Contacts of the helix formed by residues 481 - 499 (chain A) in PDB entry 1HKC
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479A LEU 4.2 0.4 + - - -
480A THR* 1.3 72.3 - - - +
482A ASP* 1.3 59.7 + - - +
484A LEU* 3.8 13.3 - - - +
485A LEU* 2.9 44.0 + - + +
881A GLU* 3.9 50.7 + - - +
882A LEU* 4.3 12.6 - - + -
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Residues in contact with ASP 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A THR* 2.9 10.1 + - - +
481A LYS* 1.3 81.3 - - - +
483A MET* 1.3 64.7 + - + +
485A LEU* 3.1 24.3 + - - +
486A GLU* 3.1 15.1 + - - +
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Residues in contact with MET 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A HIS 5.9 2.0 - - - +
478A HIS 4.3 8.5 - - - +
479A LEU* 3.6 28.5 - - + -
480A THR* 2.9 44.4 + - + +
482A ASP* 1.3 77.9 - - + +
484A LEU* 1.3 59.0 + - - +
486A GLU* 2.9 12.2 + - - +
487A VAL* 2.9 31.3 + - - +
720A ASP 5.9 2.5 - - - +
721A ILE* 5.2 13.4 - - + +
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Residues in contact with LEU 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A LEU* 3.7 30.5 - - + +
480A THR 3.0 20.7 + - - +
481A LYS* 3.8 13.7 - - + +
482A ASP 3.2 0.2 - - - -
483A MET* 1.3 77.9 - - - +
485A LEU* 1.3 56.0 + - - +
487A VAL* 3.5 4.4 + - + -
488A LYS* 3.0 26.9 + - - +
832A GLN* 4.2 41.1 - - + +
833A LEU* 4.7 7.2 - - + +
836A ALA* 3.5 12.0 - - + +
878A THR* 4.1 23.3 - - + -
881A GLU* 5.8 3.6 - - - +
882A LEU* 3.8 17.2 - - + +
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Residues in contact with LEU 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A LYS* 2.9 35.2 - - + +
482A ASP* 3.1 21.2 + - - +
483A MET 3.1 0.8 - - - -
484A LEU* 1.3 74.5 - - - +
486A GLU* 1.3 56.1 + - - +
488A LYS* 3.4 11.6 + - + +
489A LYS* 2.8 33.1 + - - +
881A GLU 5.4 0.7 - - - +
882A LEU* 3.4 40.4 - - + +
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Residues in contact with GLU 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A ASP 3.1 11.5 + - - +
483A MET* 2.9 13.1 + - - +
485A LEU* 1.3 74.9 - - - +
487A VAL* 1.3 56.1 + - + +
489A LYS* 2.9 34.2 + - - +
490A ARG* 2.5 90.1 + - - +
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Residues in contact with VAL 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A LEU* 5.4 1.8 - - + -
483A MET 2.9 17.3 + - - +
484A LEU* 3.6 11.0 - - + +
486A GLU* 1.3 78.1 - - + +
488A LYS* 1.3 56.0 + - - +
490A ARG* 3.3 10.8 + - - +
491A MET* 2.9 28.8 + - + +
712A PHE* 3.8 19.3 - - + -
718A LEU* 4.2 6.1 - - + -
721A ILE* 3.7 34.1 - - + -
741A TYR* 5.2 1.1 - - + -
833A LEU* 4.2 19.7 - - + +
836A ALA* 3.5 23.6 - - + -
837A GLY* 4.9 0.9 - - - +
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Residues in contact with LYS 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A LEU 3.0 17.3 + - - +
485A LEU* 3.5 12.8 - - + +
487A VAL* 1.3 73.2 - - - +
489A LYS* 1.3 67.4 + - - +
491A MET* 3.5 1.7 + - - -
492A ARG* 3.2 24.5 + - + +
836A ALA* 3.5 25.1 - - + +
839A ALA* 4.1 15.9 - - + -
840A ALA* 3.6 12.9 - - + +
843A ASP* 2.7 32.1 + - - -
882A LEU* 2.6 36.8 + - + +
883A SER* 3.0 8.3 + - - -
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Residues in contact with LYS 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A LEU 2.8 16.4 + - - +
486A GLU* 3.0 37.0 - - + +
488A LYS* 1.3 80.4 - - - +
490A ARG* 1.3 63.5 + - - +
492A ARG* 3.3 7.1 + - - +
493A ALA* 3.2 19.2 + - - +
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Residues in contact with ARG 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A GLU* 2.5 61.6 + - - +
487A VAL* 3.8 8.4 - - - +
489A LYS* 1.3 72.1 - - + +
491A MET* 1.3 66.8 + - - +
493A ALA* 3.2 8.6 + - - +
494A GLU* 3.0 25.1 + - - +
712A PHE* 3.9 12.6 - - + -
717A CYS* 2.7 43.3 + - + -
718A LEU* 4.2 8.1 - - - +
720A ASP* 2.7 40.7 + - - -
721A ILE* 4.4 7.0 - - - +
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Residues in contact with MET 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A VAL* 2.9 17.4 + - + +
488A LYS* 3.8 6.3 - - - +
489A LYS 3.4 0.2 - - - -
490A ARG* 1.3 75.3 - - - +
492A ARG* 1.3 58.8 + - - +
494A GLU* 3.0 5.7 + - - +
495A MET* 2.9 37.0 + - + +
509A VAL* 4.9 6.7 - - - -
707A MET* 4.2 19.3 - - + -
709A TRP* 3.8 29.6 - - + -
712A PHE* 3.4 51.5 - - + -
741A TYR* 3.9 13.5 - - + +
837A GLY* 4.3 11.9 - - - +
840A ALA* 3.8 19.1 - - + -
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Residues in contact with ARG 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A LYS* 3.2 13.1 + - + +
489A LYS* 3.4 11.9 - - - +
491A MET* 1.3 80.5 - - - +
493A ALA* 1.3 58.4 + - - +
495A MET* 3.4 12.0 - - - +
496A GLU* 2.6 60.4 + - + +
840A ALA* 3.8 24.5 - - + +
843A ASP* 4.8 3.0 - - - +
844A LYS* 3.5 43.6 + - + +
847A GLU* 3.1 34.6 + - - +
848A ASN* 5.2 2.0 - - - +
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Residues in contact with ALA 493 (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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489A LYS 3.2 8.7 + - - +
490A ARG* 3.2 12.0 + - - +
492A ARG* 1.3 75.4 - - - +
494A GLU* 1.3 69.1 + - + +
496A GLU* 3.2 9.8 + - - +
497A LEU* 3.1 28.5 + - + +
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Residues in contact with GLU 494 (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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490A ARG* 3.0 15.8 + - + +
491A MET 3.2 10.1 - - - +
493A ALA* 1.3 79.0 - - - +
495A MET* 1.3 62.9 + - - +
497A LEU* 3.2 23.1 + - - +
498A GLY* 3.2 17.3 + - - -
507A ALA* 5.0 0.9 - - - +
508A VAL* 3.4 30.1 + - + +
509A VAL* 3.7 24.3 + - + +
712A PHE* 3.7 24.7 - - + -
715A ASN* 3.5 20.5 + - - +
717A CYS* 4.4 8.8 - - - +
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Residues in contact with MET 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A MET* 2.9 28.9 + - - +
492A ARG* 3.4 18.6 - - - +
494A GLU* 1.3 75.6 - - - +
496A GLU* 1.3 62.4 + - - +
498A GLY 3.2 2.4 + - - -
499A LEU* 3.1 26.4 + - + +
509A VAL* 4.8 1.3 - - + -
511A MET* 3.6 17.9 - - + +
686A TYR* 3.2 40.4 - - + +
707A MET* 3.8 25.6 - - + -
840A ALA 4.6 9.0 - - - +
841A VAL* 4.5 13.2 - - - -
844A LYS* 3.6 27.4 - - + -
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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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492A ARG* 2.6 46.0 + - + +
493A ALA* 3.2 9.8 + - - +
495A MET* 1.3 74.8 - - + +
497A LEU* 1.3 68.0 + - + +
499A LEU* 3.0 10.4 + - - +
500A ARG* 3.0 40.1 + - + +
844A LYS* 4.2 12.0 - - - -
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Residues in contact with LEU 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 ALA* 3.1 17.8 + - + +
494A GLU* 3.2 26.0 + - - +
496A GLU* 1.3 78.9 - - + +
498A GLY* 1.3 61.4 + - - +
500A ARG* 3.5 29.6 - - - +
503A THR* 2.9 31.0 + - + +
504A HIS 3.3 13.5 + - - -
507A ALA* 3.9 15.9 - - + -
715A ASN* 5.8 2.2 - - - +
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Residues in contact with GLY 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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494A GLU 3.2 7.7 + - - -
495A MET 3.2 4.5 + - - -
496A GLU 3.1 1.2 - - - -
497A LEU* 1.3 80.7 - - - +
499A LEU* 1.3 59.0 + - - +
500A ARG 4.2 0.4 - - - -
504A HIS* 3.0 26.4 + - - +
507A ALA* 3.7 10.7 - - - +
509A VAL 3.7 20.9 - - - -
510A LYS 3.6 5.8 - - - +
511A MET* 3.9 9.8 - - - +
695A MET* 4.9 1.7 - - - +
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Residues in contact with LEU 499 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A MET 3.1 15.7 + - - +
496A GLU* 3.0 11.0 + - - +
498A GLY* 1.3 77.1 - - - +
500A ARG* 1.3 67.1 + - + +
501A LYS 3.5 0.2 + - - -
511A MET* 3.5 31.0 - - + +
688A GLU* 3.7 17.9 - - + +
692A ASN* 3.8 20.2 - - + +
693A VAL* 4.5 6.9 - - + -
694A GLU* 3.4 21.7 + - - +
695A MET* 4.2 8.2 + - - +
705A ILE* 4.1 23.6 - - + -
844A LYS* 3.5 32.3 - - - +
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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
------------------------------------------------------------
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