Contacts of the helix formed by residues 443 - 450 (chain A) in PDB entry 1HS6
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 443 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392A TYR* 5.0 1.0 + - - -
441A GLN 3.6 3.2 + - - +
442A VAL* 1.3 72.4 - - - +
444A TRP* 1.3 58.5 + - - +
445A ASN* 3.7 8.5 + - - +
446A ALA* 3.2 30.4 + - + +
447A TRP* 2.8 33.9 + - + -
455A PRO* 4.3 15.8 - - + +
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Residues in contact with TRP 444 (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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389A LEU* 4.5 12.6 - - + -
393A LEU* 4.0 12.3 - - + -
424A TRP* 3.7 25.1 - + - -
425A LYS* 3.7 31.9 - - + -
428A LEU* 3.5 32.5 - - + -
429A TYR* 3.2 32.8 + + - -
439A LEU* 3.2 14.9 + - + -
440A ASN* 5.4 1.8 - - - -
442A VAL* 3.0 43.8 + - + -
443A ASP* 1.3 72.2 + - - +
445A ASN* 1.3 57.4 + - - +
447A TRP* 4.5 2.5 - - + +
448A LEU* 2.8 52.6 + - + +
449A TYR* 5.1 1.1 - - + -
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Residues in contact with ASN 445 (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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443A ASP* 3.2 8.1 + - - +
444A TRP* 1.3 77.7 - - - +
446A ALA* 1.3 60.1 + - - +
449A TYR* 2.9 54.2 + - + +
450A SER* 3.3 14.1 + - - -
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Residues in contact with ALA 446 (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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385A LYS* 5.0 1.7 + - - -
443A ASP* 3.1 29.8 + - - +
445A ASN* 1.3 77.9 - - - +
447A TRP* 1.3 69.8 + - - +
450A SER* 2.9 42.8 + - - +
455A PRO* 3.8 20.2 - - + +
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Residues in contact with TRP 447 (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 LEU* 3.4 22.0 + - - +
385A LYS* 3.8 24.5 + - + +
388A ALA* 3.7 21.5 - - + -
389A LEU* 3.3 47.8 - - + -
392A TYR* 3.5 34.5 + + + -
442A VAL* 4.0 16.2 - - + -
443A ASP 2.8 24.5 + - - +
444A TRP* 4.0 4.9 - - + +
446A ALA* 1.3 81.2 - - - +
448A LEU* 1.4 60.9 + - + +
450A SER 5.0 0.2 + - - -
454A PRO* 3.4 32.3 - - + -
455A PRO* 3.3 28.7 - - + +
456A ILE* 3.4 29.2 - - + +
458A PRO* 5.0 0.7 - - + -
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Residues in contact with LEU 448 (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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315A TRP* 4.5 3.4 - - + -
365A LEU* 3.6 24.5 + - + -
366A VAL* 3.0 31.6 + - + +
389A LEU* 4.3 13.9 - - + -
421A THR* 4.0 27.1 - - + -
424A TRP* 4.9 1.6 - - + -
425A LYS* 4.2 23.3 - - + +
444A TRP* 2.8 39.3 + - + +
447A TRP* 1.4 72.5 - - - +
449A TYR* 1.3 98.5 + - + +
450A SER 3.9 0.2 - - - -
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Residues in contact with TYR 449 (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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364A LYS* 3.3 30.5 - - + -
366A VAL* 4.0 25.1 - - + -
421A THR* 5.1 3.8 - - - +
444A TRP* 5.2 0.4 - - + -
445A ASN* 2.9 42.3 + - + +
448A LEU* 1.3 115.5 - - + +
450A SER* 1.3 60.7 + - - +
451A PRO* 4.3 0.2 - - - +
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Residues in contact with SER 450 (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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364A LYS* 3.7 6.8 - - - -
365A LEU 4.7 0.5 + - - -
385A LYS* 3.1 21.3 + - - -
445A ASN* 3.3 11.1 + - - -
446A ALA* 2.9 38.4 + - - +
449A TYR* 1.3 80.4 - - - +
451A PRO* 1.3 73.3 - - - +
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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
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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