Contacts of the helix formed by residues 577 - 587 (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 GLY 577 (chain M).
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Specific contacts
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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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Residues in contact with VAL 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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577M GLY* 1.3 69.2 - - - -
579M ALA* 1.3 60.4 + - + +
581M LYS* 3.1 23.3 + - + +
582M GLU* 2.9 36.7 + - - +
601M ILE* 3.7 28.7 - - + -
602M PRO* 5.3 0.7 - - + -
604M THR* 5.0 1.8 - - - +
11N G 2.5 29.7 + - - +
12N G 3.4 21.5 + - - +
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Residues in contact with ALA 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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578M VAL* 1.3 69.0 - - + +
580M GLN* 1.3 61.1 + - - +
582M GLU* 3.1 13.6 + - + +
583M ARG* 2.9 26.2 + - - +
586M GLU* 5.2 0.3 - - - +
10N T 3.7 22.2 - - - +
11N G 2.3 27.5 + - - +
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Residues in contact with GLN 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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553M HIS* 4.0 32.8 + - + +
556M LEU* 3.6 10.4 - - + +
576M PHE* 3.1 40.9 + - + +
577M GLY* 3.1 9.1 + - - +
579M ALA* 1.3 76.8 - - - +
581M LYS* 1.3 58.4 + - - +
583M ARG* 3.3 6.5 + - + +
584M ILE* 2.9 34.6 + - - +
9N T 5.0 5.5 + - - -
10N T 3.2 16.4 + - - +
11N G 2.9 28.8 + - - +
31T A 5.5 4.2 - - - -
32T C 6.0 2.2 + - - -
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Residues in contact with LYS 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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573M GLU* 2.8 63.2 + - - +
574M HIS* 4.1 3.8 - - - +
577M GLY* 2.5 32.8 + - - +
578M VAL* 3.1 34.2 + - + +
580M GLN* 1.3 73.9 - - - +
582M GLU* 1.3 61.3 + - - +
584M ILE* 3.2 5.3 + - - +
585M ARG* 2.4 52.8 + - - +
601M ILE* 3.9 30.3 - - + +
605M LEU* 4.8 7.2 - - + -
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Residues in contact with GLU 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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407M ALA* 5.7 5.2 - - - +
410M LEU* 3.8 24.4 - - + +
578M VAL* 2.9 23.5 + - - +
579M ALA* 3.1 13.6 + - + +
581M LYS* 1.3 84.1 - - - +
583M ARG* 1.3 57.6 + - - +
585M ARG* 3.1 13.8 + - - +
586M GLU* 2.9 36.4 + - - +
605M LEU* 4.6 13.7 - - - +
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Residues in contact with ARG 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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553M HIS* 6.3 2.0 - - + -
556M LEU* 2.7 52.8 + - + -
557M GLN* 4.2 10.7 + - - +
558M GLU 5.2 2.2 + - - -
559M ASP* 5.9 2.4 - - - +
579M ALA 2.9 14.8 + - - +
580M GLN* 3.7 7.9 - - + +
581M LYS 3.3 0.2 - - - -
582M GLU* 1.3 72.9 - - - +
584M ILE* 1.3 60.9 + - - +
586M GLU* 3.2 36.8 + - - +
587M LEU* 2.9 44.2 + - - +
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Residues in contact with ILE 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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497M LEU* 3.6 23.3 - - + -
556M LEU* 4.0 9.9 - - + -
568M LEU* 5.4 7.1 - - + +
570M VAL* 4.0 10.8 - - + -
573M GLU* 3.3 23.1 - - - +
576M PHE* 3.6 24.9 - - + -
580M GLN 2.9 18.6 + - - +
581M LYS* 3.3 8.1 - - - +
583M ARG* 1.3 77.7 - - - +
585M ARG* 1.3 68.6 + - - +
587M LEU* 3.0 7.9 + - - +
588M LYS* 2.9 38.1 + - + +
593M THR* 5.8 0.7 - - + -
595M TYR* 3.6 14.1 - - + +
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Residues in contact with ARG 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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410M LEU* 3.7 31.0 - - + +
413M LEU* 4.9 3.8 - - - +
414M GLN* 4.3 17.5 + - + +
573M GLU* 4.0 6.3 + - - -
581M LYS* 2.4 63.4 + - - +
582M GLU* 3.1 21.7 + - - +
584M ILE* 1.3 93.8 - - - +
586M GLU* 1.3 61.3 + - - +
588M LYS* 3.1 47.7 + - - +
595M TYR* 3.6 22.1 + - - -
605M LEU* 5.4 8.2 - - - +
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Residues in contact with GLU 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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409M ARG* 4.7 16.7 + - - +
410M LEU* 4.8 4.6 - - + +
582M GLU* 2.9 25.9 + - - +
583M ARG* 3.3 45.1 + - - +
585M ARG* 1.3 78.3 - - - +
587M LEU* 1.3 58.0 + - - +
588M LYS 3.1 3.7 + - - -
589M ALA* 4.4 6.9 + - - +
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Residues in contact with LEU 587 (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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555M LEU 4.2 9.2 - - - +
556M LEU* 3.7 23.6 - - + +
560M VAL* 3.8 29.8 - - + -
562M PHE* 4.4 13.2 - - + -
565M LEU* 3.9 12.3 - - - +
568M LEU* 3.9 18.6 - - + +
583M ARG* 2.9 59.6 + - - +
584M ILE* 3.1 7.9 - - - +
586M GLU* 1.3 74.1 - - - +
588M LYS* 1.3 55.4 + - - +
589M ALA 3.6 2.8 + - - -
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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