Contacts of the helix formed by residues 456 - 464 (chain M) in PDB entry 5NSS
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 ARG 456 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84H G 5.0 4.0 - - - -
85H T 4.0 27.1 - - + -
454M ALA 2.9 8.4 + - - +
455M ARG* 1.3 80.6 - - - +
457M THR* 1.3 61.7 + - - +
458M VAL 3.4 0.4 - - - -
459M ALA* 3.2 4.8 + - - +
460M LYS* 2.9 28.1 + - - +
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Residues in contact with THR 457 (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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83H C 4.7 13.9 - - - -
84H G 4.7 8.5 + - - -
454M ALA* 4.1 12.9 - - - +
456M ARG* 1.3 74.8 - - - +
458M VAL* 1.3 61.7 + - - +
460M LYS* 3.0 8.4 + - - +
461M TYR* 2.9 27.9 + - - +
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Residues in contact with VAL 458 (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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424M VAL* 5.3 1.0 - - - +
443M THR* 5.8 2.0 - - - -
446M LEU* 6.1 2.9 - - + -
452M MET 5.3 0.9 - - - +
453M VAL* 4.2 12.8 - - + -
454M ALA* 3.7 28.5 - - + +
455M ARG 4.6 0.7 - - - +
456M ARG 3.4 0.2 - - - -
457M THR* 1.3 78.0 - - - +
459M ALA* 1.3 56.9 + - - +
461M TYR* 4.0 6.2 - - - +
462M ARG* 2.9 32.1 + - - +
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Residues in contact with ALA 459 (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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439M ASP* 3.7 37.1 - - + +
443M THR* 5.0 2.4 - - - +
455M ARG* 3.6 22.6 - - - +
456M ARG* 3.2 12.0 + - - +
457M THR 3.2 0.8 - - - -
458M VAL* 1.3 79.3 - - - +
460M LYS* 1.3 48.9 + - - +
462M ARG* 3.9 3.7 - - - +
463M GLU* 2.7 36.4 + - - +
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Residues in contact with LYS 460 (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 ARG 2.9 12.6 + - - +
457M THR* 3.4 10.8 - - - +
459M ALA* 1.3 76.4 - - - +
461M TYR* 1.3 59.2 + - - +
462M ARG 3.3 0.2 - - - -
463M GLU* 3.0 7.1 + - - +
464M SER* 2.9 30.3 + - - -
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Residues in contact with TYR 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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421M ARG* 4.8 22.3 - - + +
424M VAL* 4.5 11.4 - - + +
425M LYS* 5.3 0.5 + - - -
457M THR 2.9 15.4 + - - +
458M VAL* 4.0 7.0 - - - +
460M LYS* 1.3 77.8 - - - +
462M ARG* 1.3 59.5 + - - +
464M SER* 3.5 16.9 + - - +
465M LEU* 5.1 3.1 - - - +
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Residues in contact with ARG 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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424M VAL* 4.0 29.3 - - + +
427M LEU* 6.3 0.9 - - + -
428M ILE* 3.2 25.2 - - + +
442M LEU* 5.8 9.0 - - + -
446M LEU* 6.2 3.6 - - + -
458M VAL 2.9 18.3 + - - +
459M ALA* 4.4 4.3 - - - +
461M TYR* 1.3 76.1 - - - +
463M GLU* 1.3 61.9 + - - +
464M SER 3.3 3.2 - - - +
467M ILE* 3.3 3.3 - - - +
469M PRO* 5.3 0.4 - - - +
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Residues in contact with GLU 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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439M ASP* 5.3 2.7 - - + -
459M ALA 2.7 23.8 + - - +
460M LYS* 3.0 10.2 + - - +
462M ARG* 1.3 73.8 - - - +
464M SER* 1.3 63.6 + - - +
467M ILE* 3.3 26.2 - - - +
469M PRO* 4.1 26.5 - - + +
470M SER* 4.6 10.1 - - - -
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Residues in contact with SER 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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425M LYS* 5.4 0.2 - - - -
428M ILE* 4.5 1.0 - - - +
460M LYS 2.9 14.0 + - - -
461M TYR* 3.5 10.4 + - - +
462M ARG* 3.2 11.6 - - - +
463M GLU* 1.3 82.5 - - - +
465M LEU* 1.3 75.6 + - - +
466M SER 3.4 1.3 - - - -
467M ILE* 3.4 3.3 + - - +
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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