Contacts of the helix formed by residues 637 - 652 (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 VAL 637 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578B THR* 4.4 7.2 - - + +
581B LEU* 3.7 29.8 - - + +
582B SER* 4.0 17.0 - - - +
585B CYS* 3.7 24.5 - - + -
619B PHE* 3.9 11.4 - - + -
634B CYS* 4.0 10.3 - - - +
635B GLN 3.3 0.4 - - - -
636B LYS* 1.3 86.2 - - + +
638B ILE* 1.3 62.2 + - - +
639B GLN 3.1 1.8 - - - -
640B GLU* 2.9 11.1 + - - +
641B ILE* 2.8 44.6 + - + +
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Residues in contact with ILE 638 (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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619B PHE* 4.6 8.5 - - + -
634B CYS 4.3 1.8 - - - +
635B GLN* 3.7 23.3 - - + +
637B VAL* 1.3 77.2 - - - +
639B GLN* 1.3 77.9 + - + +
641B ILE* 4.2 9.5 - - + +
642B TRP* 2.7 37.4 + - - +
669B ALA* 4.5 20.9 - - + +
673B VAL* 3.8 24.5 - - + -
676B GLY 4.9 6.1 - - - +
677B SER* 4.7 9.6 - - - +
679B ALA* 6.0 2.9 - - + -
680B LEU* 4.0 40.6 - - + +
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Residues in contact with GLN 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635B GLN* 4.1 29.1 - - - +
636B LYS* 4.4 19.0 - - - +
638B ILE* 1.3 89.3 - - + +
640B GLU* 1.3 63.8 + - + +
642B TRP* 4.2 2.7 - - - +
643B PRO* 3.1 26.5 - - - +
679B ALA* 6.1 3.0 - - - +
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Residues in contact with GLU 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B SER* 3.0 29.2 + - - +
589B VAL* 4.3 6.9 - - + +
636B LYS* 2.7 46.9 + - - +
637B VAL* 2.9 10.9 + - - +
639B GLN* 1.3 79.7 - - + +
641B ILE* 1.3 68.6 + - + +
642B TRP 3.7 0.2 - - - -
643B PRO* 4.1 4.5 - - - +
644B VAL* 4.0 13.5 - - - +
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Residues in contact with ILE 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B SER 5.9 0.2 - - - +
585B CYS* 3.8 8.7 - - + -
586B SER 5.3 0.4 - - - +
589B VAL* 3.3 32.3 - - + -
615B LEU* 4.1 19.1 - - + -
619B PHE* 4.4 14.4 - - + -
637B VAL* 2.8 36.0 + - + +
638B ILE* 4.0 8.7 - - + +
640B GLU* 1.3 86.9 - - + +
642B TRP* 1.3 66.2 - - - +
643B PRO* 3.4 1.6 - - - -
644B VAL* 3.2 7.0 + - - +
645B LEU* 3.2 46.3 + - + +
669B ALA* 6.1 1.6 - - + -
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Residues in contact with TRP 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B ILE 2.7 22.7 + - - +
639B GLN* 4.2 3.1 - - - +
641B ILE* 1.3 76.1 - - - +
643B PRO* 1.3 68.8 - - + +
644B VAL 3.2 0.3 + - - -
645B LEU* 3.2 3.3 + - + -
646B SER* 2.8 43.1 + - - -
649B LEU* 5.6 1.6 - - + -
666B LEU* 3.8 23.3 - - + -
680B LEU* 3.4 30.3 - - + +
683B PRO* 3.9 22.1 - - + +
684B LEU* 3.6 50.7 - - + -
687B GLN* 3.5 27.6 - - - -
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Residues in contact with PRO 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639B GLN 3.1 19.5 - - - +
640B GLU 4.1 6.1 - - - +
641B ILE 3.5 3.6 - - - -
642B TRP* 1.3 99.9 - - + +
644B VAL* 1.3 57.5 + - + +
646B SER* 3.5 6.1 - - - -
647B GLU* 2.9 32.7 + - - +
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Residues in contact with VAL 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589B VAL* 4.0 33.2 - - + +
592B LEU* 3.6 39.0 - - + -
593B LYS* 4.3 22.0 - - + +
596B LEU* 6.3 2.5 - - + -
640B GLU 4.0 10.5 - - - +
641B ILE* 3.6 10.3 - - - +
642B TRP 3.1 0.6 - - - -
643B PRO* 1.3 77.7 - - + +
645B LEU* 1.3 59.0 + - + +
647B GLU* 3.3 8.9 + - + +
648B THR* 2.6 38.4 + - - +
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Residues in contact with LEU 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592B LEU* 4.2 13.5 - - + -
612B LEU* 4.4 11.4 - - + -
615B LEU* 3.9 23.1 - - + -
619B PHE* 5.9 0.2 - - + -
641B ILE* 3.2 32.4 + - + +
642B TRP* 3.8 7.6 - - + +
644B VAL* 1.3 73.6 - - + +
646B SER* 1.3 57.4 + - - +
648B THR* 3.6 4.5 - - - -
649B LEU* 2.8 37.2 + - - +
662B CYS* 3.7 15.0 - - - -
665B CYS* 3.8 23.8 - - + -
666B LEU* 3.7 33.2 - - + -
669B ALA* 6.0 2.0 - - + -
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Residues in contact with SER 646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642B TRP* 2.8 37.8 + - - -
643B PRO* 3.5 8.3 - - - -
645B LEU* 1.3 76.0 - - - +
647B GLU* 1.3 58.0 + - - +
649B LEU* 3.2 1.2 + - - -
650B ASN* 2.8 22.0 + - - +
687B GLN* 2.5 49.7 + - - +
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Residues in contact with GLU 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B LYS* 5.5 6.8 - - - +
596B LEU* 3.4 32.8 - - + +
643B PRO 2.9 18.6 + - - +
644B VAL* 3.7 8.2 - - + +
646B SER* 1.3 75.3 - - - +
648B THR* 1.3 58.3 + - - +
650B ASN* 3.1 10.0 + - + +
651B LYS* 2.8 31.1 + - + +
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Residues in contact with THR 648 (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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592B LEU* 4.6 10.2 + - - +
596B LEU* 5.3 9.7 - - + +
608B PRO* 3.8 33.9 - - + -
612B LEU* 4.3 17.7 - - + -
644B VAL* 2.6 33.7 + - - +
645B LEU* 3.6 8.4 - - - -
647B GLU* 1.3 74.3 - - - +
649B LEU* 1.3 62.7 + - - +
651B LYS* 3.3 4.7 + - - -
652B HIS* 3.1 31.5 + - + +
658B ILE* 4.9 3.7 - - + +
662B CYS* 4.9 2.7 - - - -
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Residues in contact with LEU 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642B TRP* 5.6 0.9 - - + -
645B LEU 2.8 20.7 + - - +
646B SER* 3.5 5.6 - - - +
648B THR* 1.3 73.0 - - - +
650B ASN* 1.3 60.9 + - - +
652B HIS* 3.9 1.0 - - - -
653B ARG* 3.4 25.3 + - - +
659B VAL* 3.8 35.7 - - + +
662B CYS* 3.8 24.0 - - + -
663B CYS* 4.8 2.2 - - - -
666B LEU* 4.5 20.0 - - + -
684B LEU* 5.4 5.2 - - + -
687B GLN* 3.6 24.5 - - + +
688B MET* 5.7 0.4 - - + +
691B VAL* 4.9 4.6 - - + +
700B PHE* 4.0 25.4 - - + -
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Residues in contact with ASN 650 (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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646B SER* 2.8 18.7 + - - +
647B GLU* 3.1 8.9 + - + +
649B LEU* 1.3 76.9 - - - +
651B LYS* 1.3 66.4 + - - +
653B ARG* 2.7 51.1 + - - +
687B GLN* 3.3 28.3 + - - +
690B ASN* 5.0 1.7 - - - +
691B VAL* 4.0 6.9 - - - +
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Residues in contact with LYS 651 (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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595B LEU 4.0 7.9 + - - -
596B LEU* 3.3 43.9 - - + +
597B SER* 4.4 11.5 + - - -
606B SER* 5.6 5.1 + - - -
647B GLU* 2.8 21.8 + - + +
648B THR* 3.3 6.0 + - - +
650B ASN* 1.3 75.6 - - - +
652B HIS* 1.3 81.1 + - + +
653B ARG* 3.1 9.9 + - - +
654B ALA 4.9 0.3 + - - -
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Residues in contact with HIS 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B LEU* 4.7 8.3 - - + -
606B SER* 4.0 19.3 + - - -
608B PRO* 3.8 26.0 - - + +
648B THR* 3.1 21.1 + - + +
649B LEU 3.9 3.6 - - - -
651B LYS* 1.3 105.4 + - + +
653B ARG* 1.3 63.8 + - - +
654B ALA* 3.1 5.3 + - - +
655B ASP* 3.2 15.3 + - + +
658B ILE* 3.9 37.7 - - + -
659B VAL* 3.2 13.3 - - - +
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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
------------------------------------------------------------
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