Contacts of the helix formed by residues 373 - 379 (chain A) in PDB entry 1XRB
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 ALA 373 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284A ASN* 2.9 11.9 - - - +
287A ALA* 4.7 15.3 - - + +
288A ALA* 3.2 23.8 - - + +
370A THR* 3.1 16.6 - - - +
371A ASP 2.8 4.5 + - - +
372A LYS* 1.3 78.3 - - - +
374A GLN* 1.3 64.2 + - + +
376A LEU* 3.2 1.6 + - - +
377A ARG 3.1 14.2 + - - -
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Residues in contact with GLN 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 ASP 4.6 1.8 + - - -
372A LYS 3.7 0.2 - - - -
373A ALA* 1.3 75.2 - - + +
375A LEU* 1.3 60.1 + - + +
377A ARG* 2.6 53.4 + - - +
378A ASP* 2.8 44.9 + - - +
382A LEU* 3.4 21.0 - - - +
383A LYS* 4.4 1.1 + - - +
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Residues in contact with LEU 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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332A PHE* 3.4 33.1 - - + -
371A ASP 4.5 4.7 - - - +
372A LYS* 3.7 32.3 - - + +
374A GLN* 1.3 77.7 - - + +
376A LEU* 1.3 60.3 + - - +
378A ASP* 3.6 13.2 + - - +
379A ALA 3.5 12.3 + - - -
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Residues in contact with LEU 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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284A ASN* 4.0 7.6 - - + +
285A ILE* 3.8 43.3 - - + +
288A ALA* 4.6 1.8 - - + -
290A LEU* 4.4 10.5 - - + -
325A LEU* 6.2 0.2 - - + -
328A LEU* 3.2 43.4 - - + +
329A VAL* 6.2 0.4 - - + -
332A PHE* 3.3 37.2 - - + -
333A PHE* 4.1 19.1 - - + -
372A LYS* 2.9 18.2 + - + +
373A ALA 3.4 4.0 - - - +
374A GLN 3.0 0.2 - - - -
375A LEU* 1.3 76.3 - - - +
377A ARG* 1.3 64.8 + - - +
380A ALA* 3.2 6.9 + - - +
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Residues in contact with ARG 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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288A ALA* 3.0 36.2 + - + +
289A GLY* 4.0 11.5 + - - -
290A LEU* 3.9 10.3 - - - -
373A ALA 3.1 10.5 + - - +
374A GLN* 2.6 41.3 + - - +
376A LEU* 1.3 71.0 - - - +
378A ASP* 1.3 63.2 + - - +
380A ALA* 3.0 12.8 + - - +
381A GLY 3.1 17.5 - - - +
383A LYS* 2.8 82.0 + - + +
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Residues in contact with ASP 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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374A GLN* 2.8 46.8 + - - +
375A LEU* 3.7 17.1 - - + +
376A LEU 3.3 0.2 - - - -
377A ARG* 1.3 66.8 - - - +
379A ALA* 1.3 53.3 - - - +
380A ALA 3.0 2.9 - - - -
381A GLY* 2.7 27.2 + - - -
382A LEU* 3.0 33.1 + - + +
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Residues in contact with ALA 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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327A LEU* 5.7 4.2 - - - +
328A LEU* 3.5 24.8 - - + +
331A GLU* 5.6 1.1 - - + -
332A PHE* 3.7 23.1 - - + -
375A LEU 3.5 3.6 + - - +
378A ASP* 1.3 78.1 - - - +
380A ALA* 1.3 56.0 + - - +
381A GLY 3.3 3.5 + - - -
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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