Contacts of the helix formed by residues 588 - 607 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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587A ILE* 1.3 79.9 - - - +
589A LEU* 1.3 62.2 + - - +
590A LYS* 4.3 3.4 - - - -
591A GLU* 3.9 17.9 - - - +
592A VAL* 3.0 27.9 + - - +
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Residues in contact with LEU 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A SER* 1.3 72.5 - - - +
590A LYS* 1.3 60.6 + - - +
592A VAL* 3.4 5.7 + - - +
593A MET* 2.9 28.6 + - - +
635A TYR 5.4 2.1 - - - +
212T GLN* 6.3 2.5 - - + -
215T VAL* 5.3 13.7 - - + -
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Residues in contact with LYS 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A SER* 4.3 3.9 - - - -
589A LEU* 1.3 75.1 - - - +
591A GLU* 1.3 60.6 + - - +
593A MET* 3.4 7.3 + - - +
594A GLN* 2.9 29.6 + - - +
640A ALA 6.0 0.7 - - - +
641A ASP* 6.1 4.7 - - - +
644A GLU* 4.7 19.2 - - + +
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Residues in contact with GLU 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A ILE* 4.5 9.0 - - + -
588A SER* 3.6 25.2 + - - +
589A LEU 3.3 0.4 - - - -
590A LYS* 1.3 77.4 - - - +
592A VAL* 1.3 59.3 + - - +
594A GLN* 3.4 6.9 + - - +
595A VAL* 2.9 29.1 + - - +
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Residues in contact with VAL 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582A LYS* 4.6 21.3 - - + -
587A ILE* 4.8 7.5 - - + +
588A SER 3.0 19.0 + - - +
589A LEU* 3.8 6.3 - - - +
591A GLU* 1.3 74.4 - - - +
593A MET* 1.3 61.0 + - - +
595A VAL* 3.8 6.9 - - - +
596A LEU* 2.9 30.0 + - - +
635A TYR* 6.1 0.7 - - - -
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Residues in contact with MET 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A LEU 2.9 17.2 + - - +
590A LYS* 3.7 7.6 - - - +
591A GLU 3.3 0.2 - - - -
592A VAL* 1.3 77.9 - - - +
594A GLN* 1.3 56.3 + - - +
596A LEU* 3.4 6.6 + - - +
597A SER* 2.9 29.3 + - - -
635A TYR* 4.6 26.5 - - + +
636A ILE* 5.2 7.6 - - + +
641A ASP* 5.2 11.9 - - + +
644A GLU* 5.5 4.5 - - + -
645A ALA* 5.7 5.8 - - + +
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Residues in contact with GLN 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A LYS 2.9 18.1 + - - +
591A GLU* 3.7 6.7 - - - +
593A MET* 1.3 75.2 - - - +
595A VAL* 1.3 57.0 + - - +
597A SER* 3.4 2.1 + - - -
598A HIS* 2.9 29.5 + - - +
644A GLU* 5.3 7.8 - - + +
648A ALA* 4.4 20.6 - - + +
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Residues in contact with VAL 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A ILE* 5.7 2.7 - - + +
553A PHE* 5.7 3.4 - - + -
554A GLN* 4.8 24.6 - - + +
557A VAL* 5.3 6.8 - - + +
591A GLU 2.9 17.2 + - - +
592A VAL* 3.8 7.0 - - - +
593A MET 3.3 0.2 - - - -
594A GLN* 1.3 76.8 - - - +
596A LEU* 1.3 57.8 + - - +
598A HIS* 3.4 6.2 + - - +
599A VAL* 2.9 29.8 + - - +
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Residues in contact with LEU 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A VAL* 5.6 5.6 - - + +
592A VAL 2.9 18.3 + - - +
593A MET* 3.7 7.2 - - - +
595A VAL* 1.3 74.1 - - - +
597A SER* 1.3 59.4 + - - +
599A VAL* 3.3 6.6 + - - +
600A VAL* 2.9 29.7 + - - +
635A TYR* 5.2 11.2 - - + -
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Residues in contact with SER 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A MET 2.9 17.6 + - - -
594A GLN 3.8 4.3 - - - -
596A LEU* 1.3 75.9 - - - +
598A HIS* 1.3 57.9 + - - +
600A VAL* 3.4 6.4 + - - +
601A LEU* 2.9 29.8 + - - +
645A ALA* 5.0 12.8 - - - -
648A ALA* 3.8 24.9 - - - -
649A ILE* 5.3 1.1 - - - -
652A PHE* 5.6 0.6 - - - +
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Residues in contact with HIS 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554A GLN* 6.4 1.8 - - + -
594A GLN 2.9 17.6 + - - +
595A VAL* 3.7 7.6 - - - +
597A SER* 1.3 75.2 - - - +
599A VAL* 1.3 58.0 + - - +
601A LEU* 3.4 6.3 + - - +
602A GLU* 2.9 30.2 + - - +
648A ALA* 5.2 2.4 - - + +
652A PHE* 5.9 2.7 - - - -
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Residues in contact with VAL 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A GLN* 4.9 5.2 - - + +
557A VAL* 4.8 5.6 - - + +
558A LEU* 4.5 31.2 - - + +
561A LEU* 5.6 4.9 - - + -
595A VAL 2.9 18.3 + - - +
596A LEU* 3.8 7.9 - - - +
598A HIS* 1.3 75.3 - - - +
600A VAL* 1.3 58.0 + - - +
602A GLU* 3.3 5.2 + - - +
603A PHE* 2.9 31.0 + - - +
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Residues in contact with VAL 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A LEU 2.9 17.9 + - - +
597A SER* 3.8 7.2 - - - +
598A HIS 3.3 0.2 - - - -
599A VAL* 1.3 77.1 - - - +
601A LEU* 1.3 61.3 + - - +
603A PHE* 3.8 6.3 + - - +
604A PRO* 3.8 17.7 - - - +
621A LEU* 5.7 2.1 - - - +
624A LEU* 5.5 8.6 - - + +
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Residues in contact with LEU 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A SER 2.9 17.4 + - - +
598A HIS* 3.8 5.4 - - - +
600A VAL* 1.3 78.2 - - - +
602A GLU* 1.3 60.1 + - - +
603A PHE 3.4 0.2 - - - -
604A PRO* 3.9 5.3 - - - +
605A LEU* 3.3 21.0 + - - +
652A PHE* 3.7 29.6 - - + -
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Residues in contact with GLU 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558A LEU* 6.5 0.2 - - + -
598A HIS 2.9 18.9 + - - +
599A VAL* 3.3 6.0 + - - +
601A LEU* 1.3 75.4 - - - +
603A PHE* 1.3 56.2 + - - +
604A PRO 3.4 0.2 - - - -
605A LEU* 3.5 8.2 - - + +
606A GLN* 2.7 36.2 + - - +
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Residues in contact with PHE 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561A LEU* 6.1 4.5 - - + -
599A VAL 2.9 16.8 + - - +
600A VAL* 4.1 7.4 - - - +
601A LEU 3.4 0.4 - - - -
602A GLU* 1.3 77.0 - - - +
604A PRO* 1.3 56.7 - - - +
606A GLN* 3.3 5.3 + - - +
607A GLN* 2.9 28.2 + - - +
624A LEU* 5.9 6.3 - - + -
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Residues in contact with PRO 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600A VAL 3.8 9.4 - - - +
601A LEU* 4.2 7.2 - - - +
602A GLU 3.4 0.2 - - - -
603A PHE* 1.3 77.1 - - - +
605A LEU* 1.3 60.5 + - - +
607A GLN* 3.7 11.4 + - + +
608A MET* 4.1 7.3 + - - +
616A ARG 5.2 0.2 - - - +
617A TYR* 4.0 19.5 - - + +
620A LEU* 3.8 32.2 - - + +
621A LEU* 3.9 22.4 - - + +
624A LEU* 6.0 0.9 - - + -
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Residues in contact with LEU 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A LEU 3.3 18.7 + - - +
602A GLU* 3.3 9.3 + - + +
603A PHE 3.2 0.8 - - - -
604A PRO* 1.3 76.7 - - - +
606A GLN* 1.3 58.6 + - - +
608A MET* 2.9 20.2 + - - +
617A TYR* 6.1 1.6 - - - -
656A HIS* 5.7 9.0 - - + -
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Residues in contact with GLN 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A GLU 2.7 20.2 + - - +
603A PHE* 3.6 5.8 - - - +
605A LEU* 1.3 70.9 - - - +
607A GLN* 1.3 65.1 + - - +
608A MET 3.2 6.6 + - - +
609A ASP* 5.4 0.7 - - - -
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Residues in contact with GLN 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603A PHE 2.9 16.8 + - - +
604A PRO 3.8 8.1 - - - +
605A LEU 3.4 0.6 - - - -
606A GLN* 1.3 78.4 - - - +
608A MET* 1.3 57.9 + - + +
609A ASP 4.3 0.3 + - - -
620A 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