Contacts of the helix formed by residues 407 - 420 (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 ALA 407 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406M LEU* 1.3 79.9 - - + +
408M GLY* 1.3 60.4 + - - +
409M ARG* 3.1 11.0 - - - +
410M LEU* 3.0 10.6 + - + +
411M LEU* 2.9 34.2 + - + +
582M GLU* 5.7 5.2 - - - +
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Residues in contact with GLY 408 (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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406M LEU 4.3 3.2 - - - +
407M ALA* 1.3 74.1 - - - +
409M ARG* 1.3 59.0 + - - +
411M LEU* 3.5 19.0 - - - +
412M VAL* 2.8 32.8 + - - +
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Residues in contact with ARG 409 (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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406M LEU* 4.1 23.1 + - - +
407M ALA* 3.9 13.4 - - - +
408M GLY* 1.3 70.6 - - - +
410M LEU* 1.3 101.4 + - - +
412M VAL* 3.2 11.6 - - - +
413M LEU* 2.9 29.8 + - - +
586M GLU* 4.7 12.3 + - - +
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Residues in contact with LEU 410 (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* 3.0 10.7 + - + +
409M ARG* 1.3 110.8 - - - +
411M LEU* 1.3 59.7 + - - +
413M LEU* 3.7 15.9 - - + -
414M GLN* 2.9 62.9 + - + +
582M GLU* 3.8 34.1 - - + +
585M ARG* 3.7 31.0 - - + +
586M GLU* 4.8 4.9 - - + +
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Residues in contact with LEU 411 (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* 2.9 20.4 + - + +
408M GLY* 3.5 22.7 - - - +
409M ARG 3.2 0.4 - - - -
410M LEU* 1.3 77.2 - - - +
412M VAL* 1.3 56.8 + - - +
414M GLN* 3.5 3.2 + - + +
415M ALA* 2.9 29.5 + - - +
605M LEU* 5.8 9.2 - - + -
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Residues in contact with VAL 412 (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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408M GLY 2.8 15.8 + - - +
409M ARG* 3.2 18.6 - - - +
411M LEU* 1.3 74.4 - - - +
413M LEU* 1.3 60.8 + - + +
415M ALA* 3.5 5.6 - - + +
416M LYS* 2.9 27.7 + - - +
818M LEU* 4.6 9.4 - - + +
821M GLU* 5.5 6.5 - - + +
822M ALA* 3.8 26.4 - - + +
825M LYS* 5.4 9.4 - - + -
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Residues in contact with LEU 413 (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* 2.9 19.7 + - - +
410M LEU* 3.7 19.3 - - + +
411M LEU 3.2 0.2 - - - -
412M VAL* 1.3 78.1 - - + +
414M GLN* 1.3 74.8 + - - +
416M LYS* 3.2 29.1 + - - +
417M ARG* 2.9 23.8 + - + +
585M ARG 4.9 5.4 - - - +
588M LYS 5.5 3.1 - - - +
589M ALA* 6.0 5.4 - - - -
590M GLU* 5.5 4.3 - - + +
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Residues in contact with GLN 414 (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* 2.9 38.2 + - + +
411M LEU* 4.2 2.9 - - - +
413M LEU* 1.3 95.7 - - - +
415M ALA* 1.3 60.6 + - - +
417M ARG* 3.3 22.4 + - - +
418M LYS* 2.9 26.0 + - - +
585M ARG* 4.3 26.3 + - + +
588M LYS* 3.3 31.3 + - - +
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Residues in contact with ALA 415 (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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411M LEU 2.9 19.6 + - - +
412M VAL* 3.5 11.4 - - + +
414M GLN* 1.3 77.9 - - - +
416M LYS* 1.3 56.4 + - - +
418M LYS* 3.3 9.3 - - - +
419M ALA* 2.9 21.0 + - - +
815M TYR* 5.8 7.0 - - + -
818M LEU 5.3 1.1 - - - +
819M LEU* 3.5 34.8 - - + +
822M ALA* 4.4 7.6 - - + -
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Residues in contact with LYS 416 (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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412M VAL* 2.9 14.5 + - + +
413M LEU* 3.2 26.7 + - - +
415M ALA* 1.3 74.3 - - - +
417M ARG* 1.3 60.5 + - - +
419M ALA* 2.9 9.1 + - + -
420M THR* 2.8 47.0 + - + +
590M GLU* 2.8 41.4 + - - +
822M ALA* 4.6 18.5 - - + +
825M LYS* 5.8 4.3 - - + -
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Residues in contact with ARG 417 (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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413M LEU* 2.9 14.7 + - + +
414M GLN* 3.2 26.6 + - - +
416M LYS* 1.3 73.1 - - - +
418M LYS* 1.3 61.8 + - - +
420M THR 2.9 21.1 - - - +
463M PRO* 3.3 43.7 + - + +
464M MET 4.9 0.8 + - - -
465M ASP* 4.0 20.8 + - - +
588M LYS* 3.3 36.2 - - - +
590M GLU* 3.3 44.8 + - + +
591M VAL 2.4 32.5 + - - -
592M ASP* 4.6 1.4 - - - +
593M THR* 4.7 6.3 + - - +
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Residues in contact with LYS 418 (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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414M GLN 2.9 13.5 + - - +
415M ALA* 3.3 10.8 - - - +
416M LYS 3.2 0.2 - - - -
417M ARG* 1.3 78.5 - - - +
419M ALA* 1.3 59.8 + - - +
420M THR 3.2 4.6 + - - -
421M PRO* 4.8 1.6 - - - +
463M PRO* 5.1 6.0 - - - +
612M LEU* 4.6 15.5 - - + +
815M TYR* 2.7 40.7 + - - +
819M LEU* 3.9 21.3 - - + +
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Residues in contact with ALA 419 (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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415M ALA 2.9 15.7 + - - +
416M LYS* 2.9 14.4 + - + +
418M LYS* 1.3 75.9 - - - +
420M THR* 1.3 60.1 + - - +
421M PRO* 4.1 6.2 - - - +
819M LEU* 4.9 4.5 - - + -
822M ALA 5.4 1.1 - - - +
823M ILE* 4.3 28.7 - - + +
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Residues in contact with THR 420 (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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416M LYS* 2.8 26.9 + - + +
417M ARG 2.9 19.6 - - - +
418M LYS 3.2 1.3 - - - -
419M ALA* 1.3 79.4 + - - +
421M PRO* 1.3 71.9 - - + +
422M GLY* 4.6 7.6 - - - +
463M PRO* 3.6 0.7 - - - +
590M GLU* 3.4 28.0 - - - +
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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