Contacts of the helix formed by residues 428 - 438 (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 LEU 428 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424A GLU* 2.9 43.0 + - + +
427A GLY* 1.3 78.5 - - - +
429A LEU* 1.3 64.1 + - - +
430A GLY 3.5 1.8 - - - -
431A SER* 3.3 4.6 + - - +
432A THR* 2.7 37.7 + - - +
517A SER* 3.7 0.4 - - - +
519A ASN* 3.3 34.3 - - - +
520A ASP* 3.7 13.9 - - - +
522A GLU* 3.6 34.3 - - + +
699A LYS* 4.9 2.2 - - - +
1801A QUS 3.5 28.0 - - + +
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Residues in contact with LEU 429 (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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115A VAL* 3.8 15.9 - - + -
116A LEU 3.7 23.3 - - - +
117A LEU* 3.7 20.0 - - + -
164A PHE* 4.9 0.2 - - + -
261A LEU* 3.9 3.8 - - + -
265A GLY 3.5 27.6 - - - +
266A ASP* 3.7 5.8 - - - +
267A PRO* 4.3 5.4 - - + -
355A ILE* 4.2 7.6 - - + -
423A ALA* 3.2 17.3 + - + +
426A PHE* 3.5 25.4 - - + +
427A GLY 3.4 17.0 - - - +
428A LEU* 1.3 77.8 - - - +
430A GLY* 1.3 57.7 + - - +
432A THR* 3.9 2.4 - - - -
433A GLU* 2.9 34.8 + - - +
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Residues in contact with GLY 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A TYR* 5.3 0.2 - - - -
355A ILE* 3.7 14.1 - - - +
357A ASN* 2.9 36.5 + - - -
422A ASP 3.0 23.7 + - - -
428A LEU 3.5 0.2 - - - -
429A LEU* 1.3 75.1 - - - +
431A SER* 1.4 64.0 + - - +
433A GLU* 4.1 1.6 - - - +
434A TRP* 3.0 14.2 + - - +
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Residues in contact with SER 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A TRP* 3.7 38.1 - - - +
422A ASP 4.4 0.2 + - - -
428A LEU* 3.3 7.8 + - - +
430A GLY* 1.4 74.7 - - - +
432A THR* 1.3 62.1 + - - +
434A TRP* 3.3 2.8 + - - +
435A ALA* 2.8 31.5 + - - +
520A ASP* 2.7 46.7 + - - +
523A VAL* 4.0 3.5 - - - +
524A PHE* 4.2 7.6 - - - -
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Residues in contact with THR 432 (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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263A GLY 4.0 4.4 - - - +
264A ALA 4.1 0.7 - - - +
265A GLY* 3.6 28.1 + - - +
428A LEU* 2.7 32.4 + - - +
429A LEU 4.0 0.4 - - - -
431A SER* 1.3 81.4 + - - +
433A GLU* 1.3 57.2 + - - +
435A ALA* 3.3 2.3 + - - +
436A GLU* 2.8 36.2 + - + +
522A GLU* 4.9 4.3 + - - -
523A VAL* 4.0 23.3 - - + +
527A ARG* 3.5 28.0 - - - +
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Residues in contact with GLU 433 (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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113A TYR* 3.8 26.5 - - + -
115A VAL* 3.9 19.5 - - + -
265A GLY* 3.9 2.8 - - - -
266A ASP* 3.0 30.7 + - + -
273A PRO* 3.2 7.3 - - - +
274A ALA* 2.8 27.4 + - + +
429A LEU 2.9 22.7 + - - +
430A GLY* 4.1 0.4 - - - +
432A THR* 1.3 74.4 - - - +
434A TRP* 1.3 58.7 + - - +
436A GLU* 3.2 8.0 + - - +
437A GLU* 2.9 29.3 + - - +
1753A CA 2.5 30.0 - - - -
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Residues in contact with TRP 434 (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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111A ALA* 4.0 16.5 - - + +
113A TYR* 3.4 26.6 + - - +
357A ASN* 3.5 8.5 - - - +
359A ILE* 3.6 38.9 - - + +
373A ILE* 4.5 6.3 - - + -
417A LEU* 4.2 20.9 - - + -
421A TRP* 3.4 26.2 - + + -
430A GLY 3.0 19.0 + - - +
431A SER 3.7 2.0 - - - +
433A GLU* 1.3 77.0 - - - +
435A ALA* 1.3 61.8 + - - +
437A GLU* 3.2 1.7 + - - -
438A ASN* 2.9 60.5 + - + +
442A LEU* 3.9 32.1 - - + -
524A PHE* 3.9 14.1 - + - -
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Residues in contact with ALA 435 (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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431A SER 2.8 18.0 + - - +
432A THR 3.7 2.2 - - - +
434A TRP* 1.3 78.0 - - - +
436A GLU* 1.3 57.1 + - - +
439A SER* 2.8 35.4 + - - -
442A LEU* 3.7 22.4 - - + +
523A VAL* 3.5 32.5 - - + -
524A PHE* 4.2 6.3 - - + -
528A LEU* 4.3 6.4 - - + +
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Residues in contact with GLU 436 (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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264A ALA 3.6 6.1 - - - +
271A GLY 2.8 24.5 + - - +
272A TYR* 3.0 13.2 - - - +
273A PRO* 4.0 16.1 - - - +
432A THR* 2.8 17.3 + - + +
433A GLU* 3.2 13.9 + - - +
435A ALA* 1.3 78.9 - - - +
437A GLU* 1.3 62.7 + - - +
439A SER* 3.7 15.7 + - - -
440A ARG* 4.7 4.2 + - - -
523A VAL* 5.4 0.9 - - + -
527A ARG* 2.7 45.5 + - - +
1753A CA 2.3 30.8 - - - -
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Residues in contact with GLU 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ALA* 5.0 2.6 - - - +
113A TYR* 2.6 37.8 + - - +
273A PRO* 3.7 25.2 - - + +
275A ASN* 4.5 11.8 + - - +
433A GLU 2.9 13.2 + - - +
434A TRP* 3.2 9.0 + - - +
436A GLU* 1.3 78.3 - - - +
438A ASN* 1.3 71.6 + - - +
439A SER* 3.7 1.0 + - - -
440A ARG* 5.1 5.0 + - - -
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Residues in contact with ASN 438 (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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434A TRP* 2.9 62.5 + - + +
435A ALA 3.5 1.8 - - - -
437A GLU* 1.3 90.3 + - - +
439A SER* 1.4 65.0 + - - +
440A ARG 3.2 2.9 - - - -
441A LEU* 3.0 39.8 + - + +
442A LEU* 3.0 24.3 + - + +
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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