Contacts of the helix formed by residues 483 - 491 (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 ASN 483 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348A ARG* 3.8 15.8 - - - +
476A CYS 5.4 0.2 - - - -
479A GLU* 5.6 6.8 - - - +
480A SER* 2.7 28.0 + - - +
482A VAL* 1.3 88.6 + - - +
484A ARG* 1.3 53.4 + - - +
485A ARG 3.3 2.7 - - - -
486A PRO* 2.9 14.4 - - + +
487A CYS* 2.7 39.7 + - + +
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Residues in contact with ARG 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LEU* 4.8 0.8 - - - +
201A ALA* 5.6 2.0 - - - +
205A LYS* 5.6 3.6 - - - +
206A PHE* 3.8 15.1 - - - -
454A SER* 5.1 5.0 + - - +
457A LEU* 4.0 17.3 - - + -
458A ASN* 2.9 40.4 + - - +
461A CYS* 3.6 23.6 - - - +
476A CYS 3.5 13.5 - - - +
477A CYS* 2.8 32.1 + - - +
480A SER 3.4 16.4 + - - +
481A LEU* 3.7 35.3 - - - +
482A VAL 3.4 2.0 - - - -
483A ASN* 1.3 75.3 - - - +
485A ARG* 1.3 57.7 + - - +
487A CYS* 3.1 7.7 + - - +
488A PHE* 2.8 36.8 + - + -
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Residues in contact with ARG 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A VAL* 6.2 0.2 - - + -
348A ARG* 4.6 2.2 - - - +
383A GLU* 2.5 41.2 + - - -
384A PRO* 3.9 14.5 - - - +
387A LEU* 4.2 14.3 - - - +
411A TYR* 5.4 0.8 + - - +
450A GLU* 2.9 35.2 + - + +
453A LEU* 3.9 32.6 - - + +
454A SER* 5.8 3.4 - - - +
457A LEU* 3.4 21.8 - - + +
482A VAL 4.9 0.8 + - - -
484A ARG* 1.3 77.6 - - - +
486A PRO* 1.3 104.2 - - + +
488A PHE* 3.8 0.5 - - - +
489A SER* 2.8 50.1 + - - -
3002A T44 4.7 5.6 - - + -
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Residues in contact with PRO 486 (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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348A ARG* 3.4 35.4 - - - +
383A GLU* 4.0 8.5 - - - +
483A ASN* 2.9 28.7 - - + +
485A ARG* 1.3 110.9 - - + +
487A CYS* 1.3 51.8 + - - +
489A SER* 3.3 0.7 + - - -
490A ALA* 2.8 39.1 + - - +
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Residues in contact with CYS 487 (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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475A LYS* 4.9 7.2 - - - -
476A CYS* 2.0 56.5 - - + +
479A GLU* 4.8 12.8 - - - +
483A ASN* 2.7 21.9 + - + +
484A ARG* 3.2 11.7 - - - +
486A PRO* 1.3 73.4 - - - +
488A PHE* 1.3 62.4 + - - +
490A ALA* 3.4 5.8 + - - +
491A LEU* 3.3 23.3 + - - +
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Residues in contact with PHE 488 (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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411A TYR* 4.0 26.7 - + + +
414A LYS* 2.9 21.6 - - - -
415A VAL* 4.9 4.3 - - + -
457A LEU* 3.9 30.5 - - + -
460A LEU* 3.9 26.9 - - + -
461A CYS* 4.5 5.4 - - - -
473A VAL* 4.1 16.8 - - + -
476A CYS* 3.7 25.1 - - + -
477A CYS* 4.1 22.7 - - - -
484A ARG* 2.8 31.8 + - + +
485A ARG 3.9 2.0 - - - +
487A CYS* 1.3 70.1 - - - +
489A SER* 1.3 69.0 + - - +
491A LEU* 2.9 32.3 + - + +
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Residues in contact with SER 489 (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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383A GLU* 5.1 2.0 - - - -
387A LEU* 3.5 12.4 - - - +
411A TYR* 4.2 0.6 + - - -
414A LYS* 3.0 17.8 + - - -
485A ARG* 2.8 48.8 + - - -
486A PRO 3.6 1.1 - - - -
488A PHE* 1.3 72.5 - - - +
490A ALA* 1.3 61.0 + - - +
491A LEU 3.6 1.0 - - - +
3002A T44 2.7 40.1 + - - +
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Residues in contact with ALA 490 (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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486A PRO 2.8 22.0 + - - +
487A CYS* 3.7 6.7 - - - +
489A SER* 1.3 71.2 - - - +
491A LEU* 1.3 63.8 + - - +
492A GLU* 3.4 12.5 + - - +
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Residues in contact with LEU 491 (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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414A LYS* 3.1 36.4 + - + +
415A VAL* 4.2 19.1 - - + -
472A ARG* 3.5 39.3 - - + +
476A CYS* 4.3 10.8 - - - -
487A CYS 3.3 17.8 + - - +
488A PHE* 2.9 43.4 + - + +
489A SER 3.6 0.7 - - - +
490A ALA* 1.3 77.1 - - - +
492A GLU* 1.3 64.8 + - - +
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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