Contacts of the helix formed by residues 578 - 591 (chain M) in PDB entry 6G0L
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 GLU 578 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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574M ASN* 4.9 6.3 - - - +
575M GLN* 3.9 24.7 + - + +
576M ASP 3.5 0.2 - - - -
577M GLU* 1.3 79.5 - - + +
579M GLN* 1.3 58.6 + - - +
580M GLU 3.3 2.2 - - - -
581M GLU* 3.3 24.2 + - + +
582M TYR* 2.9 29.4 + - + +
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Residues in contact with GLN 579 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574M ASN* 4.3 7.0 - - - +
575M GLN 3.2 17.7 + - - +
576M ASP* 3.5 27.9 - - - +
577M GLU 3.2 1.6 - - - -
578M GLU* 1.3 79.5 - - - +
580M GLU* 1.3 58.2 + - - +
582M TYR* 4.2 8.7 - - + -
583M ILE* 2.9 37.0 + - + +
839M LEU* 3.4 39.0 - - - +
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Residues in contact with GLU 580 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576M ASP 4.4 2.5 + - - +
577M GLU* 3.4 16.0 - - - +
579M GLN* 1.3 79.5 - - - +
581M GLU* 1.3 78.4 + - - +
583M ILE* 3.7 8.1 - - - +
584M HIS* 2.7 35.9 + - - +
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Residues in contact with GLU 581 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577M GLU 3.2 20.0 - - - +
578M GLU* 3.3 25.7 - - - +
579M GLN 3.3 0.2 - - - -
580M GLU* 1.3 97.1 - - - +
582M TYR* 1.3 60.2 + - - +
583M ILE 3.3 0.2 - - - -
584M HIS* 3.5 8.9 + - + +
585M ASP* 2.9 31.7 + - - +
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Residues in contact with TYR 582 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549M ILE* 3.4 35.1 - - + +
553M ALA* 6.0 0.2 - - - +
564M PHE* 5.2 13.9 - + - -
574M ASN* 3.7 31.0 - - - +
578M GLU* 2.9 18.3 + - + +
579M GLN* 3.9 7.4 - - + +
581M GLU* 1.3 76.7 - - - +
583M ILE* 1.3 62.2 + - + +
585M ASP* 4.4 1.8 - - - +
586M LEU* 2.9 59.3 + - + +
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Residues in contact with ILE 583 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546M GLN* 4.7 12.1 - - - +
552M LEU* 5.8 3.8 - - + -
579M GLN* 2.9 27.7 + - + +
580M GLU* 3.7 11.0 - - - +
582M TYR* 1.3 77.7 - - + +
584M HIS* 1.3 61.2 + - - +
585M ASP 3.3 0.9 - - - -
586M LEU* 4.7 12.8 - - + -
587M HIS* 2.5 54.6 + - + +
839M LEU* 5.3 3.6 - - + -
841M TYR* 3.7 54.1 - - + +
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Residues in contact with HIS 584 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580M GLU 2.7 23.3 + - - +
581M GLU* 3.1 12.7 + - + +
583M ILE* 1.3 79.6 - - - +
585M ASP* 1.3 60.1 + - - +
587M HIS* 4.4 1.1 - - - +
588M ARG* 4.3 38.8 + - - +
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Residues in contact with ASP 585 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564M PHE* 5.0 11.3 - - - -
581M GLU 2.9 13.6 + - - +
582M TYR* 4.4 2.2 - - - +
584M HIS* 1.3 79.1 - - - +
586M LEU* 1.3 60.8 + - - +
587M HIS 3.3 1.8 - - - -
588M ARG* 3.9 1.5 + - - +
589M ARG* 2.8 39.2 + - - +
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Residues in contact with LEU 586 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549M ILE* 4.2 5.2 - - + -
552M LEU* 3.8 30.1 - - + -
556M VAL* 5.8 3.4 - - + -
564M PHE* 3.7 38.8 - - + +
582M TYR* 2.9 55.1 + - + +
583M ILE* 4.5 9.0 - - + -
585M ASP* 1.3 75.3 - - - +
587M HIS* 1.3 59.4 + - - +
589M ARG* 3.8 7.2 - - + -
590M ILE* 2.9 40.1 + - + +
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Residues in contact with HIS 587 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583M ILE* 2.5 33.7 + - + +
584M HIS* 4.7 1.8 - - - +
586M LEU* 1.3 76.9 - - - +
588M ARG* 1.3 70.8 + - + +
590M ILE* 3.1 10.8 + - + +
591M GLN* 2.9 64.1 + - + +
841M TYR* 3.8 43.5 - + + +
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Residues in contact with ARG 588 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584M HIS* 4.3 34.4 + - - +
585M ASP 3.9 1.7 + - - +
587M HIS* 1.3 88.9 + - + +
589M ARG* 1.3 61.8 + - - +
590M ILE 3.3 0.2 - - - -
591M GLN* 3.9 10.4 - - + +
592M PRO* 3.3 19.6 - - - +
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Residues in contact with ARG 589 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563M ARG* 3.6 38.3 + - - +
564M PHE* 3.8 34.4 - - + -
585M ASP* 2.8 29.3 + - - +
586M LEU* 3.6 11.4 - - + +
587M HIS 3.1 0.2 - - - -
588M ARG* 1.3 78.5 - - - +
590M ILE* 1.3 58.2 + - - +
592M PRO* 3.9 3.1 - - - +
593M PHE* 3.9 13.3 - - - -
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Residues in contact with ILE 590 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552M LEU* 4.7 21.1 - - + -
556M VAL* 4.1 23.3 - - + -
563M ARG* 4.3 18.6 - - - +
586M LEU* 2.9 27.2 + - + +
587M HIS* 3.3 15.7 - - + +
589M ARG* 1.3 77.2 - - - +
591M GLN* 1.3 69.7 + - + +
592M PRO* 3.4 1.3 - - - -
593M PHE* 3.0 31.1 + - + +
594M ILE* 3.2 19.7 - - + +
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Residues in contact with GLN 591 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587M HIS* 2.9 62.6 + - + +
588M ARG* 4.0 8.5 - - + +
590M ILE* 1.3 79.0 - - - +
592M PRO* 1.3 68.2 - - + +
593M PHE 3.0 1.6 + - - -
594M ILE* 3.2 36.2 + - - +
596M ARG* 5.1 13.2 + - - +
841M TYR 5.7 2.0 - - - -
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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