Contacts of the helix formed by residues 371 - 379 (chain A) in PDB entry 1QO0
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 ASN 371 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A ALA* 6.3 0.2 - - - -
369A VAL* 3.5 12.4 + - + +
370A HIS* 1.3 70.7 - - - +
372A LEU* 1.3 55.6 + - - +
373A ASP* 2.9 31.0 + - - +
374A ASP* 2.9 48.0 + - - +
375A TRP* 4.7 1.5 - - - -
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Residues in contact with LEU 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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129A ALA* 3.7 24.0 - - + +
132A ALA* 4.3 1.8 - - + -
133A ALA* 4.1 20.8 - - + +
136A ILE* 4.1 16.2 - - + -
137A ARG* 4.4 12.4 + - - +
163A LEU* 3.6 28.7 - - + -
167A HIS* 3.3 43.7 + - + +
370A HIS* 3.3 20.2 + - + +
371A ASN* 1.3 69.7 + - - +
373A ASP* 1.3 64.2 + - - +
374A ASP 3.0 0.7 - - - -
375A TRP* 3.1 22.5 + - + +
376A SER* 3.7 6.8 + - - -
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Residues in contact with ASP 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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137A ARG* 5.2 5.8 + - - +
167A HIS* 5.6 3.3 + - - -
371A ASN* 2.9 23.8 + - - +
372A LEU* 1.3 74.0 - - - +
374A ASP* 1.3 65.6 + - - +
375A TRP 3.0 1.4 + - - -
376A SER* 3.1 27.6 + - - -
377A ALA* 4.6 0.7 + - - +
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Residues in contact with ASP 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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371A ASN* 2.9 42.2 + - - +
373A ASP* 1.3 78.1 - - - +
375A TRP* 1.3 84.9 + - + +
376A SER 3.9 0.2 + - - -
377A ALA* 4.9 5.5 + - - +
378A SER* 5.4 0.7 + - - -
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Residues in contact with TRP 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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125A ASN 4.3 6.3 + - - -
129A ALA* 4.2 9.3 - - + +
130A PRO* 3.8 36.2 - - + +
133A ALA* 3.8 18.6 - - + -
137A ARG* 6.2 0.2 - - - -
355A TRP* 3.6 29.6 - + - -
357A SER* 4.1 7.6 - - - -
358A PRO* 4.5 7.6 - - + -
361A ILE* 3.5 42.0 - - + -
371A ASN 4.7 0.6 + - - -
372A LEU* 3.1 19.3 + - + +
374A ASP* 1.3 96.5 + - + +
376A SER* 1.3 64.6 + - - +
377A ALA 3.3 2.5 - - - -
378A SER* 3.2 10.5 + - - -
379A MET* 3.2 33.1 + - + +
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Residues in contact with SER 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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137A ARG* 5.3 16.2 - - - +
372A LEU 3.7 4.3 + - - -
373A ASP* 3.1 24.8 + - - -
375A TRP* 1.3 77.6 - - - +
377A ALA* 1.3 67.1 + - - +
379A MET* 3.3 18.5 + - - +
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Residues in contact with ALA 377 (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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373A ASP 4.6 1.4 + - - -
374A ASP 4.9 4.7 + - - +
375A TRP 3.3 0.8 - - - -
376A SER* 1.3 82.5 + - - +
378A SER* 1.3 58.6 + - - +
379A MET 3.3 2.1 + - - -
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Residues in contact with SER 378 (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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355A TRP* 3.1 37.9 + - - -
356A GLN 5.2 0.9 - - - -
358A PRO* 3.8 28.7 - - - +
374A ASP 5.4 0.6 + - - -
375A TRP* 3.2 17.5 + - - -
377A ALA* 1.3 77.4 - - - +
379A MET* 1.3 57.9 + - - +
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Residues in contact with MET 379 (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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130A PRO* 3.3 26.9 - - + +
133A ALA* 3.8 11.2 - - - +
134A TYR* 3.6 34.3 - - + +
137A ARG* 4.9 15.7 - - + +
138A HIS* 4.5 20.1 + - - +
355A TRP* 3.2 54.3 - - + +
375A TRP* 3.2 26.4 + - + +
376A SER* 3.3 12.5 + - - +
377A ALA 3.3 3.0 - - - -
378A SER* 1.3 80.3 - - - +
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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