Contacts of the helix formed by residues 655 - 674 (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 ASP 655 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLU* 3.6 6.6 - - - +
652B HIS* 3.2 11.9 + - + +
654B ALA* 1.3 75.2 - - - +
656B ASN* 1.3 64.1 + - - +
657B ARG* 3.2 26.8 + - - +
658B ILE* 3.3 36.5 + - + +
659B VAL* 3.0 25.4 + - - +
697B HIS* 4.2 0.2 - - - -
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Residues in contact with ASN 656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLU* 3.6 19.9 + - + +
654B ALA 3.3 7.0 + - - +
655B ASP* 1.3 71.7 + - - +
657B ARG* 1.3 53.7 + - - +
659B VAL* 3.4 3.1 + - - +
660B GLU* 2.8 48.1 + - - +
697B HIS* 3.2 50.5 + - + +
698B SER 4.4 4.6 - - - +
699B CYS* 4.5 3.7 - - - +
747B ASP* 5.6 3.4 + - - -
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Residues in contact with ARG 657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ARG* 6.1 3.1 - - - +
34A GLU* 3.0 27.0 + - + +
607B ASP* 2.9 25.2 + - - -
609B THR* 2.7 36.0 + - - +
655B ASP* 3.2 11.3 + - - +
656B ASN* 1.3 79.1 - - - +
658B ILE* 1.3 75.4 + - - +
660B GLU* 2.9 13.7 + - - +
661B ARG* 2.9 41.2 + - + +
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Residues in contact with ILE 658 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B ASP* 4.0 19.5 - - - +
608B PRO* 3.8 25.8 - - + -
609B THR* 4.1 3.4 - - - +
612B LEU* 3.9 9.5 - - + +
648B THR* 4.9 3.8 - - + +
652B HIS* 3.9 34.8 - - + +
655B ASP* 3.3 38.2 + - + +
657B ARG* 1.3 91.6 - - - +
659B VAL* 1.3 58.7 + - - +
661B ARG* 3.2 8.6 + - - +
662B CYS* 2.9 28.6 + - + +
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Residues in contact with VAL 659 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649B LEU* 3.8 19.3 - - + -
652B HIS 3.2 18.8 - - - +
653B ARG* 3.8 9.9 - - - +
655B ASP 3.0 17.5 + - - +
656B ASN 3.5 4.0 - - - +
658B ILE* 1.3 75.1 - - - +
660B GLU* 1.3 57.7 + - - +
662B CYS* 3.4 1.6 + - - +
663B CYS* 2.8 30.1 + - - -
691B VAL* 5.7 0.2 - - + -
697B HIS* 3.7 18.6 - - + -
699B CYS* 3.7 18.8 - - - -
700B PHE* 3.7 31.4 - - + -
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Residues in contact with GLU 660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LYS* 4.3 20.9 + - - -
656B ASN* 2.8 31.7 + - - +
657B ARG* 2.9 17.4 + - - +
659B VAL* 1.3 74.8 - - - +
661B ARG* 1.3 65.6 + - - +
663B CYS* 3.3 2.8 + - - +
664B ARG* 2.8 30.0 + - + +
699B CYS* 3.8 26.3 - - + +
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Residues in contact with ARG 661 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609B THR* 4.0 20.1 - - + +
612B LEU* 4.3 15.5 - - + +
613B ASP* 3.0 35.4 + - - +
616B ALA* 5.4 0.5 - - - +
657B ARG* 2.9 30.3 + - + +
658B ILE* 3.2 8.0 + - - +
660B GLU* 1.3 83.9 - - - +
662B CYS* 1.3 58.6 + - - +
664B ARG* 3.1 55.4 + - - +
665B CYS* 2.9 27.9 + - - +
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Residues in contact with CYS 662 (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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612B LEU* 3.8 17.4 - - + +
645B LEU* 3.7 44.0 - - - -
648B THR* 4.9 3.4 - - + -
649B LEU* 3.8 26.5 - - + -
658B ILE* 2.9 18.7 + - + +
659B VAL* 3.6 4.7 - - - +
661B ARG* 1.3 76.2 - - - +
663B CYS* 1.3 57.6 + - - +
665B CYS* 3.2 5.3 + - - +
666B LEU* 2.9 38.5 + - - +
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Residues in contact with CYS 663 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649B LEU* 4.8 5.8 - - - -
659B VAL* 2.8 28.4 + - - +
660B GLU 3.6 4.0 - - - +
662B CYS* 1.3 73.1 - - - +
664B ARG* 1.3 52.4 + - - +
666B LEU* 3.4 9.7 + - - +
667B ARG* 2.8 34.9 + - - +
699B CYS* 4.0 31.0 - - + +
700B PHE* 4.0 26.7 - - - -
703B LEU* 4.0 25.6 - - + +
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Residues in contact with ARG 664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B ASP* 3.8 12.1 + - - +
616B ALA* 3.5 21.0 - - - +
617B VAL* 5.2 9.3 - - - +
620B ARG* 4.0 15.8 - - - +
660B GLU* 2.8 15.0 + - + +
661B ARG* 3.1 51.7 - - - +
662B CYS 3.2 0.2 - - - -
663B CYS* 1.3 74.7 - - - +
665B CYS* 1.3 64.7 + - - +
667B ARG* 3.1 19.0 + - - +
668B PHE* 2.9 60.7 + - + -
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Residues in contact with CYS 665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B LEU* 3.9 16.6 - - + +
615B LEU* 3.7 33.7 - - - -
616B ALA* 3.8 16.4 - - + +
619B PHE* 4.6 8.5 - - - -
645B LEU* 3.8 25.8 - - + -
661B ARG 2.9 13.1 + - - +
662B CYS* 3.3 11.9 - - - +
664B ARG* 1.3 77.5 - - - +
666B LEU* 1.3 63.9 + - - +
668B PHE* 3.2 2.6 + - - +
669B ALA* 2.9 23.4 + - - +
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Residues in contact with LEU 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642B TRP* 3.8 26.2 - - + -
645B LEU* 3.7 24.2 - - + -
649B LEU* 4.5 10.5 - - + -
662B CYS* 2.9 31.8 + - - +
663B CYS* 3.6 10.3 - - - +
665B CYS* 1.3 72.3 - - - +
667B ARG* 1.3 58.2 + - - +
669B ALA* 3.2 8.3 + - + +
670B VAL* 2.8 36.6 + - + +
680B LEU* 5.2 7.9 - - + -
684B LEU* 3.7 33.7 - - + -
703B LEU* 4.2 18.6 - - + -
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Residues in contact with ARG 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620B ARG* 6.0 0.4 - - - +
663B CYS 2.8 18.1 + - - +
664B ARG* 3.1 21.6 + - - +
666B LEU* 1.3 74.1 - - - +
668B PHE* 1.3 91.6 + - - +
670B VAL* 3.2 4.5 + - - +
671B ARG* 2.9 46.8 + - - +
702B TYR* 3.8 34.6 + - + -
703B LEU* 4.1 13.0 - - + +
706B ILE* 3.5 36.1 - - + -
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Residues in contact with PHE 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616B ALA* 3.4 38.8 - - + +
617B VAL 5.2 0.2 - - - -
619B PHE* 4.0 3.9 - - + +
620B ARG* 3.6 48.9 - - + +
664B ARG* 2.9 55.2 + - + -
665B CYS 3.7 5.4 - - - +
667B ARG* 1.3 116.2 - - - +
669B ALA* 1.3 54.2 + - - +
671B ARG* 3.3 7.5 + - + +
672B CYS* 2.7 36.6 + - - +
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Residues in contact with ALA 669 (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* 3.9 34.2 - - + +
638B ILE* 4.5 14.6 - - + -
641B ILE* 6.1 1.6 - - + -
645B LEU* 6.0 2.0 - - + -
665B CYS* 2.9 15.4 + - - +
666B LEU* 3.5 15.0 - - + +
668B PHE* 1.3 76.6 - - - +
670B VAL* 1.3 58.4 + - + +
672B CYS* 3.2 2.5 + - - +
673B VAL* 2.9 35.1 + - - +
677B SER* 5.6 0.2 - - - -
680B LEU* 6.0 2.9 - - + -
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Residues in contact with VAL 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666B LEU* 2.8 26.1 + - + +
667B ARG* 3.6 5.6 - - - +
669B ALA* 1.3 72.7 - - - +
671B ARG* 1.3 57.3 + - - +
674B GLY* 2.7 33.8 + - - +
677B SER* 4.8 10.3 - - - +
680B LEU* 4.7 19.1 - - + -
684B LEU* 4.8 7.2 - - + -
703B LEU* 5.3 1.6 - - + -
706B ILE* 4.1 9.4 - - + -
707B LEU* 3.8 32.3 - - + -
710B GLU* 4.0 22.6 - - + -
711B TYR* 4.5 9.9 - - + +
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Residues in contact with ARG 671 (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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623B ASN* 5.5 0.5 - - - +
667B ARG* 2.9 36.1 + - - +
668B PHE* 3.9 8.1 - - + +
670B VAL* 1.3 76.7 - - - +
672B CYS* 1.3 62.5 + - - +
674B GLY* 4.3 4.1 + - - -
706B ILE* 3.8 31.5 - - + +
709B ASP* 2.6 36.7 + - - +
710B GLU* 3.2 33.6 + - - +
758B ARG* 3.2 19.2 - - - +
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Residues in contact with CYS 672 (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* 3.3 33.0 - - + +
622B THR* 3.5 26.4 - - - +
623B ASN* 4.8 8.6 - - - +
632B HIS* 3.8 12.7 + - - -
634B CYS* 4.1 23.3 - - - -
668B PHE 2.7 21.6 + - - +
669B ALA* 3.3 9.2 - - - +
670B VAL 3.1 0.2 - - - -
671B ARG* 1.3 75.0 - - - +
673B VAL* 1.3 67.9 + - - +
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Residues in contact with VAL 673 (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* 5.6 1.1 - - + -
632B HIS* 3.9 28.5 - - + +
634B CYS* 3.4 31.2 - - + +
635B GLN* 4.3 12.8 - - + -
638B ILE* 3.8 19.3 - - + -
669B ALA* 2.9 19.9 + - - +
670B VAL 4.2 0.2 - - - +
672B CYS* 1.3 77.7 - - - +
674B GLY* 1.3 58.6 + - - +
675B LYS 4.0 1.2 + - - -
676B GLY* 3.4 36.7 + - - +
677B SER* 3.5 12.3 - - - +
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Residues in contact with GLY 674 (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* 2.7 26.7 + - - +
671B ARG 4.7 3.4 - - - -
672B CYS 3.5 1.7 - - - -
673B VAL* 1.3 71.7 - - - +
675B LYS* 1.3 58.2 + - - -
676B GLY 3.1 6.3 + - - -
677B SER* 4.0 4.7 + - - -
710B GLU* 3.8 20.2 - - - +
711B TYR* 3.1 19.5 + - - -
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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