Contacts of the helix formed by residues 364 - 375 (chain B) in PDB entry 2XI4
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 364 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362B HIS 3.7 2.6 + - - -
363B ALA* 1.3 74.2 - - - +
365B ASP* 1.3 68.6 + - - +
366B LEU* 3.4 11.5 + - - +
367B GLY* 2.7 41.4 + - - -
368B LEU* 3.0 12.6 + - - +
531B LEU* 4.1 6.8 + - - +
532B LEU* 3.6 29.1 + - - +
535B THR* 5.8 3.8 - - - +
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Residues in contact with ASP 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530A LYS* 4.4 16.8 + - - +
357B LYS* 5.3 3.6 + - - -
364B ASN* 1.3 75.2 - - - +
366B LEU* 1.3 56.2 + - - +
368B LEU* 3.4 16.2 + - - +
369B ASP* 3.0 33.8 + - - +
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Residues in contact with LEU 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527A PHE* 3.8 20.6 - - + -
530A LYS* 3.8 24.8 - - + +
531A LEU* 3.6 43.7 - - + +
534A ALA* 4.4 17.3 - - + -
535A THR* 4.5 11.0 - - + -
364B ASN* 3.1 11.5 + - - +
365B ASP* 1.3 74.3 - - - +
367B GLY* 1.3 65.4 + - - +
369B ASP* 3.2 8.2 + - + +
370B ALA* 3.0 18.9 + - - +
531B LEU* 3.7 30.3 - - + +
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Residues in contact with GLY 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B ALA* 4.2 5.8 - - - -
364B ASN* 2.7 23.1 + - - -
366B LEU* 1.3 72.6 - - - +
368B LEU* 1.3 60.8 + - - +
370B ALA* 3.1 4.7 + - - +
371B VAL* 3.1 27.8 + - - +
528B LEU* 3.9 6.5 - - - +
531B LEU* 3.6 16.5 - - - +
532B LEU* 3.9 10.5 - - - -
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Residues in contact with LEU 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B VAL* 4.1 12.1 - - + +
357B LYS* 3.7 61.9 - - + +
360B VAL* 4.1 10.5 - - + +
363B ALA* 4.0 24.7 - - + +
364B ASN 3.0 13.5 + - - +
365B ASP* 3.6 18.2 - - - +
367B GLY* 1.3 76.1 - - - +
369B ASP* 1.3 59.3 + - - +
371B VAL* 3.4 5.7 + - - +
372B THR* 2.9 34.7 + - - +
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Residues in contact with ASP 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527A PHE* 4.0 17.2 - - + -
530A LYS* 3.1 35.4 + - - +
365B ASP* 3.0 17.4 + - - +
366B LEU* 3.2 11.4 + - + +
368B LEU* 1.3 78.2 - - - +
370B ALA* 1.3 56.5 + - - +
372B THR* 3.5 6.5 + - - +
373B LEU* 2.9 30.0 + - - +
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Residues in contact with ALA 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527A PHE* 3.7 28.9 - - + -
366B LEU 3.0 9.1 + - - +
367B GLY* 3.1 8.7 + - - +
369B ASP* 1.3 73.4 - - - +
371B VAL* 1.3 60.4 + - - +
373B LEU* 3.5 4.6 + - - +
374B GLN* 2.9 31.9 + - - +
523B PHE* 3.7 20.4 - - + -
527B PHE* 4.3 2.7 - - + -
528B LEU* 4.6 1.3 - - + -
531B LEU* 3.9 13.5 - - + -
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Residues in contact with VAL 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B VAL* 3.7 21.8 - - + -
360B VAL* 4.3 10.3 - - + -
367B GLY 3.1 16.0 + - - +
368B LEU* 3.7 7.6 - - - +
369B ASP 3.4 0.2 - - - -
370B ALA* 1.3 76.1 - - - +
372B THR* 1.3 62.1 + - - +
374B GLN 3.1 1.7 + - - -
375B TYR* 3.1 26.3 + - + +
394B ILE* 4.0 22.2 - - + -
523B PHE* 3.7 20.4 - - + -
524B TRP* 3.9 28.7 - - + -
528B LEU* 4.1 9.6 - - + -
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Residues in contact with THR 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B ARG* 3.5 26.7 - - - +
352B PHE* 4.2 11.1 - - + -
353B MET* 5.5 10.0 - - + +
356B VAL* 4.0 16.5 - - - +
368B LEU* 2.9 19.6 + - - +
369B ASP* 3.7 7.6 - - - +
371B VAL* 1.3 76.9 - - - +
373B LEU* 1.3 63.0 + - - +
375B TYR 3.2 2.6 + - - -
376B THR* 2.6 31.1 + - - +
378B TRP* 4.8 8.3 - - + -
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Residues in contact with LEU 373 (chain B).
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* 4.5 13.5 - - - +
519A GLN* 3.6 34.5 + - - +
522A VAL* 3.9 28.0 - - + -
523A PHE* 4.1 24.0 - - + -
527A PHE* 3.9 34.1 - - + -
369B ASP 2.9 18.3 + - - +
370B ALA* 3.8 4.7 - - - +
371B VAL 3.3 0.2 - - - -
372B THR* 1.3 80.1 - - - +
374B GLN* 1.3 63.9 + - - +
375B TYR 3.3 1.0 + - - -
376B THR 3.5 6.9 + - - +
378B TRP* 4.1 9.9 - - + +
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Residues in contact with GLN 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A LEU* 4.6 13.7 - - - +
374A GLN* 4.3 18.8 - - - +
370B ALA 2.9 18.8 + - - +
371B VAL 3.1 5.3 + - - +
373B LEU* 1.3 79.1 - - - +
375B TYR* 1.3 65.0 + - + +
376B THR 3.6 0.6 + - - -
519B GLN* 4.4 6.1 + - - +
520B MET* 2.9 46.8 - - - +
523B PHE* 3.8 39.2 - - + +
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Residues in contact with TYR 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B PHE* 4.2 12.9 - - + -
371B VAL* 3.1 20.7 + - + +
372B THR 3.6 1.8 - - - +
374B GLN* 1.3 90.6 - - + +
376B THR* 1.3 57.9 + - - +
377B ASP 4.2 0.9 + - - -
386B LYS 5.3 1.9 - - - +
390B GLY* 3.8 19.0 - - - +
393B ASP* 3.7 18.4 - - + -
394B ILE* 3.5 38.1 - - + -
397B ASP* 2.4 32.9 + - - -
517B ARG* 4.3 1.1 - - - -
520B MET* 3.5 26.4 - - + +
523B PHE* 4.7 1.3 - + - -
524B TRP* 2.8 35.6 + + - -
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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