Contacts of the helix formed by residues 448 - 466 (chain M) in PDB entry 6FF7
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 ASN 448 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446M HIS* 3.2 8.9 + - - +
447M GLU* 1.3 79.9 - - + +
449M TYR* 1.3 60.0 + - - +
450M ASP* 3.3 10.7 + - + +
451M GLU* 4.5 2.4 + - - +
452M ALA* 4.2 11.3 + - - +
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Residues in contact with TYR 449 (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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447M GLU 3.3 5.3 + - - +
448M ASN* 1.3 70.9 - - - +
450M ASP* 1.3 54.3 + - - +
451M GLU 3.6 0.2 - - - -
452M ALA* 4.0 10.5 - - + -
453M LEU* 2.7 44.6 + - + +
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Residues in contact with ASP 450 (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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448M ASN* 3.3 8.5 - - + +
449M TYR* 1.3 78.7 - - - +
451M GLU* 1.3 60.6 + - + +
453M LEU* 3.6 2.8 - - - +
454M ARG* 2.9 27.3 + - - +
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Residues in contact with GLU 451 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448M ASN 4.5 3.1 + - - +
450M ASP* 1.3 78.8 - - - +
452M ALA* 1.3 57.7 + - - +
454M ARG* 3.8 6.7 - - - +
455M LEU* 2.9 33.1 + - - +
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Residues in contact with ALA 452 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443M GLU* 3.3 43.9 - - + +
444M LEU* 5.5 0.2 - - - -
446M HIS* 5.0 2.9 - - + -
448M ASN 4.2 5.1 + - - +
449M TYR* 3.9 17.0 + - + -
450M ASP 3.3 0.4 - - - -
451M GLU* 1.3 78.5 - - - +
453M LEU* 1.3 51.2 + - - +
455M LEU* 5.0 1.8 - - - -
456M LEU* 2.7 41.0 + - - +
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Residues in contact with LEU 453 (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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449M TYR* 2.7 26.5 + - + +
450M ASP* 3.6 2.9 - - - +
452M ALA* 1.3 76.6 - - - +
454M ARG* 1.3 52.4 + - - +
456M LEU* 4.4 2.9 - - - -
457M ARG* 2.7 37.8 + - - +
490M LEU 5.7 5.4 - - - +
499M THR* 6.1 5.4 - - - -
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Residues in contact with ARG 454 (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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450M ASP 2.9 15.6 + - - +
451M GLU* 3.8 7.2 - - - +
453M LEU* 1.3 74.4 - - - +
455M LEU* 1.3 60.3 + - - +
457M ARG* 3.1 5.4 + - - +
458M LYS* 2.9 29.8 + - - +
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Residues in contact with LEU 455 (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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451M GLU 2.9 16.1 + - - +
452M ALA* 4.6 2.2 - - - +
454M ARG* 1.3 77.3 - - - +
456M LEU* 1.3 58.2 + - - +
458M LYS* 4.2 3.7 - - - +
459M ALA* 2.9 33.7 + - - +
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Residues in contact with LEU 456 (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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440M GLY* 5.3 14.1 - - - -
443M GLU* 5.5 2.2 - - + -
452M ALA 2.7 24.4 + - - +
453M LEU* 3.9 4.0 - - - -
455M LEU* 1.3 76.0 - - - +
457M ARG* 1.3 52.0 + - - +
459M ALA* 4.6 2.9 - - - -
460M THR* 2.6 40.6 + - - +
489M MET 5.4 3.6 - - - +
490M LEU* 4.0 16.1 - - - +
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Residues in contact with ARG 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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453M LEU 2.7 23.6 + - - +
454M ARG* 3.1 7.4 + - - +
456M LEU* 1.3 75.0 - - - +
458M LYS* 1.3 60.1 + - - +
460M THR* 3.8 3.1 - - - -
461M ALA* 2.9 30.1 + - - +
490M LEU* 5.1 6.1 - - + -
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Residues in contact with LYS 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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454M ARG 2.9 14.9 + - - +
455M LEU* 4.2 4.0 - - - +
457M ARG* 1.3 74.8 - - - +
459M ALA* 1.3 59.8 + - - +
461M ALA* 3.0 6.4 + - - +
462M LEU* 2.9 28.1 + - - +
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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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436M TRP* 5.3 17.0 - - + +
455M LEU 2.9 19.4 + - - +
456M LEU* 4.6 3.4 - - - -
458M LYS* 1.3 77.2 - - - +
460M THR* 1.3 59.4 + - - +
462M LEU* 3.7 16.7 + - - +
463M PRO* 4.4 4.3 - - - +
486M VAL* 5.7 0.9 - - - +
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Residues in contact with THR 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 LEU 2.6 25.3 + - - -
457M ARG* 4.0 2.9 - - - -
459M ALA* 1.3 77.1 - - - +
461M ALA* 1.3 61.5 + - - +
462M LEU 3.3 0.4 + - - -
463M PRO* 4.1 9.8 - - - +
464M ALA* 4.5 4.9 + - - +
486M VAL* 4.0 27.3 - - - +
487M TRP* 5.1 3.9 + - - +
490M LEU* 3.8 21.3 - - - -
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Residues in contact with ALA 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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457M ARG 2.9 21.1 + - - +
458M LYS* 3.0 6.9 + - - +
460M THR* 1.3 75.8 - - - +
462M LEU* 1.3 64.2 + - - +
463M PRO 3.5 0.2 - - - -
464M ALA* 3.3 22.9 + - + +
465M ARG* 4.2 2.6 + - - +
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Residues in contact with LEU 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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458M LYS 2.9 14.3 + - - +
459M ALA* 3.8 11.9 - - - +
460M THR 3.3 1.0 - - - -
461M ALA* 1.3 77.7 - - - +
463M PRO* 1.3 62.3 - - - +
464M ALA 3.1 1.4 + - - -
465M ARG* 3.3 15.0 + - - +
466M ARG* 3.9 6.1 + - - +
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Residues in contact with PRO 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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433M ALA* 6.0 5.6 - - + -
459M ALA 4.4 4.2 - - - +
460M THR 4.1 8.1 - - - +
461M ALA 3.5 0.4 - - - -
462M LEU* 1.3 77.0 - - - +
464M ALA* 1.3 61.8 + - - +
465M ARG 3.2 0.2 - - - -
466M ARG 2.9 29.4 - - - +
467M ALA* 3.7 12.0 + - + +
483M SER* 5.2 16.8 - - - -
486M VAL* 6.1 4.0 - - + -
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Residues in contact with ALA 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 THR 4.5 3.4 + - - +
461M ALA* 3.3 21.0 + - + +
462M LEU 3.1 1.8 + - - -
463M PRO* 1.3 78.3 - - - +
465M ARG* 1.3 62.0 + - - +
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Residues in contact with ARG 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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461M ALA 4.2 1.9 + - - +
462M LEU 3.3 8.5 + - - +
463M PRO 3.2 0.4 - - - -
464M ALA* 1.3 82.4 - - - +
466M ARG* 1.3 61.6 + - + +
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Residues in contact with ARG 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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427M LYS* 5.4 6.3 - - + -
462M LEU 3.9 3.0 + - - +
463M PRO* 2.9 22.9 - - - +
465M ARG* 1.3 81.5 - - + +
467M ALA* 1.3 62.4 + - - +
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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