Contacts of the helix formed by residues 573 - 584 (chain M) in PDB entry 6FF7
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 LEU 573 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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569M GLY 3.7 16.4 - - - +
570M GLY 3.6 18.5 + - - +
571M ARG 4.4 0.7 - - - +
572M LYS* 1.3 77.6 - - - +
574M GLU* 1.3 64.3 + - - +
575M ARG* 3.4 3.8 - - + +
576M ALA* 3.5 24.4 + - + +
577M ARG* 3.5 12.3 + - - +
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Residues in contact with GLU 574 (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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572M LYS 4.1 1.0 + - - -
573M LEU* 1.3 71.4 - - - +
575M ARG* 1.3 61.3 + - - +
577M ARG* 3.3 7.0 + - - +
578M ASP* 2.9 28.4 + - - +
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Residues in contact with ARG 575 (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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573M LEU* 3.4 3.7 - - + +
574M GLU* 1.3 78.4 - - - +
576M ALA* 1.3 57.2 + - - +
578M ASP* 3.7 7.9 - - - +
579M LEU* 2.9 31.4 + - - +
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Residues in contact with ALA 576 (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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565M ILE* 3.7 33.5 - - + +
569M GLY* 6.0 2.5 - - - -
570M GLY 5.1 0.9 - - - +
573M LEU* 3.5 23.9 + - + +
574M GLU 3.2 0.6 - - - -
575M ARG* 1.3 79.8 - - - +
577M ARG* 1.3 57.6 + - - +
579M LEU* 3.9 2.9 - - - +
580M PHE* 2.9 32.2 + - - +
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Residues in contact with ARG 577 (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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573M LEU 3.5 8.9 + - - +
574M GLU* 3.3 9.6 + - - +
576M ALA* 1.3 76.7 - - - +
578M ASP* 1.3 60.3 + - - +
580M PHE* 4.4 4.7 - - - -
581M GLU* 2.9 33.8 + - - +
599M TYR* 6.4 2.5 - - + -
603M GLU* 6.4 1.8 - - + -
110p SER* 5.3 18.2 - - - -
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Residues in contact with ASP 578 (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 GLU 2.9 19.4 + - - +
575M ARG* 3.7 9.0 - - - +
576M ALA 3.3 0.2 - - - -
577M ARG* 1.3 77.7 - - - +
579M LEU* 1.3 57.6 + - - +
581M GLU* 3.8 2.6 - - - +
582M GLN* 2.9 29.7 + - - +
47p PRO 3.6 12.9 - - - -
110p SER 6.1 3.4 - - - -
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Residues in contact with LEU 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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575M ARG 2.9 17.0 + - - +
576M ALA* 4.2 3.1 - - - +
578M ASP* 1.3 74.1 - - - +
580M PHE* 1.3 61.3 + - - +
582M GLN* 3.6 4.9 - - - +
583M ALA* 2.9 33.1 + - - +
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Residues in contact with PHE 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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561M LEU* 5.7 13.7 - - + +
562M THR* 6.5 0.7 - - - -
576M ALA 2.9 20.5 + - - +
577M ARG* 4.2 4.7 - - - +
579M LEU* 1.3 75.7 - - - +
581M GLU* 1.3 60.6 + - - +
583M ALA* 4.6 1.9 - - - +
584M LEU* 3.4 26.9 + - - +
599M TYR* 5.6 10.3 - - + -
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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 ARG 2.9 21.4 + - - +
578M ASP* 4.2 2.5 - - - +
580M PHE* 1.3 75.0 - - - +
582M GLN* 1.3 59.1 + - - +
584M LEU* 5.3 1.3 - - - -
585M ASP* 3.2 29.6 - - - +
599M TYR* 5.7 9.6 - - + +
109p PRO* 6.1 1.6 - - + -
110p SER* 5.3 18.2 - - - +
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Residues in contact with GLN 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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578M ASP 2.9 20.5 + - - +
579M LEU* 3.1 8.0 + - - +
581M GLU* 1.3 78.6 - - - +
583M ALA* 1.3 64.1 + - - +
585M ASP* 3.7 12.7 - - - +
47p PRO* 3.2 28.5 - - + -
50p ARG* 5.0 9.1 - - + +
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Residues in contact with ALA 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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579M LEU 2.9 15.2 + - - +
580M PHE* 4.6 2.2 - - - +
582M GLN* 1.3 78.6 - - - +
584M LEU* 1.3 59.0 + - + +
585M ASP 3.3 1.4 + - - -
586M GLY 5.5 0.2 + - - -
587M CYS* 5.7 0.9 + - - -
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Residues in contact with LEU 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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558M SER* 6.0 6.3 - - - -
580M PHE 3.4 18.1 + - - +
581M GLU* 4.2 1.3 - - - -
583M ALA* 1.3 77.9 - - + +
585M ASP* 1.3 66.8 + - - +
586M GLY 3.7 1.1 - - - -
587M CYS* 3.2 24.4 - - + +
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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