Contacts of the helix formed by residues 534 - 540 (chain A) in PDB entry 4IM0
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 534 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440A ARG 5.1 1.4 - - - +
443A ILE* 3.1 30.4 - - - +
444A ARG* 4.1 23.7 - - - +
447A ILE* 3.6 13.5 - - + +
532A LEU 3.8 0.6 + - - -
533A ALA* 1.3 72.4 - - - +
535A ALA* 1.3 53.9 + - - +
536A TRP* 3.2 5.0 + - - +
537A ALA* 2.8 40.4 + - - +
538A HIS* 4.0 25.6 + - - +
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Residues in contact with ALA 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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528A PRO 5.8 2.0 - - - +
533A ALA* 3.5 9.1 - - + -
534A ASP* 1.3 77.1 - - - +
536A TRP* 1.3 63.2 + - - +
538A HIS* 3.0 26.2 + - - +
539A GLN* 3.1 33.0 - - - +
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Residues in contact with TRP 536 (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 ILE* 3.7 25.4 - - + -
533A ALA* 3.2 29.1 + - + +
534A ASP* 3.0 3.8 + - - +
535A ALA* 1.3 77.7 - - - +
537A ALA* 1.3 81.0 + - + +
539A GLN* 2.9 15.3 + - - +
540A GLU* 2.7 47.4 + - + +
612A PHE* 3.6 25.4 - + - -
615A LYS* 3.6 26.9 - - + -
616A SER* 3.0 35.2 - - - -
619A TRP* 3.3 36.5 - + + +
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Residues in contact with ALA 537 (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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440A ARG* 3.1 50.8 + - + -
443A ILE* 5.1 2.9 - - + -
534A ASP* 2.8 21.4 + - - +
536A TRP* 1.3 107.8 - - + +
538A HIS* 1.3 65.4 + - + +
540A GLU 3.4 4.5 - - - +
612A PHE* 3.7 4.1 - - + -
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Residues in contact with HIS 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ARG* 4.3 15.4 - - + +
444A ARG* 5.3 10.7 - - - -
534A ASP* 4.1 32.1 + - - +
535A ALA* 3.0 18.5 + - - +
537A ALA* 1.3 84.3 - - + +
539A GLN* 1.3 60.7 + - + +
543A HIS* 3.3 26.0 + - + +
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Residues in contact with GLN 539 (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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535A ALA* 3.1 38.9 - - - +
536A TRP* 2.9 12.7 + - - +
538A HIS* 1.3 83.0 - - + +
540A GLU* 1.3 67.4 + - + +
541A GLY 4.9 1.7 - - - +
543A HIS* 4.9 3.4 - - - -
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Residues in contact with GLU 540 (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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440A ARG* 3.3 19.9 + - - -
536A TRP* 2.7 24.5 + - + +
537A ALA 3.4 3.6 - - - +
539A GLN* 1.3 89.5 - - + +
541A GLY* 1.3 68.5 + - - +
543A HIS* 3.9 2.8 + - - -
611A ALA* 3.5 24.7 - - - +
612A PHE* 3.5 22.0 - - + -
615A LYS* 3.9 36.9 + - + -
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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