Contacts of the helix formed by residues 494 - 515 (chain B) in PDB entry 1K2P
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 GLN 494 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492B ARG* 3.4 17.4 - - - +
493B PHE* 1.3 82.0 - - - +
495B THR* 1.3 64.7 + - - +
496B GLN* 2.8 25.6 + - + +
497B GLN* 2.9 20.7 + - + +
498B LEU* 3.0 12.5 + - - +
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Residues in contact with THR 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493B PHE 4.3 0.4 + - - -
494B GLN* 1.3 71.7 - - - +
496B GLN* 1.3 63.2 + - - +
498B LEU* 3.3 12.3 - - - +
499B LEU* 2.8 31.5 + - + +
591B TYR* 3.6 25.8 - - + +
621B LEU* 3.4 20.6 + - - +
622B ALA* 5.6 0.2 - - - -
623B SER* 5.6 4.0 - - - +
626B VAL* 5.1 8.1 - - + -
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Residues in contact with GLN 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B GLN* 2.8 28.7 - - + +
495B THR* 1.3 82.9 + - - +
497B GLN* 1.3 61.3 + - - +
499B LEU* 3.5 5.2 + - - +
500B GLU* 3.2 23.0 + - - +
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Residues in contact with GLN 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B PHE* 4.3 23.8 - - + -
494B GLN* 2.9 17.3 + - + +
496B GLN* 1.3 77.5 - - + +
498B LEU* 1.3 64.0 + - - +
499B LEU 3.2 0.7 - - - -
500B GLU* 3.2 25.9 - - - +
501B MET* 3.2 26.5 + - + +
504B ASP* 5.1 2.2 + - - -
533B GLY* 4.3 14.5 + - - -
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Residues in contact with LEU 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B LEU* 4.5 2.5 - - + -
493B PHE* 3.9 32.1 - - + -
494B GLN 3.0 6.9 + - - +
495B THR* 3.1 21.3 + - - +
497B GLN* 1.3 75.9 - - - +
499B LEU* 1.3 62.4 + - - +
501B MET* 3.3 24.5 + - - +
502B CYS* 3.5 4.3 + - - -
590B ILE* 3.4 31.4 - - + +
591B TYR* 3.6 33.7 - - + -
593B LEU* 4.0 15.3 - - + -
621B LEU* 4.0 28.0 - - + -
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Residues in contact with LEU 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B THR* 2.8 15.5 + - + +
496B GLN* 3.7 5.8 - - - +
498B LEU* 1.3 76.2 - - - +
500B GLU* 1.3 66.1 + - - +
502B CYS* 2.9 15.5 + - + +
503B LYS* 2.9 22.2 + - + +
587B MET* 6.1 1.3 - - - -
591B TYR* 3.2 21.9 + - + +
626B VAL* 4.8 12.1 - - + -
629B ILE* 5.7 1.1 - - + -
651B ILE* 3.4 56.1 - - + +
652B LEU* 5.6 1.8 - - + -
654B VAL* 5.0 10.3 - - + -
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Residues in contact with GLU 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496B GLN 3.2 16.3 + - - +
497B GLN* 3.2 32.3 - - - +
499B LEU* 1.3 79.9 - - - +
501B MET* 1.3 56.5 + - - +
503B LYS* 3.1 32.5 + - - +
504B ASP* 2.8 43.2 + - - +
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Residues in contact with MET 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482B LEU* 3.6 29.2 - - + -
485B TYR* 3.7 26.9 - - + -
486B LEU* 4.1 16.6 - - + -
493B PHE* 3.8 22.7 - - + -
497B GLN* 3.2 25.1 - - + +
498B LEU* 3.4 9.0 - - - +
499B LEU 3.1 0.4 - - - -
500B GLU* 1.3 76.1 - - - +
502B CYS* 1.3 63.3 + - - +
504B ASP* 3.1 12.1 + - - +
505B VAL* 3.0 29.5 + - - +
533B GLY 4.9 2.0 - - - +
535B VAL* 3.7 21.5 - - + +
590B ILE* 4.0 18.8 - - + -
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Residues in contact with CYS 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B LEU 3.5 15.3 - - - -
499B LEU* 2.9 12.7 + - + +
501B MET* 1.3 79.0 - - - +
503B LYS* 1.3 56.4 + - - +
505B VAL* 4.6 3.1 - - - -
506B CYS* 2.9 31.3 + - - +
583B PHE* 3.6 7.2 - - - -
587B MET* 3.9 21.5 - - + -
590B ILE* 3.6 23.1 - - - -
591B TYR* 3.6 25.6 - - - -
651B ILE* 4.0 18.8 - - + -
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Residues in contact with LYS 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456B LYS* 6.2 0.8 - - - +
499B LEU* 2.9 12.9 + - + +
500B GLU* 3.2 35.4 + - - +
502B CYS* 1.3 76.0 - - - +
504B ASP* 1.3 69.2 + - - +
506B CYS* 3.7 5.2 - - - +
507B GLU* 2.9 54.6 + - - +
648B LEU* 4.3 11.0 - - + -
651B ILE* 4.2 17.9 - - + +
652B LEU* 4.0 27.4 - - + -
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Residues in contact with ASP 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456B LYS* 3.2 53.1 - - + +
497B GLN* 5.1 1.7 + - - -
500B GLU* 2.8 36.4 + - - +
501B MET* 3.5 6.8 - - - +
503B LYS* 1.3 80.4 - - - +
505B VAL* 1.3 60.7 + - - +
507B GLU* 4.6 0.7 - - - -
508B ALA* 3.3 5.7 + - - +
533B GLY 4.6 1.7 - - - +
534B VAL* 3.9 8.8 - - - +
535B VAL* 3.0 44.1 + - + +
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Residues in contact with VAL 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482B LEU* 5.0 2.5 - - + -
501B MET 3.0 17.3 + - - +
502B CYS 3.9 3.6 - - - +
504B ASP* 1.3 74.3 - - - +
506B CYS* 1.3 59.8 + - - +
508B ALA* 3.3 6.5 + - - +
509B MET* 2.8 43.0 + - + +
522B LEU* 4.4 7.2 - - + -
527B CYS* 4.2 12.1 - - - -
535B VAL* 3.8 24.7 - - + +
537B VAL* 4.9 8.1 - - + +
583B PHE* 4.1 6.3 - - + -
586B LEU* 4.0 38.4 - - + -
590B ILE* 5.0 0.2 - - + -
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Residues in contact with CYS 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502B CYS 2.9 20.8 + - - +
503B LYS* 3.2 4.7 + - - +
505B VAL* 1.3 77.4 - - - +
507B GLU* 1.3 51.8 + - - +
509B MET* 3.5 3.3 - - - -
510B GLU* 2.6 38.6 + - - +
583B PHE* 3.8 19.7 - - + -
644B PHE* 3.5 31.6 - - - -
647B LEU* 3.8 15.3 - - - -
648B LEU* 3.7 24.9 - - + -
651B ILE* 4.5 3.1 - - + -
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Residues in contact with GLU 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B HIS* 3.9 20.0 + - + +
456B LYS* 3.4 29.5 + - + +
503B LYS* 2.9 61.2 + - - +
504B ASP 3.8 4.0 - - - +
506B CYS* 1.3 75.0 - - - +
508B ALA* 1.3 57.4 + - - +
510B GLU* 3.2 9.1 + - - +
511B TYR* 3.0 29.8 + - - +
648B LEU* 3.8 22.3 - - + +
652B LEU* 5.6 0.3 - - - +
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Residues in contact with ALA 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B HIS* 4.1 7.0 - - - -
456B LYS* 3.2 29.3 - - + +
457B LEU* 3.9 6.8 - - + +
504B ASP 3.3 3.0 + - - +
505B VAL 3.3 6.4 + - - +
506B CYS 3.3 0.2 - - - -
507B GLU* 1.3 80.4 - - - +
509B MET* 1.3 57.4 + - - +
511B TYR* 3.4 2.9 + - - +
512B LEU* 3.0 32.9 + - - +
537B VAL* 3.2 31.4 - - + -
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Residues in contact with MET 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505B VAL* 2.8 28.5 + - + +
506B CYS 3.7 0.4 - - - +
508B ALA* 1.3 74.7 - - - +
510B GLU* 1.3 60.6 + - - +
512B LEU* 3.7 24.6 - - + +
513B GLU* 2.8 28.9 + - - +
517B PHE 5.3 0.2 - - - +
519B HIS* 4.1 15.0 - - + -
522B LEU* 3.9 27.4 - - + -
537B VAL* 4.6 6.5 - - - -
579B ASP* 3.9 25.1 - - + +
644B PHE* 3.3 54.1 - - + -
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Residues in contact with GLU 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506B CYS 2.6 22.5 + - - +
507B GLU* 3.3 9.3 - - - +
509B MET* 1.3 74.2 - - - +
511B TYR* 1.3 71.2 + - - +
513B GLU* 3.1 6.7 + - - +
514B SER* 2.9 29.6 + - - -
644B PHE* 3.5 15.5 - - + +
645B LYS* 3.3 60.6 + - + +
648B LEU* 3.3 11.4 - - + +
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Residues in contact with TYR 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B SER 4.4 11.7 - - - -
454B HIS* 3.3 41.5 - + + +
457B LEU* 6.0 1.3 - - + -
507B GLU 3.0 11.0 + - - +
508B ALA 4.1 3.1 - - - +
510B GLU* 1.3 88.7 - - - +
512B LEU* 1.3 62.8 + - + +
514B SER* 2.6 29.1 + - - -
515B LYS* 2.9 18.7 + - + +
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Residues in contact with LEU 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452B LEU* 3.9 26.2 - - + -
457B LEU* 3.9 35.0 - - + -
508B ALA 3.0 19.3 + - - +
509B MET* 3.7 30.7 - - + +
511B TYR* 1.3 73.7 - - - +
513B GLU* 1.3 64.9 + - - +
515B LYS* 3.2 4.2 + - + -
516B GLN 2.9 4.9 + - - -
517B PHE* 2.8 60.4 + - + +
519B HIS* 4.4 16.6 - - + -
540B PHE* 5.1 2.5 - - + -
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Residues in contact with GLU 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509B MET* 2.8 15.2 + - - +
510B GLU* 3.1 11.0 - - - +
512B LEU* 1.3 77.2 - - - +
514B SER* 1.3 58.0 + - - +
516B GLN* 2.9 28.9 + - - -
517B PHE 4.9 2.9 - - - +
576B SER* 5.2 12.6 - - - +
577B LYS* 5.4 1.0 + - - -
580B ILE* 4.2 5.0 - - - +
643B THR* 3.4 25.1 - - - +
644B PHE* 3.0 44.3 + - + +
645B LYS* 3.5 11.8 + - - +
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Residues in contact with SER 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510B GLU* 2.9 16.3 + - - -
511B TYR* 2.6 45.4 + - - -
513B GLU* 1.3 76.6 + - - +
515B LYS* 1.3 58.7 + - - +
516B GLN* 3.1 21.0 + - - +
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Residues in contact with LYS 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448B VAL* 5.0 6.0 - - - +
451B ASN* 4.7 17.5 - - - +
452B LEU* 3.4 34.1 - - + -
511B TYR* 2.9 16.9 + - + +
512B LEU* 3.2 3.1 + - + +
514B SER* 1.3 78.9 + - - +
516B GLN* 1.3 66.9 + - - +
517B PHE* 3.3 26.3 - - + +
545B TYR* 3.9 27.3 + - - -
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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