Contacts of the helix formed by residues 494 - 509 (chain A) in PDB entry 4KXA
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 LYS 494 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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490A GLU 2.7 9.5 + - - -
491A ASP 3.6 7.5 + - - +
492A TRP 3.3 6.9 - - - +
493A ILE* 1.3 91.0 - - - +
495A PRO* 1.3 78.2 - - + +
496A GLU* 3.3 4.5 - - + +
497A ASN* 3.3 13.4 + - - +
498A PHE* 3.1 14.0 + - - +
584A LYS* 6.2 1.1 - - - +
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Residues in contact with PRO 495 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336A TYR* 4.6 3.3 + - - +
437A ARG* 5.6 3.1 - - - +
490A GLU* 3.5 38.6 - - + +
491A ASP* 5.1 4.5 - - - +
494A LYS* 1.3 87.2 - - + +
496A GLU* 1.3 52.5 + - - +
498A PHE* 3.0 3.5 + - - +
499A GLN* 2.7 36.5 + - - +
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Residues in contact with GLU 496 (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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494A LYS* 3.3 4.3 - - + +
495A PRO* 1.3 80.1 - - - +
497A ASN* 1.3 68.9 + - - +
499A GLN* 3.3 23.9 + - - +
500A LYS* 3.1 46.3 + - + +
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Residues in contact with ASN 497 (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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493A ILE* 3.0 26.0 - - + +
494A LYS* 3.3 13.7 + - - +
496A GLU* 1.3 84.2 - - - +
498A PHE* 1.3 61.4 + - - +
500A LYS* 3.4 5.3 + - - +
501A GLY* 2.8 27.7 + - - -
523A LEU* 4.1 1.3 - - - +
526A ALA* 3.7 28.6 + - - +
527A SER* 4.1 12.9 + - - +
528A ARG* 6.0 1.9 - - - +
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Residues in contact with PHE 498 (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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336A TYR* 4.4 9.0 - - - -
418A PHE* 5.5 0.4 - + - -
421A PHE* 4.0 18.4 - + - -
422A PHE* 3.7 29.8 - + - -
486A LEU* 4.3 36.8 - - + -
489A LEU* 4.3 5.4 - - + -
490A GLU* 3.7 31.6 - - + -
493A ILE* 3.7 11.8 - - + +
494A LYS 3.1 12.7 + - - +
495A PRO 3.0 8.2 + - - +
497A ASN* 1.3 77.6 - - - +
499A GLN* 1.3 63.9 + - - +
501A GLY 3.4 0.5 + - - -
502A CYS* 3.0 39.1 + - - -
519A PHE* 4.4 1.3 - + - -
523A LEU* 3.7 30.7 - - + +
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Residues in contact with GLN 499 (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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335A GLU 5.1 1.2 + - - -
336A TYR* 3.3 66.5 + - + +
337A PHE* 6.1 0.2 - - - -
495A PRO 2.7 16.5 + - - +
496A GLU* 3.3 27.8 - - - +
498A PHE* 1.3 73.8 - - - +
500A LYS* 1.3 72.2 + - - +
502A CYS* 3.2 7.1 + - - +
503A GLN* 3.1 40.3 + - - +
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Residues in contact with LYS 500 (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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496A GLU* 3.1 35.8 + - + +
497A ASN* 3.8 7.4 - - - +
499A GLN* 1.3 93.1 + - - +
501A GLY* 1.3 63.6 + - - +
503A GLN* 3.2 29.4 + - - +
504A MET* 3.0 34.4 + - + +
526A ALA* 4.9 5.2 - - + -
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Residues in contact with GLY 501 (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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497A ASN 2.8 15.6 + - - -
499A GLN 3.3 0.2 - - - -
500A LYS* 1.3 73.0 - - - +
502A CYS* 1.3 61.6 + - - +
504A MET* 3.4 5.0 + - - +
505A TYR* 3.2 22.7 + - - +
519A PHE* 5.0 0.4 - - - -
522A ALA* 3.9 11.6 - - - +
523A LEU* 3.4 25.6 - - - -
526A ALA* 3.7 14.5 - - - +
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Residues in contact with CYS 502 (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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336A TYR* 5.7 0.7 - - + -
337A PHE* 5.0 6.7 - - + -
400A PHE* 4.0 21.5 - - + -
418A PHE* 4.6 0.9 - - - -
422A PHE* 3.9 14.6 - - + -
498A PHE* 3.0 47.9 + - - -
499A GLN* 3.5 10.3 - - - +
501A GLY* 1.3 71.9 - - - +
503A GLN* 1.3 67.0 + - - +
505A TYR* 3.4 7.8 + - - +
506A LEU* 3.0 25.8 + - - +
519A PHE* 4.0 19.7 - - - -
523A LEU* 5.0 0.2 - - - -
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Residues in contact with GLN 503 (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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335A GLU 4.8 1.2 + - - -
336A TYR 2.8 24.6 + - - +
337A PHE* 3.4 27.6 - - + +
338A ALA* 3.6 22.2 - - + +
499A GLN* 3.1 29.6 + - - +
500A LYS* 3.4 35.4 + - - +
502A CYS* 1.3 76.5 - - + +
504A MET* 1.3 59.0 + - + +
506A LEU* 3.2 6.2 + - - +
507A GLU* 2.9 36.7 + - + +
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Residues in contact with MET 504 (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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500A LYS* 3.0 22.4 + - + +
501A GLY* 3.8 4.7 - - - +
502A CYS 3.3 0.2 - - - -
503A GLN* 1.3 75.0 - - + +
505A TYR* 1.3 59.0 + - - +
507A GLU* 3.2 9.3 + - - +
508A LYS* 2.9 32.2 + - - +
522A ALA* 4.7 10.1 - - + +
525A GLU* 5.0 23.1 - - - +
526A ALA* 4.5 22.4 - - - -
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Residues in contact with TYR 505 (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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400A PHE* 3.5 38.0 - + - -
404A VAL* 3.3 32.2 - - + +
405A THR 5.2 0.5 + - - -
414A LEU* 3.8 22.3 + - + +
418A PHE* 5.1 1.1 - + - -
501A GLY 3.2 11.3 + - - +
502A CYS 3.5 6.7 - - - +
504A MET* 1.3 77.7 - - - +
506A LEU* 1.3 63.6 + - - +
508A LYS* 3.3 5.1 + - - -
509A TYR* 3.2 40.3 + + - +
514A ALA* 3.3 25.5 - - + +
515A LYS 4.8 0.4 - - - -
518A ASP 4.3 1.3 - - - -
519A PHE* 3.8 48.9 - + + -
522A ALA* 3.8 13.2 - - + +
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Residues in contact with LEU 506 (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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337A PHE* 3.8 35.4 - - + +
339A MET* 3.9 21.0 - - - +
399A TRP* 3.9 28.3 - - + +
400A PHE* 3.7 43.3 - - + -
403A ILE* 4.4 2.4 - - + +
404A VAL* 3.9 21.4 - - + +
502A CYS 3.0 14.4 + - - +
503A GLN* 3.4 6.3 - - - +
505A TYR* 1.3 75.5 - - + +
507A GLU* 1.3 61.7 + - - +
510A GLN* 3.4 24.3 + - - +
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Residues in contact with GLU 507 (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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338A ALA* 4.2 15.2 - - - +
339A MET* 5.1 14.4 - - + +
503A GLN* 2.9 21.6 + - + +
504A MET* 3.2 11.6 + - - +
506A LEU* 1.3 76.6 - - - +
508A LYS* 1.3 62.4 + - - +
510A GLN* 3.5 25.8 - - - +
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Residues in contact with LYS 508 (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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504A MET 2.9 17.2 + - - +
505A TYR* 3.3 5.8 + - - +
507A GLU* 1.3 80.5 - - - +
509A TYR* 1.3 102.2 + - + +
510A GLN* 3.4 1.0 + - - +
512A LYS* 3.4 19.6 + - - -
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Residues in contact with TYR 509 (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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404A VAL* 3.5 23.1 - - + +
505A TYR* 3.2 38.1 + + - +
508A LYS* 1.3 117.5 + - + +
510A GLN* 1.3 55.2 + - - +
511A PHE 3.2 0.5 + - - -
512A LYS* 2.8 44.9 + - + +
513A ASN 4.0 18.8 - - - +
514A ALA* 4.1 5.8 - - + -
518A ASP* 3.3 50.1 + - + +
522A ALA* 5.8 1.3 - - + -
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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