369B ALA* 3.8 15.7 - - + -
370B GLY* 1.3 83.5 - - - +
372B ASP* 1.3 61.3 + - - +
373B VAL* 3.6 4.0 + - - +
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Residues in contact with ASP 372 (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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343B THR* 3.8 21.2 - - + +
344B ARG 3.0 12.4 + - - +
345B LYS* 3.4 35.1 + - + +
346B ALA 3.1 21.2 + - - -
371B PHE* 1.3 69.2 - - - +
373B VAL* 1.3 68.3 + - - +
374B ALA* 3.5 7.8 + - - +
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Residues in contact with VAL 373 (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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346B ALA* 3.6 18.8 - - + +
348B VAL* 4.5 7.4 - - + -
363B LYS* 3.7 45.1 - - + +
366B LEU* 3.7 33.7 - - + -
367B ALA* 4.4 2.9 - - + +
371B PHE 3.6 8.0 + - - +
372B ASP* 1.3 78.8 + - - +
374B ALA* 1.3 59.2 + - - +
375B CYS 4.3 9.4 + - - +
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Residues in contact with ALA 374 (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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345B LYS* 6.5 0.7 - - + -
346B ALA 3.3 12.2 + - - +
347B LEU* 4.3 4.0 - - - +
372B ASP* 3.5 10.8 + - - +
373B VAL* 1.3 74.3 - - - +
375B CYS* 1.3 75.9 + - + +
397B LYS* 6.3 1.1 - - - +
398B LEU* 6.1 0.7 - - - +
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Residues in contact with CYS 375 (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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346B ALA 4.2 0.5 - - - +
347B LEU* 3.4 17.6 - - + +
348B VAL* 3.5 10.2 + - - -
363B LYS* 5.5 3.1 - - - +
373B VAL* 4.2 7.9 + - - +
374B ALA* 1.3 82.6 - - - +
376B GLU* 1.3 74.7 + - - +
377B GLU* 5.7 2.2 - - - +
394B ALA* 6.4 1.1 - - + -
397B LYS* 5.6 8.7 - - - +
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Residues in contact with GLU 376 (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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347B LEU* 4.0 1.1 - - - -
348B VAL* 2.9 15.9 - - + +
359B THR* 2.8 30.3 + - + +
363B LYS* 3.1 37.8 + - - +
375B CYS* 1.3 86.7 - - - +
377B GLU* 1.3 76.9 + - - +
378B GLU* 4.8 8.0 - - + +
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Residues in contact with GLU 377 (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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273B MET* 4.7 1.7 - - - +
277B ILE* 5.3 0.7 - - + -
347B LEU* 4.3 6.7 - - + -
348B VAL 2.9 7.1 + - - -
349B PHE* 3.1 14.5 - - + +
350B GLY 2.9 26.7 + - - +
359B THR* 4.3 0.7 - - - +
375B CYS* 5.7 2.4 - - - +
376B GLU* 1.3 83.4 - - - +
378B GLU* 1.3 61.7 + - - +
379B VAL* 4.2 5.4 - - + +
387B GLU 4.7 0.7 - - - +
390B ALA* 3.6 36.4 - - - +
391B CYS* 4.0 22.9 + - - -
394B ALA* 4.0 23.2 - - + +
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Residues in contact with GLU 378 (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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350B GLY 3.4 9.4 - - - +
352B MET* 2.7 46.9 - - + +
355B ASN 4.9 2.5 - - - +
356B GLY* 4.2 5.9 - - - -
357B GLY 4.3 10.1 + - - -
359B THR* 3.4 30.3 + - + +
376B GLU* 4.1 9.1 - - + +
377B GLU* 1.3 73.9 + - - +
379B VAL* 1.3 66.9 + - - +
380B TYR 4.3 0.5 + - - -
387B GLU* 5.5 0.5 - - - +
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Residues in contact with VAL 379 (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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273B MET* 3.7 29.4 - - + -
350B GLY 2.9 5.9 + - - -
351B SER* 3.1 4.0 - - - -
352B MET* 2.8 32.9 + - - +
377B GLU* 5.1 4.3 - - - +
378B GLU* 1.3 81.0 - - - +
380B TYR* 1.3 65.0 + - - +
381B TYR 3.3 23.0 + - - +
383B PRO* 3.8 27.6 - - + -
387B GLU* 4.3 29.2 - - + +
391B CYS* 5.0 6.1 - - - -
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Residues in contact with TYR 380 (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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109A VAL* 4.8 8.7 + - - +
112A LYS* 4.2 23.4 - - + +
113A GLY* 3.7 13.2 + - - -
116A LYS* 3.0 47.6 + - + +
352B MET* 3.4 31.8 - - + +
353B GLY 3.3 28.5 + - - -
354B GLY* 4.3 3.4 - - - -
378B GLU 4.3 0.8 + - - -
379B VAL* 1.3 68.8 - - - +
381B TYR* 1.3 90.3 + + - +
387B GLU* 4.7 4.0 + - - +
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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