Contacts of the helix formed by residues 507 - 521 (chain B) in PDB entry 4KIK
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 SER 507 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497B TYR* 2.8 18.8 + - - -
505B ILE* 4.0 11.2 - - - -
506B THR* 1.3 72.0 - - - +
508B ASP* 1.4 56.3 + - - +
509B LYS* 3.1 7.9 + - - +
510B LEU* 2.9 52.8 + - - +
511B LEU 3.2 9.4 + - - -
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Residues in contact with ASP 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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497B TYR* 4.6 1.3 + - - -
506B THR* 3.6 23.1 + - - +
507B SER* 1.4 70.5 - - - +
509B LYS* 1.3 64.7 + - + +
511B LEU* 3.7 14.4 + - - +
512B LEU* 3.3 35.2 + - + +
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Residues in contact with LYS 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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507B SER* 3.1 7.4 - - - +
508B ASP* 1.3 79.0 - - + +
510B LEU* 1.4 62.9 + - - +
512B LEU* 4.1 6.4 - - - +
513B ALA* 3.2 24.1 + - - +
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Residues in contact with LEU 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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497B TYR* 5.3 9.2 - - + -
507B SER* 2.9 32.1 + - - +
509B LYS* 1.4 74.1 - - - +
511B LEU* 1.4 54.1 + - - +
513B ALA* 3.1 7.9 + - + +
514B TRP* 2.8 88.0 + - + +
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Residues in contact with LEU 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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494B LEU* 4.4 11.7 - - + +
497B TYR* 3.7 39.6 - - + +
498B SER* 5.4 7.0 - - - -
507B SER 3.2 4.6 + - - +
508B ASP* 3.9 16.6 - - - +
510B LEU* 1.4 76.8 - - - +
512B LEU* 1.4 72.4 + - + +
514B TRP* 3.5 7.3 + - - +
515B ARG* 2.9 47.9 + - - +
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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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508B ASP* 3.3 23.8 + - + +
509B LYS* 4.1 5.2 - - - +
510B LEU 3.3 0.4 - - - -
511B LEU* 1.4 85.7 - - + +
513B ALA* 1.3 59.8 - - - +
515B ARG* 3.5 8.5 + - + +
516B GLU* 3.0 34.0 + - + +
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Residues in contact with ALA 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 LYS 3.2 18.9 + - - +
510B LEU* 3.1 10.4 + - + +
512B LEU* 1.3 76.8 - - - +
514B TRP* 1.3 69.1 + - + +
516B GLU* 3.3 8.4 + - - +
517B MET* 3.1 29.4 + - + +
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Residues in contact with TRP 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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655A TRP* 3.7 26.2 - + - -
490B ILE* 3.3 13.1 - - + +
493B ASP* 3.7 42.6 - - + -
494B LEU* 3.8 22.7 - - + -
497B TYR* 4.4 10.5 - + + -
510B LEU* 2.8 58.4 + - + +
511B LEU* 3.9 2.9 - - - +
513B ALA* 1.3 81.2 - - + +
515B ARG* 1.4 62.1 + - - +
517B MET* 3.2 33.0 + - + +
518B GLU* 3.1 18.2 + - - +
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Residues in contact with ARG 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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491B GLN* 5.7 2.2 - - - +
494B LEU* 3.7 39.6 + - - +
511B LEU* 2.9 34.7 + - - +
512B LEU* 3.9 9.9 - - + +
514B TRP* 1.4 77.2 - - - +
516B GLU* 1.4 60.2 - - - +
518B GLU* 3.1 30.9 + - - +
519B GLN* 3.2 23.0 + - + +
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Residues in contact with GLU 516 (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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512B LEU* 3.0 18.3 + - + +
513B ALA* 3.6 10.8 - - - +
514B TRP 3.2 0.4 - - - -
515B ARG* 1.4 74.6 - - + +
517B MET* 1.4 55.0 + - - +
519B GLN* 3.1 35.4 + - - +
520B ALA* 2.8 34.5 + - - +
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Residues in contact with MET 517 (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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486B PHE* 4.2 15.9 - - + -
490B ILE* 3.6 16.8 - - + -
513B ALA* 3.1 20.7 + - + +
514B TRP* 3.2 36.3 - - + +
516B GLU* 1.4 73.8 - - - +
518B GLU* 1.3 56.6 + - - +
520B ALA* 3.3 7.0 + - - +
521B VAL* 3.1 36.0 + - - +
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Residues in contact with GLU 518 (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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487B LYS* 5.5 2.6 - - + +
490B ILE* 3.8 25.3 - - + +
491B GLN* 3.7 18.7 + - - +
494B LEU* 3.3 21.8 - - + +
514B TRP 3.1 8.6 + - - +
515B ARG* 3.1 38.8 + - - +
517B MET* 1.3 79.3 - - - +
519B GLN* 1.4 60.4 + - - +
521B VAL* 3.3 16.8 - - + +
522B GLU* 3.2 26.6 + - - +
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Residues in contact with GLN 519 (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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515B ARG 3.2 12.8 + - - +
516B GLU* 3.1 47.0 + - - +
518B GLU* 1.4 77.7 - - - +
520B ALA* 1.4 76.5 + - - +
521B VAL 3.4 0.2 - - - -
522B GLU* 3.3 21.1 - - + +
523B LEU* 3.6 21.4 - - - +
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Residues in contact with ALA 520 (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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516B GLU 2.8 19.2 + - - +
517B MET* 3.3 8.7 + - - +
519B GLN* 1.4 85.3 - - - +
521B VAL* 1.3 61.4 + - + +
522B GLU 3.2 2.3 + - - -
523B LEU* 3.5 24.8 + - - +
524B CYS* 4.0 7.3 + - - +
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Residues in contact with VAL 521 (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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483B LEU* 3.7 14.0 - - + +
486B PHE* 3.5 43.1 - - + -
487B LYS* 3.6 26.6 + - + -
490B ILE* 5.7 0.2 - - + -
517B MET* 3.1 13.8 + - - +
518B GLU* 3.3 18.8 - - + +
520B ALA* 1.3 75.7 - - + +
522B GLU* 1.3 62.9 + - - +
523B LEU 3.3 0.4 - - - -
524B CYS* 3.4 31.3 - - - +
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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