Contacts of the helix formed by residues 657 - 674 (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 ASN 657 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653A PHE* 3.7 4.0 - - - -
654A ASP* 3.0 25.4 + - + +
655A LYS 3.3 1.7 - - - -
656A SER* 1.3 77.8 + - - +
658A PRO* 1.4 59.5 - - - +
659A ILE* 3.0 23.2 + - - +
660A VAL* 3.1 28.8 + - + +
661A LEU* 2.9 27.0 + - - +
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Residues in contact with PRO 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ARG* 6.3 0.7 - - - +
656A SER 3.3 11.6 - - - +
657A ASN* 1.4 86.5 - - - +
659A ILE* 1.3 73.0 + - + +
661A LEU* 3.6 14.3 - - + +
662A ARG* 2.8 30.5 + - - +
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Residues in contact with ILE 659 (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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657A ASN* 3.0 9.9 + - - +
658A PRO* 1.3 90.0 - - + +
660A VAL* 1.3 63.1 + - + +
662A ARG* 3.4 7.4 + - + +
663A MET* 2.9 30.7 + - + +
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Residues in contact with VAL 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653A PHE* 3.5 33.7 - - + -
654A ASP* 5.0 2.9 - - + +
657A ASN* 3.1 33.4 + - + +
659A ILE* 1.3 74.8 - - + +
661A LEU* 1.3 53.6 + - - +
663A MET* 3.2 22.9 + - + +
664A MET* 2.4 46.7 + - + +
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Residues in contact with LEU 661 (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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413A ARG* 4.0 17.9 - - - +
591A ILE* 3.4 26.0 - - + +
592A VAL* 3.5 25.8 - - + -
653A PHE* 3.3 31.7 - - + -
655A LYS* 5.5 5.4 - - + +
657A ASN 2.9 15.6 + - - +
658A PRO* 3.6 12.3 - - + +
660A VAL* 1.3 76.5 - - - +
662A ARG* 1.3 51.5 + - - +
664A MET* 3.0 5.9 + - + +
665A ASN* 2.6 49.3 + - - +
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Residues in contact with ARG 662 (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* 2.5 41.6 + - - +
369A ASP* 3.1 30.1 + - - -
370A ARG* 3.3 29.5 - - - +
658A PRO 2.8 22.5 + - - +
659A ILE* 4.0 8.3 - - + +
661A LEU* 1.3 71.1 - - - +
663A MET* 1.3 56.2 + - - +
665A ASN* 4.1 9.2 - - - +
666A ASP* 2.6 54.2 + - - +
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Residues in contact with MET 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A ARG* 6.1 1.8 - - - +
659A ILE* 2.9 21.2 + - + +
660A VAL* 3.5 20.4 - - + +
662A ARG* 1.3 75.2 - - - +
664A MET* 1.3 85.8 + - - +
666A ASP* 3.8 7.2 - - - +
667A GLN* 2.9 45.3 + - + +
748A GLU* 6.5 0.2 - - - -
749A VAL* 3.8 37.7 - - + +
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Residues in contact with MET 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A PHE* 3.8 16.5 - - + -
649A ARG* 4.1 21.3 - - + +
650A LEU* 3.8 47.3 - - + +
653A PHE* 4.1 11.4 - - + -
660A VAL* 2.4 41.7 + - + +
661A LEU* 3.1 9.2 - - + +
663A MET* 1.3 106.2 - - - +
665A ASN* 1.3 58.0 + - - +
667A GLN* 3.2 14.5 + - - +
668A LEU* 2.9 32.3 + - - +
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Residues in contact with ASN 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A GLU* 4.3 7.5 + - - +
370A ARG* 6.3 0.2 - - - +
413A ARG* 5.0 1.0 - - - +
414A ARG* 3.4 9.2 - - - +
591A ILE 3.0 23.2 + - - -
592A VAL* 3.5 9.8 - - - +
593A LEU* 2.8 44.0 + - + +
661A LEU* 2.6 30.9 + - - +
662A ARG* 3.0 15.7 + - - +
664A MET* 1.3 73.3 - - - +
666A ASP* 1.3 52.1 + - - +
668A LEU* 3.1 8.0 + - - +
669A MET* 2.8 35.3 + - - +
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Residues in contact with ASP 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ARG* 2.8 35.6 + - - -
662A ARG* 2.6 41.6 + - - +
663A MET* 3.8 8.0 - - - +
665A ASN* 1.3 70.7 - - - +
667A GLN* 1.3 56.5 + - + +
669A MET* 4.0 5.9 - - - +
670A PHE* 2.8 55.9 + - + +
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Residues in contact with GLN 667 (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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646A PHE* 3.4 25.0 - - + -
649A ARG* 4.5 2.9 + - - +
663A MET* 2.9 32.4 + - + +
664A MET* 3.5 17.6 - - - +
666A ASP* 1.3 71.4 - - + +
668A LEU* 1.3 63.2 + - - +
670A PHE* 3.9 2.9 - - - -
671A LEU* 3.2 23.6 + - - +
745A THR* 2.8 32.8 + - - +
746A LEU* 3.7 19.3 + - + +
747A SER 3.1 22.6 + - - -
748A GLU* 5.1 0.2 - - - +
749A VAL* 3.7 19.8 - - + +
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Residues in contact with LEU 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A LEU* 4.4 2.6 - - - +
592A VAL* 4.1 16.8 - - + -
593A LEU* 3.8 26.0 - - + +
595A PHE* 3.7 46.9 - - + +
597A CYS* 4.7 14.4 - - + +
646A PHE* 3.6 24.7 - - + -
650A LEU* 4.2 14.4 - - + -
664A MET 2.9 16.9 + - - +
665A ASN* 3.1 14.8 + - - +
667A GLN* 1.3 76.8 - - - +
669A MET* 1.3 63.3 - - - +
671A LEU* 3.3 21.3 + - + +
672A GLU 4.4 1.7 + - - -
746A LEU* 5.2 0.9 - - + -
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Residues in contact with MET 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ARG* 3.6 38.6 - - - +
444A GLU 3.4 14.4 - - - +
445A ARG 4.0 3.6 - - - -
446A GLY 3.5 28.0 - - - +
447A VAL* 4.0 15.3 - - - +
531A ALA* 5.8 0.5 + - - +
593A LEU* 4.1 12.3 - - + +
595A PHE* 4.4 8.2 - - - -
665A ASN 2.8 18.0 + - - +
666A ASP* 3.7 5.2 - - - +
668A LEU* 1.3 75.4 - - - +
670A PHE* 1.3 100.8 + - + +
671A LEU 3.4 1.0 + - - -
672A GLU* 4.0 7.1 + - - +
673A ARG* 3.5 19.4 + - - +
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Residues in contact with PHE 670 (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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370A ARG* 5.0 1.3 - - - -
443A GLN 3.4 23.3 - - - -
444A GLU* 3.5 24.7 - - + -
666A ASP* 2.8 41.5 + - + +
667A GLN* 3.9 4.0 - - - +
669A MET* 1.3 104.6 - - + +
671A LEU* 1.3 57.3 + - - +
672A GLU 3.4 0.4 - - - -
673A ARG* 3.2 26.9 + - + +
674A ALA* 2.9 28.8 + - - +
745A THR* 4.8 8.4 + - + +
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Residues in contact with LEU 671 (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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469A LEU* 3.8 21.3 - - + -
597A CYS* 3.5 32.1 - - + -
600A TYR* 4.9 1.6 - - + -
639A PHE* 3.9 24.9 - - + -
667A GLN 3.2 13.5 + - - +
668A LEU* 3.5 15.5 - - + +
669A MET 3.3 1.2 - - - -
670A PHE* 1.3 73.3 - - - +
672A GLU* 1.3 69.3 + - - +
674A ALA* 3.0 17.9 + - - +
675A PHE* 3.5 15.5 - - + -
742A ALA* 3.8 25.6 - - + +
745A THR* 3.9 7.0 - - - +
746A LEU* 4.0 14.1 - - + -
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Residues in contact with GLU 672 (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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467A THR* 2.6 29.0 + - - -
469A LEU* 3.7 16.2 - - + +
525A PHE* 3.5 16.9 - - + -
529A GLY* 3.3 25.1 - - - +
531A ALA* 3.7 24.5 - - + +
600A TYR* 2.5 31.4 + - - -
669A MET 4.0 7.0 + - - +
670A PHE 3.4 0.2 - - - -
671A LEU* 1.3 78.9 - - - +
673A ARG* 1.3 62.5 + - - +
675A PHE* 3.1 21.7 + - - +
676A ILE 4.1 1.7 + - - -
689A HIS* 2.9 18.4 + - - +
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Residues in contact with ARG 673 (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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442A LEU 3.9 0.6 + - - -
443A GLN* 2.8 37.8 + - - +
446A GLY 3.0 28.5 + - - +
447A VAL 5.5 0.2 + - - -
528A LEU 3.0 26.7 - - - +
529A GLY* 2.9 24.7 + - - -
530A ILE* 3.6 18.3 - - - +
531A ALA 4.8 1.4 - - - +
669A MET* 3.5 31.9 + - - +
670A PHE* 3.2 31.7 + - + +
671A LEU 3.1 0.4 - - - -
672A GLU* 1.3 77.2 - - - +
674A ALA* 1.3 61.6 - - - +
676A ILE* 3.1 24.4 + - + +
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Residues in contact with ALA 674 (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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670A PHE 2.9 11.3 + - - +
671A LEU 3.0 13.3 + - - +
673A ARG* 1.3 78.4 - - - +
675A PHE* 1.4 58.4 + - - +
676A ILE 3.1 6.7 + - - +
738A THR* 3.7 14.6 - - - +
741A ALA* 4.9 3.8 - - + +
742A ALA* 3.6 30.6 + - + +
745A THR* 4.0 17.3 - - + +
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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
------------------------------------------------------------
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