Contacts of the helix formed by residues 698 - 712 (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 698 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656B ASN* 4.4 4.6 - - - +
692B TYR* 4.6 1.1 - - - -
696B GLN 3.3 6.1 + - - -
697B HIS* 1.3 71.4 - - - +
699B CYS* 1.3 54.9 + - - +
700B PHE 3.0 0.4 - - - -
701B LEU* 2.7 37.2 + - - +
702B TYR 3.2 7.6 + - - -
747B ASP* 3.6 36.5 + - - +
748B THR* 3.9 17.3 - - - -
751B ASP* 2.2 32.0 + - - +
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Residues in contact with CYS 699 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656B ASN* 4.5 4.7 - - - +
659B VAL* 3.7 31.2 - - - -
660B GLU* 3.8 39.3 - - + +
663B CYS* 4.0 13.1 - - + +
697B HIS* 3.0 14.1 + - - -
698B SER* 1.3 80.2 + - - +
700B PHE* 1.3 59.3 + - - +
702B TYR* 3.4 10.7 + - + +
703B LEU* 2.9 30.1 + - - +
751B ASP* 4.5 1.1 - - - -
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Residues in contact with PHE 700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649B LEU* 4.0 19.5 - - + -
659B VAL* 3.7 26.7 - - + -
663B CYS* 4.0 15.9 - - - -
688B MET* 3.7 46.4 - - + +
691B VAL* 3.8 34.1 - - + -
692B TYR* 3.6 27.8 - + + -
695B HIS 4.4 2.0 - - - -
697B HIS* 2.9 35.3 + + + +
699B CYS* 1.3 77.9 - - - +
701B LEU* 1.3 58.5 + - - +
703B LEU* 3.8 3.7 - - - +
704B GLY* 3.0 24.6 + - - -
728B LEU* 4.6 6.9 - - + +
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Residues in contact with LEU 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692B TYR* 3.6 36.8 - - + +
698B SER* 2.7 17.4 + - - +
700B PHE* 1.3 71.0 - - - +
702B TYR* 1.3 66.2 + - - +
704B GLY* 3.5 2.1 + - - -
705B SER* 3.1 19.8 + - - -
728B LEU* 4.0 26.9 - - + -
732B THR* 4.0 9.9 - - - +
748B THR* 3.6 33.7 - - + +
751B ASP* 3.7 15.7 - - + +
752B LEU* 3.7 17.9 - - + +
755B LEU* 3.8 19.7 - - + +
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Residues in contact with TYR 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667B ARG* 3.8 38.2 + - + -
698B SER 3.2 2.2 + - - -
699B CYS* 3.6 12.3 - - + +
701B LEU* 1.3 76.1 - - - +
703B LEU* 1.3 59.5 + - - +
705B SER* 2.5 41.1 + - - -
706B ILE* 3.2 27.9 - - + +
751B ASP* 3.7 20.7 - - - +
754B ARG* 3.6 46.6 + - - -
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Residues in contact with LEU 703 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663B CYS* 4.0 40.2 - - + +
666B LEU* 4.2 24.5 - - + +
667B ARG* 4.1 22.2 - - + +
670B VAL* 5.3 0.9 - - + -
684B LEU* 4.4 2.5 - - + -
688B MET* 3.5 36.6 - - + -
699B CYS 2.9 18.5 + - - +
700B PHE* 3.8 4.7 - - + +
702B TYR* 1.3 76.3 - - - +
704B GLY* 1.3 58.6 + - - +
706B ILE* 2.8 29.6 + - + +
707B LEU* 3.3 19.6 + - + +
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Residues in contact with GLY 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688B MET* 4.3 7.2 - - - -
700B PHE 3.0 17.9 + - - -
701B LEU* 3.7 3.1 - - - -
702B TYR 3.2 0.2 - - - -
703B LEU* 1.3 78.1 - - - +
705B SER* 1.3 60.7 + - - +
707B LEU* 3.5 4.4 + - - +
708B VAL* 3.3 26.9 + - - +
724B MET* 4.2 22.8 - - - +
728B LEU* 5.4 0.7 - - - -
755B LEU* 3.5 9.4 - - - +
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Residues in contact with SER 705 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701B LEU 3.1 7.1 + - - -
702B TYR* 2.5 34.2 + - - -
704B GLY* 1.3 74.0 - - - +
706B ILE* 1.3 69.5 + - - +
708B VAL* 3.6 3.3 - - - +
709B ASP* 3.2 15.2 + - - +
754B ARG* 4.0 6.9 - - - +
755B LEU* 3.5 39.7 - - - +
758B ARG* 3.4 24.5 + - - +
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Residues in contact with ILE 706 (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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667B ARG* 3.5 26.2 - - + -
670B VAL* 4.1 20.0 - - + -
671B ARG* 3.8 41.1 - - + +
702B TYR* 3.2 54.1 - - + +
703B LEU* 2.8 12.0 + - + +
705B SER* 1.3 86.6 + - - +
707B LEU* 1.3 60.4 + - + +
709B ASP* 2.7 31.7 + - - +
710B GLU* 3.1 8.5 + - + +
758B ARG* 5.1 2.9 - - - +
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Residues in contact with LEU 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670B VAL* 3.8 34.8 - - + -
677B SER* 6.5 0.2 - - - -
681B LEU* 4.2 21.8 - - + -
684B LEU* 4.3 10.3 - - + -
685B VAL* 4.1 10.8 - - + -
688B MET* 3.4 31.0 - - + -
703B LEU* 3.3 11.8 + - + +
704B GLY* 3.5 6.0 + - - +
706B ILE* 1.3 76.5 - - + +
708B VAL* 1.3 52.3 - - - +
710B GLU* 2.8 5.2 + - - -
711B TYR* 2.7 48.5 + - + +
721B LEU* 4.5 10.3 - - + -
724B MET* 3.8 16.6 - - + -
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Residues in contact with VAL 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704B GLY 3.3 14.5 + - - +
705B SER 3.6 8.5 - - - +
706B ILE 3.2 0.2 - - - -
707B LEU* 1.3 76.5 - - - +
709B ASP* 1.3 58.4 + - - +
712B GLY* 2.8 33.4 + - - +
721B LEU* 4.3 15.2 - - + +
724B MET* 5.4 1.8 - - - -
755B LEU* 3.7 8.7 - - + -
758B ARG* 3.5 32.1 - - + +
759B PHE* 3.3 43.7 - - + -
762B ARG* 3.4 8.9 - - + +
763B SER* 5.7 1.1 - - - +
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Residues in contact with ASP 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671B ARG* 2.6 31.9 + - - +
705B SER 3.2 7.3 + - - +
706B ILE 2.7 15.5 + - - +
708B VAL* 1.3 73.7 - - - +
710B GLU* 1.3 62.2 + - - +
713B MET* 6.1 0.2 - - - +
758B ARG* 3.2 38.2 + - - +
762B ARG* 3.0 49.2 + - - -
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Residues in contact with GLU 710 (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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670B VAL* 4.0 21.1 - - + -
671B ARG* 3.2 33.5 + - - +
674B GLY* 3.8 26.9 - - - +
675B LYS* 3.0 38.9 + - - +
706B ILE* 3.1 12.5 + - + +
707B LEU 2.8 6.4 + - - +
709B ASP* 1.3 83.1 - - - +
711B TYR* 1.3 79.1 + - + +
712B GLY 3.7 0.7 - - - -
713B MET* 5.0 1.5 + - - -
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Residues in contact with TYR 711 (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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670B VAL* 4.5 2.7 - - + -
674B GLY 3.1 22.4 + - - -
675B LYS* 3.7 22.4 - - + -
677B SER* 3.1 29.7 + - - -
678B ALA* 4.3 12.6 - - + -
681B LEU* 3.6 29.4 - - + -
707B LEU* 2.7 42.2 + - + +
710B GLU* 1.3 86.5 - - + +
712B GLY* 1.3 64.7 + - - +
713B MET 3.1 3.1 - - - -
714B GLU* 3.0 32.2 + - + +
717B CYS* 3.6 33.7 - - + +
718B ARG 4.8 0.2 + - - -
721B LEU* 3.9 11.2 - - + +
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Residues in contact with GLY 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708B VAL* 2.8 25.0 + - - -
710B GLU 3.7 0.4 - - - -
711B TYR* 1.3 78.4 - - - +
713B MET* 1.3 55.8 + - - +
714B GLU 3.6 0.2 + - - -
718B ARG* 3.0 32.7 + - - +
721B LEU* 4.0 12.1 - - - +
762B ARG* 3.4 18.6 - - - +
763B SER* 3.8 6.4 - - - -
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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