Contacts of the helix formed by residues 677 - 693 (chain B) in PDB entry 4OL0
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 SER 677 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638B ILE* 4.7 6.4 - - - +
669B ALA 5.6 0.2 - - - -
670B VAL* 4.8 11.6 - - - -
673B VAL* 3.5 21.7 - - - +
674B GLY 4.2 2.5 + - - -
676B GLY* 1.3 81.0 + - - +
678B ALA* 1.3 61.1 + - - +
679B ALA* 3.2 3.8 - - - +
680B LEU* 3.4 30.1 + - - +
681B LEU* 3.1 27.6 + - - +
707B LEU* 6.5 0.2 - - - -
711B TYR* 3.1 20.6 + - - -
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Residues in contact with ALA 678 (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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675B LYS 4.0 8.9 + - - +
676B GLY 3.7 1.8 - - - -
677B SER* 1.3 78.1 - - - +
679B ALA* 1.3 63.7 + - - +
681B LEU* 3.2 24.3 + - + +
682B GLN* 4.4 1.7 + - - +
711B TYR* 3.7 12.2 + - + -
717B CYS* 5.8 3.8 - - - -
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Residues in contact with ALA 679 (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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635B GLN* 6.0 3.6 - - - +
638B ILE* 6.0 2.9 - - + -
639B GLN* 6.1 3.1 - - - +
677B SER* 3.2 1.3 - - - -
678B ALA* 1.3 77.1 - - - +
680B LEU* 1.3 60.7 + - - +
681B LEU 3.1 5.6 + - - -
682B GLN* 5.5 0.3 - - - +
683B PRO* 3.6 17.0 - - - +
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Residues in contact with LEU 680 (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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638B ILE* 4.0 32.1 - - + +
642B TRP* 3.4 55.9 - - + -
666B LEU* 5.2 7.2 - - + -
669B ALA* 6.0 2.7 - - + -
670B VAL* 4.7 16.2 - - + -
677B SER* 3.4 29.0 + - - +
679B ALA* 1.3 78.1 - - - +
681B LEU* 1.3 66.7 + - - +
682B GLN 3.7 0.2 - - - -
683B PRO* 3.5 5.1 - - - +
684B LEU* 3.3 27.1 + - + +
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Residues in contact with LEU 681 (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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677B SER* 3.1 11.7 + - - +
678B ALA* 3.2 19.5 - - + +
679B ALA 3.1 2.0 - - - -
680B LEU* 1.3 77.4 - - - +
682B GLN* 1.3 65.8 + - - +
684B LEU* 3.1 8.5 + - - +
685B VAL* 2.8 38.4 + - + +
707B LEU* 4.2 23.3 - - + -
711B TYR* 3.6 37.7 - - + -
717B CYS* 4.1 28.9 - - + -
721B LEU* 5.4 7.4 - - + -
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Residues in contact with GLN 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678B ALA 4.4 1.2 + - - +
679B ALA 4.4 1.2 + - - +
681B LEU* 1.3 81.9 - - - +
683B PRO* 1.3 66.4 - - + +
685B VAL* 3.7 18.7 - - - +
686B THR* 2.8 49.4 + - - +
720B GLY* 5.3 11.9 + - - -
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Residues in contact with PRO 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642B TRP* 3.9 25.5 - - + +
679B ALA 3.6 17.0 - - - +
680B LEU* 3.5 8.1 - - - +
681B LEU 3.5 3.4 - - - -
682B GLN* 1.3 94.7 - - + +
684B LEU* 1.3 55.3 + - - +
686B THR* 3.3 6.2 + - - -
687B GLN* 2.8 31.7 + - - +
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Residues in contact with LEU 684 (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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642B TRP* 3.6 29.3 - - + -
649B LEU* 5.4 4.0 - - + -
666B LEU* 3.7 29.2 - - + -
670B VAL* 4.8 5.4 - - + -
680B LEU* 3.3 34.1 + - + +
681B LEU* 3.1 5.7 + - + +
683B PRO* 1.3 79.7 - - - +
685B VAL* 1.3 56.5 + - - +
687B GLN* 3.3 1.7 + - + -
688B MET* 2.8 64.5 + - + +
703B LEU* 4.4 4.7 - - + -
707B LEU* 4.3 19.5 - - + -
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Residues in contact with VAL 685 (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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681B LEU* 2.8 36.3 + - + +
682B GLN* 3.7 20.6 - - - +
684B LEU* 1.3 71.0 - - - +
686B THR* 1.3 58.3 + - - +
688B MET* 3.2 9.6 + - - +
689B VAL* 2.9 33.7 + - + +
707B LEU* 4.1 11.7 - - + -
720B GLY 5.0 5.2 - - - +
721B LEU* 5.5 1.6 - - + -
724B MET* 3.5 52.3 - - + -
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Residues in contact with THR 686 (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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682B GLN* 2.8 38.0 + - - +
683B PRO* 3.6 7.1 - - - +
685B VAL* 1.3 78.0 - - - +
687B GLN* 1.3 57.2 + - - +
689B VAL* 3.5 4.9 + - - +
690B ASN* 2.8 36.6 + - + +
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Residues in contact with GLN 687 (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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642B TRP* 3.5 11.3 - - + -
646B SER* 2.5 55.2 + - - -
649B LEU* 3.6 19.3 - - + +
650B ASN* 3.3 30.6 + - - +
683B PRO 2.8 17.1 + - - +
684B LEU* 3.8 5.2 - - + +
686B THR* 1.3 74.6 - - - +
688B MET* 1.3 61.7 + - - +
690B ASN* 4.1 6.1 - - + +
691B VAL* 2.8 41.2 + - + +
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Residues in contact with MET 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649B LEU* 5.7 0.6 - - + +
684B LEU* 2.8 38.5 + - + +
685B VAL* 3.2 13.0 + - + +
687B GLN* 1.3 76.6 - - - +
689B VAL* 1.3 59.0 + - + +
691B VAL* 4.1 0.9 - - - +
692B TYR* 2.8 35.2 + - - +
700B PHE* 3.7 44.6 - - + +
703B LEU* 3.5 32.1 - - + -
704B GLY* 4.3 6.1 - - - +
707B LEU* 3.4 33.9 - - + -
724B MET* 4.6 7.6 - - + +
728B LEU* 4.6 7.0 - - + -
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Residues in contact with VAL 689 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685B VAL* 2.9 27.4 + - + +
686B THR* 3.9 4.9 - - - +
688B MET* 1.3 74.3 - - + +
690B ASN* 1.3 63.8 + - - +
692B TYR* 4.0 0.7 - - - +
693B HIS* 3.2 24.6 + - + +
724B MET* 4.3 18.2 - - + -
727B ALA* 3.5 38.6 - - + +
728B LEU* 4.0 18.6 - - + -
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Residues in contact with ASN 690 (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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650B ASN* 5.0 1.2 - - - +
653B ARG* 4.2 19.6 + - - -
686B THR* 2.8 28.7 + - + +
687B GLN* 3.6 8.4 - - - +
689B VAL* 1.3 76.7 - - - +
691B VAL* 1.3 63.6 + - - +
693B HIS* 3.8 12.3 + - - +
694B VAL* 3.9 10.7 - - - +
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Residues in contact with VAL 691 (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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649B LEU* 4.9 4.9 - - + +
650B ASN* 4.0 20.6 - - - +
653B ARG* 3.9 45.1 - - + +
659B VAL* 5.7 0.4 - - + -
687B GLN* 2.8 32.8 + - + +
690B ASN* 1.3 74.5 - - - +
692B TYR* 1.3 66.1 + - - +
693B HIS 3.1 0.7 - - - -
694B VAL* 3.0 9.2 + - - +
695B HIS* 2.9 24.6 + - + +
697B HIS* 5.2 0.2 - - + -
700B PHE* 3.8 28.0 - - + -
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Residues in contact with TYR 692 (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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688B MET 2.8 19.5 + - - +
689B VAL 4.0 1.6 - - - +
691B VAL* 1.3 76.9 - - - +
693B HIS* 1.3 59.1 + - - +
694B VAL 3.2 0.5 + - - -
695B HIS 3.4 10.8 - - - +
696B GLN* 3.0 50.7 + - + +
697B HIS 3.3 31.6 - - - -
698B SER* 5.1 0.5 - - - -
700B PHE* 3.6 18.3 - + + -
701B LEU* 3.6 27.2 - - + +
728B LEU* 3.5 30.7 - - + -
731B PRO* 3.6 19.3 - - + -
732B THR* 2.9 32.6 + - - +
735B LEU* 4.9 0.2 - - - +
748B THR* 4.2 5.5 - - - +
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Residues in contact with HIS 693 (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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689B VAL* 3.2 19.1 + - + +
690B ASN* 3.9 7.9 - - - +
691B VAL 3.1 0.8 - - - -
692B TYR* 1.3 76.8 - - - +
694B VAL* 1.3 61.8 + - + +
696B GLN* 3.0 14.4 + - - +
730B ILE* 6.3 1.6 - - + -
731B PRO* 4.4 24.7 - - + -
734B GLN* 5.4 5.1 + - - -
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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