Contacts of the helix formed by residues 588 - 607 (chain B) in PDB entry 6O81
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 588 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587B ILE* 1.3 79.2 - - - +
589B LEU* 1.3 60.9 + - - +
590B LYS* 3.5 4.0 - - - -
591B GLU* 3.9 17.3 - - - +
592B VAL* 3.0 27.2 + - - +
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Residues in contact with LEU 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B SER* 1.3 73.1 - - - +
590B LYS* 1.3 61.1 + - - +
592B VAL* 3.4 5.4 + - - +
593B MET* 2.9 28.2 + - - +
635B TYR 5.4 2.2 - - - +
215S VAL* 5.3 14.1 - - + -
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Residues in contact with LYS 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B SER* 3.5 3.2 - - - -
589B LEU* 1.3 76.7 - - - +
591B GLU* 1.3 60.2 + - - +
593B MET* 3.4 7.2 + - - +
594B GLN* 2.9 28.8 + - - +
640B ALA 6.4 0.4 - - - -
641B ASP* 6.1 4.7 - - - +
644B GLU* 4.7 19.5 - - + +
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Residues in contact with GLU 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587B ILE* 4.5 8.5 - - + -
588B SER* 3.6 24.1 + - - +
589B LEU 3.3 0.6 - - - -
590B LYS* 1.3 75.5 - - - +
592B VAL* 1.3 58.7 + - - +
594B GLN* 3.4 6.6 + - - +
595B VAL* 2.9 29.7 + - - +
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Residues in contact with VAL 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B LYS* 4.6 21.1 - - + -
587B ILE* 4.8 7.6 - - + +
588B SER 3.0 20.0 + - - +
589B LEU* 3.8 6.1 - - - +
590B LYS 3.3 0.2 - - - -
591B GLU* 1.3 73.4 - - - +
593B MET* 1.3 60.6 + - - +
595B VAL* 3.4 7.1 + - - +
596B LEU* 2.9 29.3 + - - +
635B TYR* 6.1 0.9 - - - -
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Residues in contact with MET 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589B LEU 2.9 17.6 + - - +
590B LYS* 3.7 8.3 - - - +
591B GLU 3.3 0.2 - - - -
592B VAL* 1.3 77.3 - - - +
594B GLN* 1.3 57.3 + - - +
596B LEU* 3.4 6.1 + - - +
597B SER* 2.9 29.5 + - - -
635B TYR* 4.6 25.4 - - + +
636B ILE* 5.2 9.0 - - + +
641B ASP* 5.2 11.0 - - + +
644B GLU* 5.5 3.8 - - + -
645B ALA* 5.7 6.2 - - + +
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Residues in contact with GLN 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B LYS 2.9 17.0 + - - +
591B GLU* 3.7 7.4 - - - +
593B MET* 1.3 76.5 - - - +
595B VAL* 1.3 57.9 + - - +
597B SER* 3.4 1.9 + - - -
598B HIS* 2.9 29.5 + - - +
644B GLU* 5.3 7.8 - - + +
648B ALA* 4.4 22.1 - - + +
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Residues in contact with VAL 595 (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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550B ILE* 5.7 1.8 - - + +
553B PHE* 5.7 2.9 - - + -
554B GLN* 4.8 25.3 - - + +
557B VAL* 5.3 6.9 - - + +
591B GLU 2.9 17.8 + - - +
592B VAL* 3.8 7.4 - - - +
594B GLN* 1.3 75.5 - - - +
596B LEU* 1.3 57.8 + - - +
598B HIS* 3.4 6.6 + - - +
599B VAL* 2.9 29.7 + - - +
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Residues in contact with LEU 596 (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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557B VAL* 5.6 5.6 - - + +
592B VAL 2.9 17.2 + - - +
593B MET* 3.7 7.2 - - - +
595B VAL* 1.3 74.6 - - - +
597B SER* 1.3 58.9 + - - +
599B VAL* 3.3 6.8 + - - +
600B VAL* 2.9 29.8 + - - +
635B TYR* 5.2 11.0 - - + -
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Residues in contact with SER 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B MET 2.9 17.6 + - - -
594B GLN* 3.8 4.5 - - - -
596B LEU* 1.3 76.3 - - - +
598B HIS* 1.3 57.7 + - - +
600B VAL* 3.4 6.8 + - - +
601B LEU* 2.9 29.8 + - - +
645B ALA* 4.9 12.8 - - - -
648B ALA* 3.8 24.9 - - - -
649B ILE 5.3 0.4 - - - -
652B PHE* 6.3 0.4 - - - -
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Residues in contact with HIS 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554B GLN* 6.4 2.0 - - + -
594B GLN 2.9 18.3 + - - +
595B VAL* 3.7 7.4 - - - +
596B LEU 3.3 0.2 - - - -
597B SER* 1.3 75.6 - - - +
599B VAL* 1.3 57.3 + - - +
601B LEU* 3.4 6.6 + - - +
602B GLU* 2.9 30.0 + - - +
648B ALA* 5.2 2.6 - - + +
652B PHE* 5.9 2.2 - - - -
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Residues in contact with VAL 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554B GLN* 4.9 4.9 - - + +
557B VAL* 4.8 7.4 - - + +
558B LEU* 4.5 30.1 - - + +
561B LEU* 5.6 5.4 - - + -
595B VAL 2.9 17.6 + - - +
596B LEU* 3.8 6.7 - - - +
597B SER 3.3 0.2 - - - -
598B HIS* 1.3 76.0 - - - +
600B VAL* 1.3 57.6 + - - +
602B GLU* 3.7 5.8 - - - +
603B PHE* 2.9 30.7 + - - +
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Residues in contact with VAL 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B LEU 2.9 17.8 + - - +
597B SER* 3.8 7.0 - - - +
599B VAL* 1.3 77.6 - - - +
601B LEU* 1.3 60.2 + - - +
603B PHE* 3.8 5.7 + - - +
604B PRO* 3.8 18.2 - - - +
621B LEU* 5.7 2.6 - - - +
624B LEU* 5.5 8.6 - - + +
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Residues in contact with LEU 601 (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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597B SER 2.9 17.3 + - - +
598B HIS* 3.8 5.4 - - - +
599B VAL 3.3 0.2 - - - -
600B VAL* 1.3 78.1 - - - +
602B GLU* 1.3 60.1 + - - +
604B PRO* 3.9 4.6 - - - +
605B LEU* 3.3 21.0 + - - +
652B PHE* 3.7 29.6 - - + -
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Residues in contact with GLU 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B LEU* 6.5 0.4 - - + -
598B HIS 2.9 17.3 + - - +
599B VAL* 3.3 6.7 + - - +
601B LEU* 1.3 75.2 - - - +
603B PHE* 1.3 57.1 + - - +
605B LEU* 3.5 7.8 - - - +
606B GLN* 2.7 36.3 + - - +
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Residues in contact with PHE 603 (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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561B LEU* 6.1 5.2 - - + -
599B VAL 2.9 15.7 + - - +
600B VAL* 4.1 7.2 - - - +
601B LEU 3.4 0.4 - - - -
602B GLU* 1.3 77.2 - - - +
604B PRO* 1.3 57.8 - - - +
606B GLN* 3.3 5.8 + - - +
607B GLN* 2.9 27.0 + - - +
624B LEU* 5.9 6.7 - - + -
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Residues in contact with PRO 604 (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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600B VAL 3.8 9.4 - - - +
601B LEU* 3.9 7.4 - - - +
602B GLU 3.4 0.4 - - - -
603B PHE* 1.3 77.9 - - - +
605B LEU* 1.3 61.2 + - - +
607B GLN* 3.7 11.2 + - - +
608B MET* 4.1 6.8 + - - +
616B ARG 5.2 0.3 - - - +
617B TYR* 4.0 19.4 - - + +
620B LEU* 3.8 31.8 - - + +
621B LEU* 3.9 23.1 - - + +
624B LEU* 6.0 0.9 - - + -
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Residues in contact with LEU 605 (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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601B LEU 3.3 17.7 + - - +
602B GLU* 3.3 9.4 + - + +
603B PHE 3.2 1.0 - - - -
604B PRO* 1.3 77.6 - - - +
606B GLN* 1.3 58.5 + - - +
607B GLN 3.4 0.2 - - - -
608B MET* 2.9 20.4 - - - +
609B ASP 5.2 0.2 - - - +
617B TYR* 6.1 1.3 - - - -
656B HIS* 5.7 8.3 - - + -
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Residues in contact with GLN 606 (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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602B GLU 2.7 20.9 + - - +
603B PHE* 3.3 5.4 + - - +
605B LEU* 1.3 70.5 - - - +
607B GLN* 1.3 64.3 + - - +
608B MET 3.2 6.9 + - - +
609B ASP* 5.4 0.5 - - - -
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Residues in contact with GLN 607 (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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603B PHE 2.9 15.5 + - - +
604B PRO 3.8 8.3 - - - +
605B LEU 3.4 0.4 - - - -
606B GLN* 1.3 79.3 - - - +
608B MET* 1.3 57.5 + - + +
609B ASP 4.3 0.3 + - - -
620B LEU* 3.8 20.6 - - + -
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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