Contacts of the helix formed by residues 677 - 694 (chain B) in PDB entry 2O8C
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
----------------------------------------------------------
572B GLN* 3.1 11.7 - - - +
661B GLY 5.0 0.5 + - - -
662B MET* 3.5 57.8 - - - +
673B PRO* 5.1 0.2 - - - -
674B GLY 3.1 7.5 + - - -
676B LYS* 1.3 83.7 + - - +
678B GLU* 1.3 66.1 + - - +
680B ALA* 4.1 2.1 - - - +
681B LEU* 3.4 27.2 + - - +
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Residues in contact with GLU 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B LYS* 5.5 0.4 - - - -
545B LYS* 4.9 10.6 + - - -
572B GLN* 3.3 2.3 + - - +
630B ALA* 3.4 16.4 - - + +
673B PRO* 4.9 9.2 - - + +
674B GLY 3.8 14.4 - - - +
675B GLU* 4.2 13.1 + - - +
677B SER* 1.3 78.0 - - - +
679B LEU* 1.3 66.9 + - + +
682B SER* 3.3 23.0 + - - -
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Residues in contact with LEU 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B LYS* 3.6 31.2 - - + +
544B GLU 3.9 15.9 - - - +
545B LYS* 3.9 17.9 - - + -
555B ALA* 3.4 38.1 - - + +
556B TYR 3.6 15.7 - - - +
557B GLY* 3.7 13.0 - - - +
572B GLN* 3.1 20.0 + - - +
678B GLU* 1.3 79.8 - - + +
680B ALA* 1.3 59.1 + - - +
682B SER* 3.3 3.2 + - - -
683B ALA* 2.8 29.8 + - - +
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Residues in contact with ALA 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B GLY* 4.0 4.4 - - - -
558B VAL 4.6 0.4 - - - -
570B ILE* 3.9 11.1 - - + +
571B GLY 3.3 32.8 - - - +
572B GLN* 3.3 11.6 + - + +
662B MET* 3.4 25.8 - - + -
677B SER 4.4 0.7 - - - +
678B GLU 3.5 0.4 - - - -
679B LEU* 1.3 78.9 - - - +
681B LEU* 1.3 57.8 + - - +
683B ALA* 3.2 5.1 + - - +
684B LEU* 2.9 27.9 + - - +
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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
----------------------------------------------------------
570B ILE* 4.5 0.2 - - + -
630B ALA* 3.7 14.8 - - + +
633B THR* 3.2 13.3 + - + +
634B LEU* 4.1 26.5 - - + -
637B LEU* 5.6 0.2 - - + -
659B LEU* 4.1 21.8 - - + +
662B MET* 3.8 40.6 - - + +
673B PRO* 3.8 26.2 - - + -
677B SER 3.4 20.5 + - - +
680B ALA* 1.3 78.2 - - - +
682B SER* 1.3 57.5 + - - +
684B LEU* 3.2 16.7 + - + +
685B GLY 3.0 21.8 + - - -
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Residues in contact with SER 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B LYS* 3.5 27.8 + - - -
627B PHE* 3.2 9.1 - - - -
628B TRP 2.8 34.2 + - - +
629B ASP* 3.6 6.0 - - - -
630B ALA* 3.6 15.8 - - - +
678B GLU 3.3 18.1 + - - -
679B LEU 3.3 4.2 + - - -
680B ALA 3.2 0.4 - - - -
681B LEU* 1.3 74.2 - - - +
683B ALA* 1.3 65.9 + - - +
685B GLY 3.1 6.8 + - - -
686B GLY 3.2 6.1 + - - -
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Residues in contact with ALA 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B SER* 2.7 36.5 + - - +
543B LYS* 4.0 4.7 - - + -
557B GLY 3.3 30.3 - - - +
558B VAL 4.2 5.2 - - - -
559B CYS* 4.2 2.2 - - - -
627B PHE* 3.7 12.3 - - - -
679B LEU 2.8 15.3 + - - +
680B ALA 3.4 5.6 - - - +
682B SER* 1.3 73.5 - - - +
684B LEU* 1.3 61.5 + - - +
686B GLY 3.1 2.4 + - - -
687B CYS 2.9 11.3 + - - -
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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
----------------------------------------------------------
559B CYS* 3.6 26.8 - - - +
568B PHE* 4.9 4.7 - - + -
570B ILE* 3.8 20.6 - - + -
633B THR* 3.9 7.4 - - + -
637B LEU* 3.9 29.6 - - + -
659B LEU* 4.0 15.3 - - + -
680B ALA 2.9 12.9 + - - +
681B LEU* 3.2 12.8 + - + +
683B ALA* 1.3 76.2 - - - +
685B GLY* 1.3 52.6 + - - +
687B CYS* 3.1 3.7 + - + +
688B VAL* 2.6 56.6 + - + +
701B LEU* 5.3 0.2 - - + -
706B PHE* 4.1 20.0 - - + -
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Residues in contact with GLY 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628B TRP* 3.4 27.2 - - - -
633B THR* 3.2 24.8 + - - +
681B LEU 3.0 10.3 + - - -
682B SER 3.1 4.6 + - - -
683B ALA 3.1 0.8 - - - -
684B LEU* 1.3 76.5 - - - +
686B GLY* 1.3 51.7 + - - +
688B VAL* 3.2 0.6 + - - -
689B PHE* 2.8 32.9 + - - +
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Residues in contact with GLY 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B SER* 3.6 5.2 - - - -
595B LEU* 3.4 12.1 - - - +
621B LEU* 3.6 13.4 - - - +
627B PHE* 3.8 31.9 - - - -
628B TRP 4.0 1.6 - - - +
682B SER 3.2 7.1 + - - -
683B ALA 3.1 7.3 + - - -
685B GLY* 1.3 74.8 - - - +
687B CYS* 1.3 61.1 + - - +
689B PHE* 3.7 1.5 + - - -
690B TYR 3.4 14.9 + - - -
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Residues in contact with CYS 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B LEU* 4.9 8.9 - - - +
541B SER* 3.2 14.3 + - - -
559B CYS* 3.7 31.6 - - - -
561B VAL* 4.5 8.1 - - - -
568B PHE* 4.0 23.8 - - - -
595B LEU* 3.8 7.2 - - - +
683B ALA 2.9 12.4 + - - +
684B LEU* 3.2 9.6 - - + +
686B GLY* 1.3 77.1 - - - +
688B VAL* 1.3 61.7 + - - +
690B TYR* 3.4 5.0 + - - +
691B LEU* 3.2 32.1 + - - +
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Residues in contact with VAL 688 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B PHE* 5.8 0.2 - - + -
628B TRP* 3.6 23.8 - - + -
633B THR* 5.1 1.3 - - + -
636B THR* 4.9 0.9 - - + -
637B LEU* 4.2 15.3 - - + -
642B TYR* 4.1 14.6 - - + +
684B LEU* 2.6 44.8 + - + +
685B GLY* 3.8 4.3 - - - +
687B CYS* 1.3 70.9 - - - +
689B PHE* 1.3 65.5 + - - +
691B LEU* 3.3 8.6 + - + +
692B LYS* 2.9 23.4 + - + +
697B ASP* 4.6 0.8 - - + +
701B LEU* 4.0 33.0 - - + -
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Residues in contact with PHE 689 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B LEU* 3.9 24.2 - - + -
625B SER 4.2 3.6 - - - -
626B GLN* 3.2 66.0 - - + +
628B TRP* 4.0 27.7 - + + -
685B GLY 2.8 18.0 + - - +
686B GLY 3.8 4.3 - - - +
688B VAL* 1.3 74.2 - - - +
690B TYR* 1.3 62.3 + + - +
692B LYS* 3.2 4.8 + - + +
693B LYS* 2.9 53.8 + - + +
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Residues in contact with TYR 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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479B LYS* 3.7 13.3 - - - +
516B ILE* 5.5 2.1 - - + +
518B THR* 3.5 11.9 + - - -
521B THR* 4.0 12.1 - - + -
539B LEU* 4.5 4.9 - - + -
593B GLN* 2.8 43.1 + - - -
595B LEU* 3.5 43.3 - - + -
619B GLU* 3.7 12.2 + - + -
621B LEU* 4.6 14.1 - - + -
686B GLY 3.4 3.8 + - - +
687B CYS 3.8 1.6 - - - +
688B VAL 3.3 0.4 - - - -
689B PHE* 1.3 83.9 - + + +
691B LEU* 1.3 57.0 + - - +
693B LYS* 3.3 18.7 + - + +
694B CYS* 3.1 48.0 + - - -
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Residues in contact with LEU 691 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B THR* 4.0 13.9 - - + -
539B LEU* 4.0 6.7 - - + -
561B VAL* 4.7 3.6 - - + -
563B THR* 3.9 15.7 - - + -
568B PHE* 3.6 37.5 - - + -
687B CYS* 3.2 25.5 + - - +
688B VAL* 3.9 6.5 - - - +
689B PHE 3.3 0.2 - - - -
690B TYR* 1.3 75.0 - - - +
692B LYS* 1.3 62.2 + - - +
694B CYS* 4.0 0.9 - - - +
695B LEU 3.3 2.4 + - - -
696B ILE* 3.0 42.2 + - + +
697B ASP* 3.0 35.0 + - + +
700B LEU* 4.0 8.1 - - + -
701B LEU* 5.5 3.1 - - + -
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Residues in contact with LYS 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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628B TRP* 4.3 21.6 - - + -
636B THR* 5.0 3.1 - - - -
640B GLU* 3.6 36.2 + - + -
642B TYR* 3.9 6.7 - - - +
688B VAL 2.9 16.2 + - - +
689B PHE* 3.5 6.7 - - + +
691B LEU* 1.3 77.6 - - - +
693B LYS* 1.3 62.9 + - - +
695B LEU* 3.5 21.5 + - + +
697B ASP* 3.3 27.5 - - + +
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Residues in contact with LYS 693 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B SER* 5.0 10.5 + - - -
419B GLN 4.9 5.3 + - - -
420B ASN* 4.2 19.0 + - - -
423B LEU* 6.1 0.4 - - - -
513B ILE* 5.6 0.5 - - - +
516B ILE* 3.6 23.1 - - + +
626B GLN* 4.9 10.3 - - - +
689B PHE* 2.9 42.7 + - + +
690B TYR* 3.3 21.7 + - + +
691B LEU 3.2 0.2 - - - -
692B LYS* 1.3 76.4 - - - +
694B CYS* 1.3 61.3 + - - +
695B LEU* 3.1 13.0 + - - +
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Residues in contact with CYS 694 (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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515B ARG* 3.5 13.5 - - - +
516B ILE* 3.1 60.3 + - - +
518B THR* 4.6 0.7 - - - -
521B THR* 4.1 12.1 - - - +
690B TYR* 3.1 47.2 + - - +
691B LEU* 3.8 4.2 + - - +
692B LYS 3.4 0.2 - - - -
693B LYS* 1.3 76.3 - - - +
695B LEU* 1.3 68.8 + - - +
696B ILE* 4.5 8.3 - - + -
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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