Contacts of the helix formed by residues 438 - 445 (chain A) in PDB entry 3HU1
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 438 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429A LEU 4.9 6.0 + - - +
434A ASP* 5.6 0.4 + - - -
436A THR 3.9 2.0 + - - -
437A ILE* 1.3 78.4 - - + +
439A ALA* 1.3 74.3 + - - +
440A GLU* 3.2 22.5 + - - +
441A VAL* 3.4 23.2 + - + +
442A MET* 3.3 17.5 + - - +
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Residues in contact with ALA 439 (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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437A ILE 3.6 3.6 + - - -
438A ASP* 1.3 72.9 + - - +
440A GLU* 1.3 65.6 + - - +
442A MET* 3.3 14.3 + - - +
443A ASN* 3.0 27.9 - - - +
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Residues in contact with GLU 440 (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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429A LEU* 6.4 0.9 - - + -
438A ASP* 3.2 12.1 + - - +
439A ALA* 1.3 75.6 - - - +
441A VAL* 1.3 68.1 + - + +
443A ASN* 3.1 12.1 + - - +
444A SER* 3.1 32.7 + - - -
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Residues in contact with VAL 441 (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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426A LYS* 3.8 23.5 - - + +
429A LEU* 3.8 35.2 - - + +
430A ILE* 3.8 28.5 - - + -
437A ILE* 4.4 4.7 - - + -
438A ASP* 3.4 30.5 + - + +
439A ALA 3.3 0.4 - - - -
440A GLU* 1.3 78.6 - - + +
442A MET* 1.3 62.1 + - - +
444A SER* 3.2 19.9 + - - -
445A LEU* 3.4 15.5 - - + +
229B LEU* 6.1 0.2 - - + -
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Residues in contact with MET 442 (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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437A ILE* 3.6 48.9 - - + +
438A ASP 3.3 3.7 + - - +
439A ALA* 3.3 14.9 + - - +
441A VAL* 1.3 79.8 - - - +
443A ASN* 1.3 64.8 + - - +
445A LEU* 3.5 24.5 - - + +
228B ALA* 4.7 14.6 - - + +
229B LEU* 4.6 28.5 - - - -
232B ALA* 4.1 22.6 - - + +
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Residues in contact with ASN 443 (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 LYS* 6.0 0.5 - - - +
439A ALA* 3.0 22.3 + - - +
440A GLU* 3.1 11.2 + - - +
442A MET* 1.3 77.7 - - - +
444A SER* 1.3 61.2 + - - +
445A LEU 3.1 12.0 + - - +
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Residues in contact with SER 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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426A LYS* 3.8 27.3 + - - +
440A GLU* 3.1 26.4 + - - -
441A VAL* 3.2 17.3 + - - -
443A ASN* 1.3 73.1 - - - +
445A LEU* 1.3 57.6 + - - +
446A ALA* 3.0 14.4 + - - +
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Residues in contact with LEU 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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389A LYS* 3.4 23.7 - - + +
422A ALA* 4.0 27.1 - - + +
423A ILE* 4.5 5.6 - - + -
426A LYS* 4.1 21.8 - - + -
430A ILE* 5.6 0.7 - - + -
441A VAL* 3.4 15.7 - - + +
442A MET* 3.5 25.0 - - + +
443A ASN 3.1 7.5 - - - +
444A SER* 1.3 74.0 + - - +
446A ALA* 1.3 60.9 + - - +
229B LEU* 3.7 32.8 - - + +
232B ALA* 5.6 1.1 - - + -
233B ILE* 4.4 29.2 - - + +
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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