Contacts of the helix formed by residues 517 - 536 (chain A) in PDB entry 1HK2
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 517 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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515A THR 4.3 0.2 + - - -
516A LEU* 1.3 77.4 - - - +
518A GLU* 1.3 60.5 + - - +
519A LYS* 3.9 6.3 + - - +
520A GLU* 3.3 29.0 + - - +
521A ARG* 2.8 27.9 + - - +
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Residues in contact with GLU 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A SER* 1.3 76.6 - - - +
519A LYS* 1.3 63.6 + - - +
521A ARG* 2.4 45.1 + - - +
522A GLN* 2.9 49.2 + - - +
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Residues in contact with LYS 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A ARG* 4.3 8.0 + - - +
517A SER* 3.3 7.4 + - - +
518A GLU* 1.3 81.2 - - - +
520A GLU* 1.3 66.5 + - + +
522A GLN* 3.2 10.4 + - - +
523A ILE* 3.2 31.0 + - + +
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Residues in contact with GLU 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A LEU* 3.8 25.4 - - + -
517A SER* 3.3 22.4 + - - +
519A LYS* 1.3 81.5 - - + +
521A ARG* 1.3 62.2 + - - +
523A ILE* 3.3 14.1 + - + +
524A LYS* 3.1 30.3 + - - +
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Residues in contact with ARG 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A TYR* 4.3 10.5 + - - -
516A LEU* 4.2 19.4 - - + +
517A SER 2.8 22.2 + - - +
518A GLU* 2.4 45.3 + - - +
519A LYS 3.2 0.2 - - - -
520A GLU* 1.3 73.6 - - - +
522A GLN* 1.3 75.7 + - - +
524A LYS* 3.1 5.1 + - - +
525A LYS* 2.9 64.9 + - + +
3003A T44 4.7 14.3 + - + +
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Residues in contact with GLN 522 (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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401A TYR* 3.0 48.3 - - + +
404A GLN* 4.6 1.4 - - - +
428A ARG* 3.5 20.8 + - - +
518A GLU* 2.9 43.3 + - - +
519A LYS* 3.2 8.1 + - - +
521A ARG* 1.3 90.6 - - - +
523A ILE* 1.3 52.8 + - - +
525A LYS* 3.6 4.6 - - - +
526A GLN* 2.6 41.7 + - - +
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Residues in contact with ILE 523 (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 VAL* 4.5 12.0 - - + +
428A ARG* 3.6 37.9 - - - +
519A LYS* 3.2 20.3 + - + +
520A GLU* 3.6 12.8 - - + +
521A ARG 3.2 0.2 - - - -
522A GLN* 1.3 74.2 - - - +
524A LYS* 1.3 63.0 + - + +
526A GLN* 3.8 5.7 - - - +
527A THR* 2.7 44.0 + - - +
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Residues in contact with LYS 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A ILE* 5.6 3.4 - - + +
516A LEU* 3.5 33.0 - - + -
520A GLU* 3.1 16.5 + - - +
521A ARG 3.1 6.2 + - - +
523A ILE* 1.3 79.7 - - + +
525A LYS* 1.3 59.9 + - - +
527A THR* 3.1 3.5 + - - +
528A ALA* 2.9 26.0 + - - +
3003A T44 3.2 80.1 + - + +
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Residues in contact with LYS 525 (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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401A TYR* 3.3 24.5 + - - +
521A ARG* 2.9 44.8 + - + +
522A GLN* 3.7 4.7 - - - +
524A LYS* 1.3 77.7 - - - +
526A GLN* 1.3 56.9 + - - +
528A ALA* 3.4 7.8 - - - +
529A LEU* 3.0 22.3 + - - +
548A MET* 3.3 36.1 - - + +
549A ASP* 5.5 3.8 + - - -
552A ALA* 4.4 20.8 - - - +
3003A T44 3.9 22.2 - - + +
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Residues in contact with GLN 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A TYR* 4.0 15.7 - - + +
404A GLN* 3.4 35.7 + - - +
405A ASN* 3.1 28.5 + - - +
408A LEU* 3.5 18.8 - - + +
424A VAL* 4.1 7.1 - - + +
428A ARG* 2.8 37.2 + - - +
522A GLN 2.6 29.1 + - - +
523A ILE* 3.9 4.9 - - - +
525A LYS* 1.3 70.3 - - - +
527A THR* 1.3 65.8 + - - +
529A LEU* 3.2 7.0 + - - +
530A VAL* 3.1 28.1 + - - +
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Residues in contact with THR 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A THR* 3.6 20.3 - - + +
421A PRO* 6.1 0.2 - - - +
424A VAL* 3.8 17.4 - - - +
506A THR* 4.8 8.3 - - + -
523A ILE* 2.7 31.9 + - - +
524A LYS* 3.4 7.1 - - - +
526A GLN* 1.3 74.5 - - - +
528A ALA* 1.3 64.1 + - - +
530A VAL* 3.1 5.0 + - - +
531A GLU* 3.0 29.8 + - + +
3003A T44 4.2 13.5 - - + -
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Residues in contact with ALA 528 (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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507A PHE* 4.1 12.8 - - + -
524A LYS 2.9 13.3 + - - +
525A LYS 3.4 10.3 - - - +
527A THR* 1.3 79.7 - - - +
529A LEU* 1.3 55.8 + - - +
531A GLU* 3.3 2.3 + - - -
532A LEU* 2.9 13.3 + - - +
548A MET* 4.5 0.2 - - - -
3003A T44 3.8 30.0 - - + +
3004A T44 2.6 41.9 + - + -
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Residues in contact with LEU 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A ASN* 4.0 33.4 - - + +
408A LEU* 4.6 8.1 - - + -
409A VAL* 3.9 26.0 - - + -
525A LYS 3.0 14.3 + - - +
526A GLN* 3.4 9.9 - - - +
527A THR 3.2 0.4 - - - -
528A ALA* 1.3 78.1 - - - +
530A VAL* 1.3 57.0 + - - +
532A LEU* 3.4 10.7 - - + +
533A VAL* 3.0 36.3 + - + +
544A LEU* 4.8 9.4 - - + -
548A MET* 3.9 31.6 - - + -
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Residues in contact with VAL 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A LEU* 3.5 32.8 - - + -
412A THR* 3.5 27.8 - - + +
420A THR* 4.0 17.0 - - + +
423A LEU* 3.9 16.8 - - + -
424A VAL* 3.7 13.2 - - + -
526A GLN 3.1 17.0 + - - +
527A THR 3.6 4.0 - - - +
529A LEU* 1.3 70.6 - - - +
531A GLU* 1.3 59.5 + - - +
532A LEU 3.0 1.3 - - - -
533A VAL* 3.0 7.2 + - - +
534A LYS* 2.7 37.5 + - - +
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Residues in contact with GLU 531 (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 THR* 2.7 29.7 + - - +
500A LYS* 3.0 35.9 + - - +
506A THR* 3.8 31.1 + - + +
507A PHE* 4.3 4.9 - - + -
527A THR* 3.0 19.9 + - + +
528A ALA 3.5 8.1 - - - +
530A VAL* 1.3 75.4 - - - +
532A LEU* 1.3 61.9 + - - +
534A LYS* 3.5 6.3 + - - +
535A HIS* 3.1 23.7 + - - +
3004A T44 3.5 19.1 - - + +
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Residues in contact with LEU 532 (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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528A ALA 2.9 9.0 + - - +
529A LEU* 3.4 11.4 - - + +
531A GLU* 1.3 77.2 - - - +
533A VAL* 1.3 56.9 + - - +
535A HIS* 3.0 6.0 + - + +
536A LYS* 2.9 34.4 + - + +
544A LEU* 3.6 35.9 - - + +
547A VAL* 3.7 31.4 - - + -
548A MET* 4.4 13.0 - - + -
3004A T44 3.1 50.4 + - + +
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Residues in contact with VAL 533 (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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409A VAL* 4.4 16.6 - - + +
412A THR* 3.8 23.3 - - + +
413A LYS* 4.0 30.3 - - + +
529A LEU* 3.0 22.9 + - + +
530A VAL* 3.0 8.8 + - - +
532A LEU* 1.3 74.0 - - - +
534A LYS* 1.3 62.7 + - - +
536A LYS 4.4 5.6 - - - +
537A PRO* 3.0 27.4 - - + +
544A LEU* 4.3 27.6 - - + -
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Residues in contact with LYS 534 (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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412A THR* 3.9 13.2 - - + -
416A PRO* 3.2 26.4 + - + +
417A GLN 4.9 1.2 + - - -
418A VAL 2.9 22.9 + - - -
419A SER* 3.5 4.2 - - - +
420A THR* 3.2 34.4 + - - +
423A LEU* 4.0 11.2 - - - -
497A TYR* 2.7 39.0 + - - +
499A PRO* 3.7 0.7 - - - +
500A LYS* 3.1 31.6 + - + +
530A VAL* 2.7 21.7 + - - +
531A GLU* 3.7 14.5 + - - +
533A VAL* 1.3 74.7 - - - +
535A HIS* 1.3 58.9 + - - +
537A PRO* 3.7 0.3 - - - +
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Residues in contact with HIS 535 (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 PRO* 3.5 12.1 - - + +
500A LYS* 2.7 28.3 + - + +
501A GLU* 3.8 5.8 - - - +
502A PHE* 3.8 22.0 - - + +
531A GLU 3.1 15.9 + - - +
532A LEU* 3.0 5.8 + - + +
534A LYS* 1.3 79.1 - - - +
536A LYS* 1.3 62.1 + - + +
537A PRO* 3.3 7.4 - - - +
3004A T44 4.0 58.7 - + + +
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Residues in contact with LYS 536 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A LEU* 2.9 23.0 + - + +
533A VAL* 3.4 7.0 - - - +
535A HIS* 1.3 85.5 - - + +
537A PRO* 1.3 64.9 - - - +
538A LYS* 2.9 5.4 + - - -
539A ALA* 2.9 28.2 + - + +
543A GLN* 5.8 1.8 - - - +
3004A T44 5.9 3.1 - - + -
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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