Contacts of the helix formed by residues 365 - 370 (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 ASP 365 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A ALA* 4.6 1.2 - - - +
364A ALA* 1.3 80.2 - - + +
366A PRO* 1.3 67.1 - - - +
367A HIS* 3.7 14.1 + - - +
368A GLU* 2.8 48.5 + - + +
369A CYS* 3.4 9.9 + - - +
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Residues in contact with PRO 366 (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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316A CYS* 3.7 24.2 - - + -
360A CYS 3.4 26.7 - - - +
361A CYS* 4.2 9.9 - - - +
363A ALA 4.0 6.5 - - - +
364A ALA 3.0 12.8 - - - +
365A ASP* 1.3 85.1 - - - +
367A HIS* 1.3 63.2 + - - +
369A CYS* 3.1 3.2 + - + +
370A TYR* 3.1 34.5 + - + +
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Residues in contact with HIS 367 (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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310A VAL* 3.8 22.8 + - + -
311A GLU* 4.0 21.0 + - + -
312A SER 4.7 1.4 + - - -
313A LYS* 6.2 1.3 - - - -
365A ASP* 3.2 14.3 + - - +
366A PRO* 1.3 79.1 - - - +
368A GLU* 1.3 73.9 + - - +
370A TYR* 4.0 16.0 + - - +
371A ALA* 3.0 32.4 + - + +
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Residues in contact with GLU 368 (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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365A ASP* 2.8 31.4 + - + +
367A HIS* 1.3 94.1 - - - +
369A CYS* 1.3 67.5 + - - +
371A ALA* 3.1 20.6 + - - +
372A LYS* 4.4 2.9 + - - +
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Residues in contact with CYS 369 (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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356A THR* 4.6 2.4 - - - +
359A LYS* 4.5 3.6 - - - -
360A CYS* 2.0 62.1 - - + -
363A ALA* 4.1 15.7 - - + -
365A ASP 3.4 8.1 + - - +
366A PRO 3.1 7.2 + - - +
368A GLU* 1.3 81.1 - - - +
370A TYR* 1.3 56.1 + - - +
371A ALA 3.5 1.2 + - - -
372A LYS* 4.6 3.1 + - - +
373A VAL 5.6 0.3 + - - -
376A GLU* 5.7 0.9 - - - +
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Residues in contact with TYR 370 (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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309A PHE 4.8 1.6 - - - -
310A VAL* 3.1 31.0 - - - +
312A SER 3.2 14.2 + - - -
313A LYS* 4.5 5.0 + - - -
315A VAL* 3.2 31.9 + - + +
316A CYS* 3.7 25.7 + - - +
353A TYR* 6.1 0.2 - - + -
356A THR* 3.9 16.2 - - + -
357A LEU* 3.8 22.9 - - + -
360A CYS* 2.9 24.8 - - + -
366A PRO* 3.1 25.3 + - + +
367A HIS* 4.0 18.9 + - - +
369A CYS* 1.3 74.2 - - - +
371A ALA* 1.3 66.6 + - - +
372A LYS 3.4 1.8 - - - -
373A VAL* 3.5 20.6 + - + +
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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