Contacts of the helix formed by residues 572 - 577 (chain M) in PDB entry 6M6A
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 572 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470M GLY 5.4 3.1 - - - +
471M ASP* 5.7 3.1 - - - +
499M PRO* 4.8 1.1 - - + +
571M ASP* 1.3 77.8 - - + +
573M GLU* 1.3 64.8 + - - +
574M HIS* 3.1 13.1 + - - -
575M ARG* 3.3 45.9 - - - +
576M PHE* 3.8 2.3 + - - +
596M LEU* 2.9 26.0 + - - +
597M SER* 3.3 8.2 - - - +
598M ALA* 3.4 17.0 - - - +
599M THR* 2.4 50.1 + - - +
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Residues in contact with GLU 573 (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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570M VAL* 3.6 14.6 - - + -
571M ASP 4.1 1.1 - - - -
572M GLU* 1.3 71.7 - - - +
574M HIS* 1.3 53.8 + - - +
575M ARG 3.2 0.7 - - - -
576M PHE* 3.6 17.5 - - + -
577M GLY 3.0 18.4 + - - -
581M LYS* 2.8 55.7 + - + +
584M ILE* 3.3 22.0 - - - +
585M ARG* 4.0 4.6 + - - -
595M TYR* 3.1 39.7 + - - -
597M SER* 2.6 22.9 + - - +
601M ILE 5.9 0.7 - - - +
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Residues in contact with HIS 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 GLU 3.2 8.1 - - - -
573M GLU* 1.3 78.0 - - - +
575M ARG* 1.3 95.9 + - + +
577M GLY 4.1 1.0 + - - -
581M LYS* 4.2 3.4 - - - +
597M SER* 4.2 0.2 + - - -
599M THR* 3.0 38.3 + - - +
600M PRO 3.3 28.0 - - - +
601M ILE* 4.8 2.2 - - - +
602M PRO* 5.2 1.8 - - + -
736M ALA* 3.6 30.1 - - + +
737M THR* 6.1 1.8 - - + -
11N G 2.9 24.9 - - - +
12N G 2.9 29.6 + - - +
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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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499M PRO* 3.4 39.5 - - + +
500M THR* 6.5 0.2 - - - -
503M LEU* 4.0 14.4 - - - +
572M GLU* 3.3 41.7 - - - +
574M HIS* 1.3 99.3 + - + +
576M PHE* 1.3 65.7 + - - +
577M GLY* 3.5 0.7 - - - -
713M ILE* 6.3 2.5 - - - +
740M GLN* 5.1 13.3 - - - +
11N G 4.5 9.2 - - - +
12N G 4.7 6.1 - - - -
31T A 5.8 4.3 + - - +
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Residues in contact with PHE 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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497M LEU* 3.6 32.5 - - + -
498M VAL 3.1 26.9 - - - +
499M PRO* 4.4 9.2 - - + -
552M THR* 4.1 20.0 - - - -
553M HIS* 4.1 7.2 - - + -
556M LEU* 3.7 19.7 - - + -
570M VAL* 4.7 4.7 - - + -
571M ASP* 5.0 3.8 - - - +
572M GLU 4.4 1.8 - - - +
573M GLU* 3.1 22.3 + - + +
575M ARG* 1.3 84.7 - - - +
577M GLY* 1.3 57.8 + - - +
580M GLN* 3.1 35.7 + - + +
584M ILE* 3.6 33.2 - - + -
11N G 4.3 1.2 - - - +
32T C 6.4 0.7 - - - -
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Residues in contact with GLY 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 GLU* 3.0 9.5 + - - +
574M HIS 4.1 0.4 + - - -
575M ARG 3.5 0.6 - - - -
576M PHE* 1.3 80.4 - - - +
578M VAL* 1.3 54.0 + - - -
579M ALA 3.4 0.4 - - - -
580M GLN* 3.1 6.5 + - - +
581M LYS* 2.5 42.6 + - - +
11N G 3.1 27.8 - - - -
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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