Contacts of the helix formed by residues 460 - 471 (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 GLN 460 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-15I A 4.9 11.7 + - - +
459M ASN* 1.3 90.3 + - + +
461M LYS* 1.3 76.4 + - + +
462M SER 3.3 0.7 - - - -
463M ARG* 3.2 29.5 + - - +
464M ASP* 3.3 20.0 + - - +
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Residues in contact with LYS 461 (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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317M ASP* 3.3 26.0 - - + +
318M GLU* 5.7 3.3 + - - +
459M ASN* 4.2 3.0 + - - -
460M GLN* 1.3 89.3 - - + +
462M SER* 1.3 57.9 + - - +
464M ASP* 3.0 16.8 + - + +
465M THR* 2.9 28.3 + - - +
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Residues in contact with SER 462 (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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315M ASN* 3.0 19.2 + - - -
316M TYR* 3.4 18.1 - - - +
317M ASP* 2.5 26.5 + - - -
457M MET 3.3 23.1 - - - -
458M GLY* 3.6 9.4 - - - -
459M ASN 4.2 0.2 - - - -
460M GLN 3.3 1.0 - - - +
461M LYS* 1.3 76.4 - - - +
463M ARG* 1.3 57.1 + - - +
465M THR* 3.1 9.9 + - - -
466M ILE* 2.9 35.9 + - - +
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Residues in contact with ARG 463 (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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456M TYR* 3.8 34.1 - - + +
457M MET 4.6 1.0 + - - -
459M ASN 4.2 19.0 + - - +
460M GLN* 3.2 26.2 + - - +
462M SER* 1.3 79.7 - - - +
464M ASP* 1.3 56.4 + - - +
466M ILE* 3.3 1.9 + - - +
467M ARG* 2.9 70.0 + - + +
497M LYS* 6.1 0.4 - - - +
498M ASP* 4.0 22.0 + - - -
501M GLU* 4.9 14.4 + - + -
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Residues in contact with ASP 464 (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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460M GLN* 3.6 17.6 - - - +
461M LYS* 3.0 16.6 + - - +
463M ARG* 1.3 77.2 + - - +
465M THR* 1.3 57.1 + - - +
467M ARG* 2.3 41.4 + - - +
468M GLU* 2.9 34.6 + - - +
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Residues in contact with THR 465 (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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291M ILE* 3.8 33.0 - - + -
308M LEU* 4.8 2.5 - - + -
316M TYR* 4.1 25.8 + - + +
317M ASP* 4.9 1.0 + - - -
319M ALA* 5.7 2.6 - - + +
461M LYS 2.9 13.8 + - - -
462M SER* 3.1 13.1 + - - -
464M ASP* 1.3 74.6 - - - +
466M ILE* 1.3 62.5 - - + +
468M GLU* 3.2 22.6 + - - +
469M TYR* 2.9 29.4 + - + +
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Residues in contact with ILE 466 (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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316M TYR* 4.3 23.3 - - + -
454M ILE* 4.4 11.9 - - + -
455M CYS 3.5 22.7 - - - +
456M TYR* 3.6 38.1 - - + -
457M MET 4.9 3.4 - - - +
462M SER 2.9 20.6 + - - +
463M ARG 3.3 4.0 + - - +
465M THR* 1.3 78.2 - - + +
467M ARG* 1.3 58.6 + - + +
469M TYR* 3.7 8.4 - - + +
470M GLU* 2.9 36.9 + - + +
488M LEU* 6.4 2.0 - - + -
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Residues in contact with ARG 467 (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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456M TYR* 6.5 0.2 - - + -
463M ARG* 2.9 53.1 + - + +
464M ASP* 2.3 32.8 + - - +
466M ILE* 1.3 77.2 - - + +
468M GLU* 1.3 63.0 + - - +
470M GLU* 3.4 26.5 + - - +
471M PHE* 3.7 8.5 + - - +
501M GLU* 4.5 27.9 + - + -
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Residues in contact with GLU 468 (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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292M ASP* 4.3 14.8 - - - +
308M LEU* 3.8 21.8 - - - +
464M ASP* 2.9 19.6 + - - +
465M THR* 3.2 26.0 + - + +
467M ARG* 1.3 76.8 - - - +
469M TYR* 1.3 57.9 + - + +
471M PHE 3.3 15.4 - - - +
473M THR* 6.2 4.3 - - + +
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Residues in contact with TYR 469 (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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291M ILE* 3.7 35.4 - - + -
292M ASP* 3.4 22.0 - - - +
341M ARG* 4.1 11.6 + - - -
452M ASN* 3.9 8.0 + - - -
454M ILE* 3.5 47.0 - - + +
465M THR* 2.9 19.5 + - + +
466M ILE* 4.1 9.2 - - + +
468M GLU* 1.3 76.3 - - - +
470M GLU* 1.3 69.6 + - - +
471M PHE 4.6 0.8 - - - -
484M LYS* 3.0 41.0 + - + +
485M PHE* 4.3 12.4 - + + +
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Residues in contact with GLU 470 (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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466M ILE* 2.9 24.0 + - + +
467M ARG* 3.4 19.7 + - - +
469M TYR* 1.3 81.6 - - - +
471M PHE* 1.3 79.3 + - + +
482M THR 3.0 15.9 - - - +
484M LYS* 4.0 7.6 + - - +
485M PHE* 3.5 33.7 - - + -
501M GLU* 4.6 8.9 - - - +
505M ILE* 3.4 34.0 - - - +
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Residues in contact with PHE 471 (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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467M ARG 3.7 8.1 + - - +
468M GLU* 3.3 19.9 - - - +
469M TYR 5.1 0.7 - - - -
470M GLU* 1.3 113.8 - - + +
472M TYR* 1.3 69.4 + - - +
473M THR* 5.4 1.4 - - - +
481M LYS* 3.7 15.0 - - + +
482M THR* 3.3 29.2 - - - +
483M MET* 3.6 36.3 - - + -
484M LYS* 6.1 0.4 - - - -
485M PHE* 5.0 3.8 - + - -
505M ILE* 3.6 24.9 - - + -
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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