Contacts of the helix formed by residues 481 - 499 (chain B) in PDB entry 1HKB
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 481 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479B LEU 4.1 0.2 + - - -
480B THR* 1.3 72.5 - - - +
482B ASP* 1.3 60.9 + - - +
484B LEU* 3.1 14.6 + - + +
485B LEU* 3.0 48.6 + - + +
881B GLU* 3.1 55.4 + - - +
882B LEU* 4.5 10.8 - - + -
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Residues in contact with ASP 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B THR* 3.0 9.1 + - - +
481B LYS* 1.3 84.4 - - - +
483B MET* 1.3 63.6 + - - +
485B LEU* 3.2 25.0 + - - +
486B GLU* 3.2 15.4 + - - +
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Residues in contact with MET 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B HIS 3.7 8.5 - - - +
479B LEU* 3.4 30.1 - - + -
480B THR* 2.9 50.7 + - + +
482B ASP* 1.3 75.9 - - - +
484B LEU* 1.3 62.2 + - - +
486B GLU* 3.2 9.7 + - - +
487B VAL* 3.1 27.2 + - + +
721B ILE* 5.2 10.3 - - + -
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Residues in contact with LEU 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B LEU* 3.9 25.1 - - + +
480B THR 2.9 18.2 + - - +
481B LYS* 3.1 16.6 + - + +
483B MET* 1.3 78.9 - - - +
485B LEU* 1.3 60.3 + - - +
487B VAL* 3.6 3.5 + - + -
488B LYS* 3.2 21.1 + - - +
832B GLN* 3.9 54.1 - - + +
833B LEU* 4.5 3.6 - - + +
836B ALA* 3.6 14.8 - - + +
878B THR* 4.6 12.1 - - + +
881B GLU* 5.5 4.3 - - - +
882B LEU* 3.7 18.8 - - + +
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Residues in contact with LEU 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B LYS* 3.0 37.4 + - + +
482B ASP* 3.2 18.6 + - - +
484B LEU* 1.3 75.6 - - - +
486B GLU* 1.3 60.0 + - - +
488B LYS* 3.2 17.3 + - + +
489B LYS* 2.8 33.3 + - + +
881B GLU 5.8 0.4 - - - +
882B LEU* 4.3 31.4 - - + +
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Residues in contact with GLU 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B ASP 3.2 11.8 + - - +
483B MET* 3.4 12.3 - - - +
485B LEU* 1.3 78.6 - - - +
487B VAL* 1.3 52.4 + - + +
489B LYS* 3.1 37.5 + - - +
490B ARG* 2.7 82.1 + - - +
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Residues in contact with VAL 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B LEU* 5.6 1.3 - - + -
483B MET* 3.1 17.0 + - + +
484B LEU* 3.8 9.9 - - + +
486B GLU* 1.3 76.9 - - + +
488B LYS* 1.3 57.8 + - - +
490B ARG* 3.8 12.1 - - - +
491B MET* 2.9 28.5 + - + +
712B PHE* 4.0 19.5 - - + -
718B LEU* 4.9 4.3 - - + -
721B ILE* 4.2 26.9 - - + -
741B TYR* 4.8 3.8 - - + +
833B LEU* 4.3 24.0 - - + +
836B ALA* 3.9 18.6 - - + -
837B GLY* 5.1 0.7 - - - +
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Residues in contact with LYS 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B LEU 3.2 11.9 + - - +
485B LEU* 3.2 21.1 + - + +
487B VAL* 1.3 77.5 - - - +
489B LYS* 1.3 65.7 + - - +
491B MET* 3.3 4.7 + - - +
492B ARG* 3.1 19.4 + - - +
836B ALA* 3.8 17.0 - - + +
839B ALA* 3.9 15.5 - - + -
840B ALA* 3.6 24.8 - - - +
843B ASP* 3.4 25.5 + - - -
882B LEU* 2.8 33.6 + - + +
883B SER* 3.4 11.8 + - - -
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Residues in contact with LYS 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B LEU 2.8 14.9 + - - +
486B GLU* 3.1 38.0 + - - +
488B LYS* 1.3 76.4 - - - +
490B ARG* 1.3 64.0 + - - +
492B ARG* 2.9 18.6 + - - +
493B ALA* 3.1 11.9 + - - +
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Residues in contact with ARG 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B GLU* 2.7 64.5 + - - +
487B VAL* 3.8 7.6 - - - +
489B LYS* 1.3 72.6 - - + +
491B MET* 1.3 64.4 + - - +
493B ALA* 3.2 8.7 + - - +
494B GLU* 3.0 27.8 + - + +
712B PHE* 3.7 19.5 - - + -
717B CYS* 2.5 45.8 + - + +
718B LEU* 4.3 7.9 - - - +
720B ASP* 2.6 38.8 + - - +
721B ILE* 5.2 4.2 - - - +
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Residues in contact with MET 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B VAL 2.9 19.6 + - - +
488B LYS* 3.5 7.0 - - - +
489B LYS 3.2 0.2 - - - -
490B ARG* 1.3 75.4 - - - +
492B ARG* 1.3 57.5 + - - +
494B GLU* 3.4 1.4 + - - +
495B MET* 2.9 37.3 + - + +
509B VAL* 4.7 6.1 - - - -
707B MET* 4.3 13.5 - - + -
709B TRP* 3.3 50.0 - - + -
712B PHE* 3.7 37.4 - - + -
741B TYR* 4.1 7.4 - - + +
837B GLY* 4.0 13.2 - - - +
840B ALA* 3.6 20.2 - - + -
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Residues in contact with ARG 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B LYS 3.1 10.4 + - - +
489B LYS* 2.9 13.2 + - - +
491B MET* 1.3 74.7 - - - +
493B ALA* 1.3 64.5 + - - +
495B MET* 3.0 22.8 + - - +
496B GLU* 2.8 39.2 + - - +
840B ALA* 4.4 8.6 + - + +
843B ASP* 4.7 3.4 + - - +
844B LYS* 3.2 49.1 - - - +
847B GLU* 3.1 36.8 + - - +
848B ASN* 5.0 2.4 - - - +
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Residues in contact with ALA 493 (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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489B LYS 3.1 11.5 + - - +
490B ARG* 3.6 11.4 - - - +
492B ARG* 1.3 77.3 - - - +
494B GLU* 1.3 64.8 + - + +
496B GLU* 3.2 12.8 + - - +
497B LEU* 3.2 30.2 + - + +
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Residues in contact with GLU 494 (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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490B ARG* 3.0 17.0 + - + +
491B MET 3.7 4.0 - - - +
493B ALA* 1.3 75.2 - - + +
495B MET* 1.3 65.5 + - - +
497B LEU* 3.5 22.9 + - - +
498B GLY 3.3 16.1 + - - -
507B ALA* 4.9 1.9 - - - +
508B VAL* 3.0 25.6 + - - +
509B VAL* 3.9 28.3 - - + +
712B PHE* 3.8 18.8 - - + -
715B ASN* 2.8 26.8 + - - -
717B CYS* 3.9 10.3 - - + +
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Residues in contact with MET 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B MET* 2.9 29.3 + - - +
492B ARG* 3.2 22.0 - - - +
494B GLU* 1.3 77.9 - - - +
496B GLU* 1.3 64.0 + - - +
499B LEU* 3.5 12.1 + - - +
509B VAL* 5.0 1.6 - - + -
511B MET* 3.4 30.7 - - + +
686B TYR* 3.2 45.3 - - + +
707B MET* 4.0 26.2 - - + -
840B ALA 4.6 2.2 - - - -
841B VAL* 4.4 24.9 - - + -
844B LYS* 4.1 18.4 - - + -
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Residues in contact with GLU 496 (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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492B ARG* 2.8 52.2 + - - +
493B ALA* 3.5 11.9 - - - +
494B GLU 3.1 0.2 - - - -
495B MET* 1.3 74.8 - - - +
497B LEU* 1.3 68.3 + - + +
498B GLY 2.9 1.8 - - - -
499B LEU* 2.8 22.1 + - + +
500B ARG* 3.1 27.1 + - + +
844B LYS* 4.1 11.0 - - - -
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Residues in contact with LEU 497 (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 ALA* 3.2 19.2 + - + +
494B GLU* 3.5 27.6 + - - +
496B GLU* 1.3 78.3 - - + +
498B GLY* 1.3 58.8 + - - +
500B ARG* 3.5 19.5 - - - +
503B THR* 2.8 45.6 - - - +
504B HIS 3.1 13.0 + - - -
506B ASN 6.1 0.2 - - - +
507B ALA* 3.8 13.0 - - + -
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Residues in contact with GLY 498 (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 GLU 3.3 6.7 + - - -
495B MET 3.9 3.6 - - - -
496B GLU 2.8 2.6 + - - -
497B LEU* 1.3 79.8 - - - +
499B LEU* 1.3 60.9 + - - +
504B HIS* 2.7 30.2 + - - +
507B ALA* 3.7 8.7 - - - +
509B VAL 3.6 22.9 - - - -
510B LYS 3.9 2.4 - - - +
511B MET* 4.0 9.8 - - - +
695B MET* 4.6 1.9 - - - +
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Residues in contact with LEU 499 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B MET 3.5 16.6 + - - +
496B GLU* 2.8 15.6 + - + +
498B GLY* 1.3 73.4 - - - +
500B ARG* 1.3 64.2 + - + +
501B LYS 3.2 3.6 + - - -
511B MET* 3.9 28.7 - - + +
686B TYR* 4.1 1.1 - - - +
688B GLU* 3.7 38.6 - - + +
692B ASN* 3.6 22.4 - - + +
693B VAL* 4.4 10.4 - - + -
694B GLU* 3.4 18.9 + - - +
695B MET* 3.9 8.6 - - - +
705B ILE* 4.3 12.1 - - + -
844B LYS* 4.4 14.1 - - - +
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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
------------------------------------------------------------
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