Contacts of the helix formed by residues 371 - 376 (chain A) in PDB entry 1QM4
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 ILE 371 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ASP* 4.3 0.7 - - - -
366A ASP 4.1 9.9 - - - +
367A LEU* 5.1 1.3 - - + -
369A LYS* 2.8 52.2 + - + +
370A PRO* 1.3 75.7 - - - +
372A TYR* 1.3 77.4 + - + +
373A GLN 3.5 2.2 - - - -
374A LYS* 2.9 57.6 + - - +
375A THR* 3.6 4.6 + - - +
385A GLU 5.8 0.2 - - - +
386A PHE* 4.8 4.3 - - + -
387A PRO* 5.2 11.0 - - + -
388A TRP* 4.5 26.2 - - + -
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Residues in contact with TYR 372 (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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40A ASP* 3.4 22.6 - - + +
43A LEU* 3.4 26.7 - - + -
44A ASP* 3.1 10.0 + - - +
47A LEU* 3.6 25.4 - - + -
288A TYR* 3.6 13.4 - - + +
293A ARG* 3.4 35.2 - - - -
297A TYR* 4.2 16.6 - + - -
367A LEU* 2.7 38.9 + - - +
369A LYS 3.6 11.9 - - - -
371A ILE* 1.3 86.6 - - + +
373A GLN* 1.3 65.2 + - - +
375A THR* 2.9 29.0 - - + +
376A ALA 3.2 2.3 + - - -
388A TRP* 5.0 1.3 - + - -
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Residues in contact with GLN 373 (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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37A GLN* 4.1 25.0 + - + +
40A ASP* 3.7 11.2 - - - +
41A ALA* 3.4 29.9 - - - +
44A ASP* 3.1 20.6 + - - +
87A THR* 3.6 24.5 + - - +
90A HIS* 4.0 27.1 + - - +
372A TYR* 1.3 75.2 - - - +
374A LYS* 1.3 57.1 + - - +
375A THR 3.1 0.2 - - - -
376A ALA* 3.1 21.0 + - - +
377A CYS* 4.3 1.0 + - - +
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Residues in contact with LYS 374 (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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44A ASP* 5.0 0.2 + - - -
371A ILE* 2.9 53.4 + - - +
373A GLN* 1.3 77.2 - - - +
375A THR* 1.3 51.5 + - - +
376A ALA 3.3 0.2 - - - -
377A CYS 3.6 3.8 - - - +
383A ARG* 2.5 41.3 + - - +
385A GLU* 2.8 51.6 + - - +
386A PHE* 3.4 13.2 - - + -
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Residues in contact with THR 375 (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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40A ASP* 3.9 0.7 - - - +
270A ASP* 4.8 0.2 - - - +
293A ARG* 3.0 19.1 - - - +
297A TYR* 3.7 2.5 + - - +
371A ILE 3.6 3.5 + - - -
372A TYR* 2.9 24.1 - - + +
374A LYS* 1.3 78.3 - - - +
376A ALA* 1.3 54.9 + - - +
377A CYS 3.3 7.7 + - - -
379A GLY 4.0 9.3 + - - +
380A HIS* 2.9 52.6 + - + +
383A ARG* 3.8 5.8 - - - +
386A PHE* 3.9 10.8 - - - -
388A TRP* 3.7 28.1 - - - -
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Residues in contact with ALA 376 (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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33A LYS* 3.0 26.2 + - - +
36A ASP* 3.4 28.9 - - - +
37A GLN* 3.6 16.6 - - + +
40A ASP* 3.5 13.0 - - + +
270A ASP* 4.9 0.2 - - - -
284A SER* 3.9 5.8 - - - +
372A TYR 3.2 1.1 + - - +
373A GLN 3.1 14.6 + - - +
375A THR* 1.3 80.6 - - - +
377A CYS* 1.3 61.0 + - - +
380A HIS* 4.4 2.5 - - - -
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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