Contacts of the strand formed by residues 367 - 377 (chain A) in PDB entry 2OR4
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 GLU 367 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A VAL* 1.3 83.6 - - + +
368A PRO* 1.4 55.9 - - - +
369A ASP* 3.1 10.1 - - - -
370A ARG* 3.1 26.6 + - + +
413A ARG* 2.8 53.3 + - - +
414A ARG* 3.2 40.4 + - + -
662A ARG* 2.5 48.3 + - - +
665A ASN* 4.3 5.5 + - - +
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Residues in contact with PRO 368 (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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363A ARG* 4.0 15.7 - - + -
364A GLY 3.7 21.5 - - - +
365A ALA 4.7 1.8 - - - +
366A VAL 3.3 11.2 - - - +
367A GLU* 1.4 87.1 - - - +
369A ASP* 1.3 60.3 + - + +
370A ARG 3.2 3.9 + - - -
371A TYR* 3.5 9.2 - - - -
415A THR* 2.8 30.3 + - - +
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Residues in contact with ASP 369 (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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367A GLU* 3.9 4.9 - - - -
368A PRO* 1.3 81.5 - - + +
370A ARG* 1.3 86.3 + - - +
371A TYR* 4.4 6.5 - - - -
445A ARG* 3.2 32.6 - - - +
662A ARG* 3.1 30.9 + - - -
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Residues in contact with ARG 370 (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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367A GLU* 3.1 15.8 + - + +
368A PRO 3.2 0.6 - - - -
369A ASP* 1.3 123.1 + - - +
371A TYR* 1.3 60.5 + - - +
372A VAL 4.2 0.2 - - - -
414A ARG* 3.5 15.5 - - + +
415A THR* 2.9 29.8 + - - +
444A GLU 3.6 16.6 + - - -
445A ARG* 3.5 6.0 - - - +
447A VAL* 3.9 14.6 - - + -
593A LEU* 6.2 1.1 - - - -
662A ARG* 3.3 31.5 - - - +
666A ASP* 2.8 35.6 + - - -
669A MET* 3.6 34.2 - - - +
670A PHE* 5.0 1.8 - - - -
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Residues in contact with TYR 371 (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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368A PRO 3.5 18.2 - - - -
369A ASP* 4.4 4.7 - - - -
370A ARG* 1.3 77.5 - - - +
372A VAL* 1.3 62.3 + - - +
373A ILE* 4.1 7.4 - - + +
415A THR* 3.5 21.5 - - + -
417A LEU* 4.0 31.2 - - + -
441A LEU* 4.2 22.1 - - + +
442A LEU* 4.8 11.0 - - + -
445A ARG* 2.9 66.4 + - + +
446A GLY* 3.8 4.3 - - - -
447A VAL* 2.8 30.6 + - - +
448A ALA 3.6 3.6 + - - +
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Residues in contact with VAL 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A TYR* 1.3 77.1 - - - +
373A ILE* 1.3 62.5 + - - +
414A ARG* 4.5 5.4 - - - -
415A THR 2.9 12.4 + - - +
416A ILE* 3.2 7.4 - - + +
417A LEU 2.9 22.0 + - - -
447A VAL* 4.1 13.5 - - + -
448A ALA* 3.6 7.9 - - + +
450A ILE* 5.5 0.4 - - + -
584A VAL* 4.1 30.5 - - + +
587A LEU* 3.7 51.1 - - + +
588A ALA* 3.8 11.7 - - + -
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Residues in contact with ILE 373 (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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371A TYR* 4.4 9.4 - - + +
372A VAL* 1.3 79.1 - - - +
374A LEU* 1.3 65.3 + - - +
375A GLY 4.5 0.2 - - - +
417A LEU* 3.3 31.6 - - + +
419A ALA* 5.0 4.0 - - + -
421A TRP* 4.8 11.4 - - + -
434A TRP* 4.5 6.3 - - + -
442A LEU* 3.6 31.4 - - + -
446A GLY* 5.6 2.2 - - - -
448A ALA 2.9 13.5 + - - +
449A TYR* 3.4 26.4 - - + -
450A ILE* 2.8 30.7 + - - +
524A PHE* 4.2 16.6 - - + -
530A ILE* 5.5 4.0 - - + -
584A VAL* 5.3 0.7 - - - -
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Residues in contact with LEU 374 (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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372A VAL 4.1 0.6 + - - -
373A ILE* 1.3 73.1 - - - +
375A GLY* 1.3 60.0 + - - +
395A VAL* 4.3 18.6 - - + +
398A ILE* 3.7 41.5 - - + -
416A ILE* 5.1 0.8 - - + +
417A LEU 2.8 9.1 + - - -
418A PHE* 3.3 25.4 - - + +
419A ALA 3.0 22.1 + - - +
450A ILE* 3.3 34.1 - - + +
452A ALA* 4.0 16.4 - - + -
580A ARG* 4.6 8.5 - - + -
584A VAL* 4.0 20.2 - - + -
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Residues in contact with GLY 375 (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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374A LEU* 1.3 76.4 - - - +
376A GLY* 1.3 59.6 + - - -
395A VAL* 5.2 0.9 - - - -
419A ALA* 3.4 12.6 - - - -
421A TRP* 3.8 7.0 - - - -
449A TYR* 3.1 29.2 + - - -
450A ILE 3.0 8.1 + - - -
451A ASN* 3.2 1.9 - - - +
452A ALA* 2.7 27.3 + - - -
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Residues in contact with GLY 376 (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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375A GLY* 1.3 74.8 - - - -
377A HIS* 1.3 65.4 + - - -
392A ALA* 6.1 1.3 - - - +
395A VAL* 5.1 3.1 - - - +
419A ALA 3.1 10.5 + - - +
420A SER* 3.4 2.8 - - - -
421A TRP* 2.9 30.1 + - - -
451A ASN* 4.6 3.6 - - - -
452A ALA* 3.6 23.7 - - - +
453A ASP* 4.4 0.9 - - - -
519A ASN* 5.9 0.4 - - - -
520A ASP* 4.7 0.9 - - - -
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Residues in contact with HIS 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A GLY* 1.3 76.9 - - - -
378A ARG* 1.3 58.2 + - - +
379A ASP* 2.8 37.5 + - - +
387A ASP* 3.2 1.0 + - - -
388A PRO* 3.2 29.3 - - + +
392A ALA* 4.1 12.2 + - - +
420A SER* 5.0 0.2 - - - -
421A TRP* 3.2 14.6 - - + +
424A GLU* 3.2 38.6 + - + +
425A GLU* 3.4 16.6 - - + -
452A ALA 4.5 2.9 + - - +
453A ASP* 3.2 19.4 + - + -
519A ASN* 4.4 1.1 + - - -
520A ASP* 3.4 8.3 + - - +
1752A ZN 2.0 37.4 - - - -
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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