Contacts of the helix formed by residues 450 - 468 (chain A) in PDB entry 2XAF
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 450 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446A ASN* 3.2 24.8 + - - +
447A LYS* 3.8 6.1 - - - +
449A VAL* 1.3 85.0 - - - +
451A LEU* 1.3 60.0 + - - +
453A GLU* 3.3 23.6 - - + +
454A LYS* 4.1 14.6 + - - +
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Residues in contact with LEU 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A LYS* 3.3 17.9 + - + +
448A MET* 3.3 9.0 - - - +
449A VAL 2.8 2.2 + - - -
450A ASN* 1.3 83.6 - - - +
452A LYS* 1.3 55.0 + - - +
453A GLU 2.5 13.8 + - - -
454A LYS* 3.1 7.8 + - + +
455A ILE* 2.8 31.3 + - + +
490A LEU* 4.0 25.8 - - + +
493A GLU* 3.6 27.6 - - + +
494A TYR* 3.6 39.7 - - + +
497A LEU* 4.9 7.9 - - + -
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Residues in contact with LYS 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A MET 3.0 11.4 + - - +
449A VAL* 3.7 9.0 - - + +
451A LEU* 1.3 72.4 - - - +
453A GLU* 1.3 66.8 + - - +
455A ILE* 4.2 9.4 - - + -
456A LYS* 3.3 23.4 + - + +
494A TYR* 4.2 7.9 - - + -
362B LYS 3.9 15.4 + - - +
363B LEU* 3.9 22.2 + - + -
364B ASP 3.4 26.3 + - - -
365B GLY* 4.2 3.8 - - - -
366B GLY 2.9 28.2 + - - +
367B ILE* 4.3 11.7 - - + +
370B TYR* 5.2 16.1 + - + -
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Residues in contact with GLU 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A VAL* 3.0 14.5 + - + +
450A ASN* 3.3 30.1 - - + +
451A LEU 2.5 8.5 - - - -
452A LYS* 1.3 74.9 - - - +
454A LYS* 1.3 66.8 + - + +
456A LYS* 3.2 22.3 - - - +
457A GLU* 3.4 8.3 + - - +
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Residues in contact with LYS 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A ASN 4.1 13.0 + - - +
451A LEU* 3.1 8.0 + - + +
453A GLU* 1.3 78.4 - - + +
455A ILE* 1.3 55.5 + - - +
457A GLU* 3.0 17.7 + - - +
458A LEU* 2.6 41.1 + - + +
490A LEU* 4.1 19.3 - - + -
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Residues in contact with ILE 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A LEU* 2.8 20.8 + - + +
452A LYS* 4.2 4.5 - - + -
454A LYS* 1.3 76.6 - - - +
456A LYS* 1.3 65.7 + - - +
458A LEU* 3.8 6.1 - - - +
459A HIS* 3.1 17.3 + - - +
487A LEU* 4.0 8.3 - - + +
490A LEU* 3.2 50.0 - - + +
491A CYS* 3.8 20.2 - - - -
494A TYR* 4.4 12.8 - - + -
367B ILE* 4.4 16.6 - - + -
370B TYR* 3.6 31.6 - - + -
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Residues in contact with LYS 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452A LYS* 3.3 16.5 + - + +
453A GLU* 3.2 15.7 + - - +
455A ILE* 1.3 83.4 - - - +
457A GLU* 1.3 64.7 + - + +
458A LEU 3.3 0.3 + - - -
459A HIS* 3.3 15.8 + - - +
460A GLN* 3.4 6.1 + - - +
370B TYR* 3.0 39.0 - - + +
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Residues in contact with GLU 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A GLU 3.4 7.8 + - - +
454A LYS* 3.0 21.3 + - - +
456A LYS* 1.3 79.7 - - + +
458A LEU* 1.3 62.0 + - - +
459A HIS 3.5 0.2 - - - -
460A GLN* 3.2 25.9 - - + +
461A GLN* 3.4 31.4 + - + +
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Residues in contact with LEU 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A LYS* 2.6 25.2 + - + +
455A ILE* 3.8 5.2 - - - +
457A GLU* 1.3 74.4 - - - +
459A HIS* 1.3 66.3 + - - +
460A GLN 3.1 0.2 - - - -
461A GLN* 3.1 24.1 + - - +
462A TYR* 3.0 21.3 + - - +
483A LYS* 3.8 33.2 - - + +
486A ASP* 3.9 14.1 - - + +
487A LEU* 3.6 46.7 - - + +
490A LEU* 5.4 7.6 - - + -
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Residues in contact with HIS 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A ILE 3.1 12.5 + - - +
456A LYS 3.3 11.2 - - - +
458A LEU* 1.3 71.7 - - - +
460A GLN* 1.3 70.4 + - - +
462A TYR* 3.0 9.9 + + - +
463A LYS* 2.7 55.5 + - + +
487A LEU* 3.6 14.2 - - + +
369B PRO 3.9 21.7 + - - -
370B TYR* 4.0 33.1 + + + -
371B ARG 5.6 1.1 - - - -
372B LEU* 4.9 15.4 - - + +
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Residues in contact with GLN 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456A LYS 3.4 4.8 + - - +
457A GLU* 3.2 24.2 - - + +
459A HIS* 1.3 85.1 - - - +
461A GLN* 1.3 64.5 + - + +
463A LYS* 3.0 8.0 + - - +
464A GLU* 2.9 53.1 + - - +
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Residues in contact with GLN 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457A GLU* 3.4 36.9 + - + +
458A LEU* 3.1 24.5 + - + +
460A GLN* 1.3 83.1 - - + +
462A TYR* 1.3 60.8 + - - +
464A GLU* 3.7 15.1 - - - +
465A ALA* 3.1 25.1 + - - +
479A LEU* 5.3 0.7 - - - +
483A LYS* 3.4 35.2 + - + +
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Residues in contact with TYR 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A LEU 3.0 12.0 + - - +
459A HIS* 3.6 14.1 - + - +
461A GLN* 1.3 74.2 - - - +
463A LYS* 1.3 86.1 + - + +
465A ALA* 3.1 4.2 + - - -
466A SER* 2.9 37.7 + - - -
480A VAL* 4.0 32.4 - - + +
483A LYS* 4.1 17.9 - - + +
484A HIS* 3.8 37.5 - + + -
487A LEU* 5.5 2.7 - - + -
372B LEU* 3.8 35.6 - - + +
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Residues in contact with LYS 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459A HIS* 2.7 40.3 + - + +
460A GLN* 3.4 14.4 - - - +
462A TYR* 1.3 87.8 - - + +
464A GLU* 1.3 57.9 + - - +
466A SER* 3.0 21.7 + - - -
467A GLU* 3.1 35.2 + - - +
372B LEU* 6.3 1.0 - - - +
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Residues in contact with GLU 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A GLN* 2.9 43.5 + - - +
461A GLN* 3.7 14.2 - - - +
463A LYS* 1.3 75.0 - - - +
465A ALA* 1.3 59.4 + - + +
467A GLU* 3.5 25.6 + - + +
468A VAL* 4.0 7.1 + - - +
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Residues in contact with ALA 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461A GLN 3.1 19.1 + - - +
462A TYR* 3.1 5.4 + - - +
464A GLU* 1.3 75.5 - - + +
466A SER* 1.3 59.5 + - - +
467A GLU 3.4 0.9 - - - -
468A VAL* 4.1 20.8 - - + +
472A ARG* 4.1 1.2 + - - -
476A ALA 4.7 2.0 - - - +
479A LEU* 3.6 30.1 - - + -
480A VAL* 3.0 27.2 - - + +
483A LYS* 5.6 0.9 - - + -
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Residues in contact with SER 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A TYR* 2.9 33.2 + - - -
463A LYS* 3.0 9.6 + - - -
465A ALA* 1.3 78.1 - - - +
467A GLU* 1.3 65.1 + - - +
468A VAL 3.4 5.5 - - - +
469A LYS* 3.3 16.3 + - - -
472A ARG* 4.2 8.7 + - - +
480A VAL* 3.9 20.5 - - - +
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Residues in contact with GLU 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463A LYS* 3.1 36.3 + - - +
464A GLU* 3.5 19.5 - - + +
465A ALA 3.4 0.2 - - - -
466A SER* 1.3 81.1 - - - +
468A VAL* 1.3 52.8 + - - +
469A LYS* 2.6 39.1 + - - +
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Residues in contact with VAL 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464A GLU 4.0 7.8 + - - +
465A ALA* 4.1 16.8 - - + +
466A SER 3.4 0.7 - - - +
467A GLU* 1.3 73.8 - - - +
469A LYS* 1.3 60.7 + - - +
472A ARG* 2.4 53.8 + - + +
476A ALA* 5.1 11.2 - - + +
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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