Contacts of the helix formed by residues 497 - 514 (chain A) in PDB entry 4KM5
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 ASP 497 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429A HIS* 6.1 0.5 - - - -
432A LYS* 5.2 8.3 + - - +
493A SER 4.6 8.5 - - - +
496A ILE* 1.3 75.9 - - - +
498A LYS* 1.3 65.6 + - - +
499A ARG* 4.3 8.5 - - + +
500A SER* 3.1 30.1 + - - +
501A LYS* 3.1 11.5 + - - -
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Residues in contact with LYS 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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476A ARG 5.7 1.8 + - - -
478A GLU* 2.3 40.0 + - + +
493A SER* 5.6 5.6 - - - +
496A ILE 3.7 0.4 + - - -
497A ASP* 1.3 70.4 - - - +
499A ARG* 1.3 66.5 + - - +
501A LYS* 3.2 15.5 + - + +
502A GLU* 3.0 45.3 + - + +
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Residues in contact with ARG 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LYS* 5.2 11.2 - - - +
429A HIS* 5.7 5.6 - - + +
497A ASP* 3.3 6.4 - - + +
498A LYS* 1.3 78.4 - - - +
500A SER* 1.3 57.8 + - - +
502A GLU* 4.1 19.8 + - - +
503A PHE* 2.9 61.3 + - - +
506A LYS* 5.3 11.5 - - - +
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Residues in contact with SER 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A HIS* 4.0 36.8 + - - +
432A LYS* 5.8 2.9 - - - +
433A PHE* 3.8 6.6 - - - -
496A ILE* 3.7 17.6 - - - +
497A ASP* 3.1 25.1 + - - +
498A LYS 3.1 0.2 - - - -
499A ARG* 1.3 77.7 - - - +
501A LYS* 1.3 59.6 + - - +
503A PHE* 3.3 6.1 + - - +
504A LEU* 2.9 28.9 + - - +
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Residues in contact with LYS 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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433A PHE* 3.9 11.9 - - + -
475A LEU* 3.6 41.3 - - + +
478A GLU* 3.0 34.2 + - + -
491A PHE* 3.8 20.6 + - + +
496A ILE* 2.4 54.3 + - + +
497A ASP 3.1 17.8 + - - +
498A LYS* 3.2 8.4 + - + +
500A SER* 1.3 77.9 - - - +
502A GLU* 1.3 53.2 + - + +
504A LEU* 3.3 1.7 + - - +
505A THR* 2.5 41.9 + - - -
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Residues in contact with GLU 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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475A LEU 6.1 0.7 - - - +
498A LYS* 3.0 42.9 + - + +
499A ARG* 3.8 27.2 + - - +
501A LYS* 1.3 73.5 - - + +
503A PHE* 1.3 59.9 + - - +
505A THR* 3.6 8.1 - - - -
506A LYS* 3.1 29.1 + - - +
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Residues in contact with PHE 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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424A PHE* 3.5 42.0 - + + -
427A LYS* 3.7 35.2 - - + +
429A HIS* 4.9 4.5 - - + -
430A LEU* 3.8 25.1 - - + -
499A ARG* 2.9 39.6 + - - +
500A SER* 3.5 6.7 - - - +
502A GLU* 1.3 77.2 - - - +
504A LEU* 1.3 63.7 + - - +
506A LYS* 3.4 8.8 + - + +
507A GLN* 3.1 52.3 + - + +
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Residues in contact with LEU 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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417A LEU* 4.5 13.2 - - + -
420A LEU* 4.0 15.7 - - + -
430A LEU* 3.8 24.5 - - + -
433A PHE* 3.7 42.0 - - + -
471A PHE* 3.9 22.2 - - + -
475A LEU* 3.9 5.4 - - + -
500A SER 2.9 17.2 + - - +
501A LYS 3.6 4.3 - - - +
503A PHE* 1.3 74.8 - - - +
505A THR* 1.3 60.6 + - - +
507A GLN* 3.4 2.4 + - + +
508A ILE* 3.0 54.6 + - + +
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Residues in contact with THR 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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472A LEU* 3.8 14.7 - - + +
475A LEU* 3.2 28.3 - - + +
476A ARG* 4.1 20.0 + - + +
501A LYS 2.5 29.6 + - - -
502A GLU* 3.6 9.3 - - - -
504A LEU* 1.3 74.2 - - - +
506A LYS* 1.3 57.0 + - - +
508A ILE 3.4 0.3 + - - -
509A GLU* 2.9 57.0 + - - +
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Residues in contact with LYS 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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499A ARG* 5.3 10.6 - - - +
502A GLU 3.1 17.4 + - - +
503A PHE* 3.7 8.7 - - + +
504A LEU 3.3 0.2 - - - -
505A THR* 1.3 75.3 - - - +
507A GLN* 1.3 76.0 + - - +
509A GLU* 3.5 13.4 + - - +
510A TYR* 3.1 23.6 + - + +
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Residues in contact with GLN 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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420A LEU* 4.3 18.8 - - + -
424A PHE* 3.2 31.5 - - + -
430A LEU* 5.6 1.3 - - + -
503A PHE* 3.1 51.5 + - + +
504A LEU* 3.8 6.1 - - + +
506A LYS* 1.3 92.3 - - - +
508A ILE* 1.3 61.7 + - - +
510A TYR* 3.3 14.7 + - - +
511A GLU* 3.2 30.9 + - - +
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Residues in contact with ILE 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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413A MET* 6.3 1.1 - - + -
416A LEU* 4.7 17.0 - - + -
417A LEU* 6.2 0.7 - - + -
420A LEU* 4.0 11.0 - - + -
468A VAL* 3.7 26.0 - - + +
471A PHE* 3.8 30.5 - - + -
472A LEU* 3.7 18.4 - - + -
475A LEU* 4.0 6.7 - - + -
504A LEU* 3.0 43.7 + - + +
507A GLN* 1.3 71.9 - - - +
509A GLU* 1.3 66.8 - - - +
511A GLU* 3.0 10.3 + - - +
512A ARG* 2.9 21.1 + - - +
516A PHE* 5.0 0.4 - - + -
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Residues in contact with GLU 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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472A LEU* 4.0 11.4 - - + -
476A ARG* 2.9 39.0 + - - +
505A THR* 2.9 31.7 + - - +
506A LYS* 3.7 12.8 - - - +
508A ILE* 1.3 76.6 - - - +
510A TYR* 1.3 59.1 + - - +
512A ARG* 3.4 7.2 + - - +
513A ASN* 3.0 40.4 + - - +
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Residues in contact with TYR 510 (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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506A LYS* 3.1 15.4 + - + +
507A GLN* 3.4 15.7 - - - +
508A ILE 3.2 0.4 - - - -
509A GLU* 1.3 77.4 - - - +
511A GLU* 1.3 81.5 + - - +
513A ASN* 3.5 3.9 + - - +
514A ASN* 3.0 57.3 + - + +
517A PRO* 4.3 17.7 - - + +
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Residues in contact with GLU 511 (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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416A LEU* 4.3 13.2 - - + -
420A LEU* 4.4 10.1 - - + +
423A ARG* 5.8 3.3 + - - -
507A GLN* 3.2 18.9 - - - +
508A ILE* 3.0 10.5 + - - +
510A TYR* 1.3 93.7 - - - +
512A ARG* 1.3 64.4 + - - +
515A GLU 3.1 3.5 + - - -
516A PHE* 2.5 49.2 + - + +
517A PRO* 3.2 27.9 - - - +
518A VAL* 3.4 30.3 - - - +
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Residues in contact with ARG 512 (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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465A ASP* 3.1 36.7 + - - +
468A VAL* 4.2 14.4 - - + -
469A THR* 3.4 26.8 - - - +
472A LEU* 4.5 10.3 - - - +
476A ARG* 6.2 0.2 - - - +
508A ILE 2.9 14.6 + - - +
509A GLU* 3.8 6.5 - - - +
511A GLU* 1.3 78.0 - - - +
513A ASN* 1.3 73.0 + - - +
514A ASN 3.6 0.2 + - - -
515A GLU* 3.8 11.3 + - - +
516A PHE* 3.8 20.9 - - + -
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Residues in contact with ASN 513 (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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509A GLU* 3.0 26.5 + - - +
510A TYR* 4.0 2.6 - - - +
511A GLU 3.3 0.2 - - - -
512A ARG* 1.3 93.0 + - - +
514A ASN* 1.3 70.7 + - - +
515A GLU* 3.5 1.8 + - - +
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Residues in contact with ASN 514 (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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164A LYS* 4.8 0.9 + - - -
510A TYR* 3.0 56.1 + - + +
513A ASN* 1.3 86.1 - - - +
515A GLU* 1.3 70.4 + - - +
516A PHE 3.2 3.3 + - - -
517A PRO* 3.4 23.9 - - + +
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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