Contacts of the helix formed by residues 558 - 566 (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 THR 558 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A PRO* 4.3 7.4 - - + -
151A TYR* 3.9 20.4 - - + -
242A TYR* 3.0 23.3 + - - +
383A PHE* 4.0 16.8 - - + -
385A GLY* 3.8 7.8 - - - -
555A VAL 3.6 18.6 - - - +
556A TYR 2.9 9.5 + - - +
557A GLU* 1.3 79.6 - - - +
559A TYR* 1.3 67.4 + - - +
560A GLU* 3.4 11.6 + - - -
561A LEU* 3.1 23.7 + - - +
562A VAL* 3.3 10.9 + - - +
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Residues in contact with TYR 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LYS* 3.2 39.5 + - - +
74A LEU* 4.0 12.8 - - + -
75A TYR* 3.6 55.7 - + + +
78A THR* 3.4 24.0 + - - +
79A GLN* 4.3 6.3 - - - +
151A TYR* 4.6 2.5 + - - +
385A GLY* 4.2 6.1 - - - -
558A THR* 1.3 72.7 - - - +
560A GLU* 1.3 79.7 + - + +
562A VAL* 3.0 8.0 + - - +
563A GLU* 2.9 44.6 + - + +
570A PHE* 4.3 13.7 - + - -
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Residues in contact with GLU 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TYR* 5.1 5.7 - - - -
79A GLN* 5.3 1.6 + - - +
151A TYR* 2.7 40.2 + - - -
242A TYR* 3.4 15.3 + - - +
558A THR* 3.1 4.9 + - - -
559A TYR* 1.3 95.1 - - + +
561A LEU* 1.3 65.7 + - - +
563A GLU* 4.5 4.9 - - - +
564A LYS* 2.9 53.4 + - - +
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Residues in contact with LEU 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A TYR* 3.7 11.7 + - + -
246A TRP* 3.7 13.7 - - + -
386A ILE* 3.9 25.4 - - + -
551A LEU* 3.7 39.3 - - + -
556A TYR 3.9 4.7 - - - +
557A GLU* 4.0 19.3 - - + -
558A THR* 3.1 21.8 + - - +
560A GLU* 1.3 76.1 - - - +
562A VAL* 1.3 59.2 + - - +
565A PHE* 3.0 37.4 + - + +
566A TYR* 3.4 28.0 + - + +
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Residues in contact with VAL 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 3.9 15.5 - - + -
385A GLY 3.4 25.8 - - - +
386A ILE* 3.5 25.6 - - + -
390A SER* 5.5 0.4 - - - -
456A ILE* 3.8 9.6 - - + -
558A THR 3.3 8.3 + - - +
559A TYR 3.0 7.6 + - - +
561A LEU* 1.3 75.6 - - + +
563A GLU* 1.3 62.2 + - - +
566A TYR* 3.0 12.4 + - + -
567A ASP* 2.9 31.7 + - + -
570A PHE* 4.0 7.9 - - + -
573A HIS* 3.6 30.5 - - + -
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Residues in contact with GLU 563 (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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71A LYS* 4.2 16.5 + - - -
559A TYR* 2.9 50.4 + - + +
560A GLU* 4.4 3.6 - - - +
562A VAL* 1.3 76.1 - - - +
564A LYS* 1.3 77.5 + - - +
568A PRO* 3.2 36.1 - - - +
570A PHE* 4.3 14.6 - - + -
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Residues in contact with LYS 564 (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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242A TYR* 5.5 1.3 - - + +
243A PRO 4.9 4.5 - - - +
560A GLU* 2.9 42.9 + - + +
563A GLU* 1.3 95.1 + - - +
565A PHE* 1.3 92.4 + - + +
568A PRO* 4.7 9.3 - - - +
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Residues in contact with PHE 565 (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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242A TYR* 4.0 8.7 - + - -
243A PRO 3.5 19.3 - - - -
244A ASP* 3.5 29.4 - - - -
245A GLY* 3.6 27.4 - - - -
246A TRP* 4.0 22.2 - + + -
561A LEU* 3.0 25.4 + - + +
564A LYS* 1.3 104.7 - - + +
566A TYR* 1.3 62.3 + - - +
568A PRO* 5.1 1.8 - - - -
1760A NAG 3.1 27.2 + - - +
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Residues in contact with TYR 566 (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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246A TRP* 3.8 17.8 + - + +
386A ILE* 4.0 16.2 - - + -
456A ILE* 3.4 31.9 - - + -
457A GLU 3.7 7.8 + - - -
458A GLY* 3.7 32.5 - - - -
459A ASN* 3.3 28.8 + - - +
549A TYR* 3.7 23.6 - - - +
550A PRO* 4.3 1.6 - - - +
551A LEU* 5.5 0.9 + - - +
561A LEU* 3.6 40.6 - - + +
562A VAL* 3.0 9.2 + - - +
565A PHE* 1.3 79.1 - - - +
567A ASP* 1.3 62.0 + - - +
568A PRO* 3.8 4.9 - - - +
572A TYR* 4.0 3.8 - - - -
1760A NAG 3.4 30.0 - - + +
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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
------------------------------------------------------------
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