Contacts of the helix formed by residues 360 - 373 (chain A) in PDB entry 1XI1
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 PHE 360 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A PHE* 3.5 34.3 - + - -
211A PHE* 4.7 2.0 - + - -
258A MET* 3.3 60.1 + - + +
263A LEU* 3.6 23.3 - - + -
358A GLY 3.4 0.4 - - - -
359A LEU* 1.3 84.9 - - + +
361A LYS* 1.3 60.4 + - - +
362A ASP 3.4 2.7 - - - -
363A PHE* 3.3 6.0 + + + +
364A ILE* 2.9 44.3 + - + +
389A LEU* 3.8 13.5 - - + -
393A PHE* 4.0 21.8 - + - -
429A MET* 3.9 23.3 - - + -
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Residues in contact with LYS 361 (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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258A MET 4.9 0.8 + - - -
259A TYR* 3.1 59.3 + - + +
260A SER* 4.3 7.2 - - - +
357A THR* 3.0 39.3 + - - +
358A GLY* 4.1 12.0 + - - +
359A LEU 3.8 0.8 - - - -
360A PHE* 1.3 76.5 - - - +
362A ASP* 1.3 55.1 + - - +
364A ILE* 3.6 0.4 - - - +
365A ASP* 2.7 47.0 + - - +
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Residues in contact with ASP 362 (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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201A ILE* 4.1 20.7 - - + +
202A ILE* 6.3 0.4 - - + -
358A GLY 5.2 1.2 + - - -
359A LEU 5.4 0.8 + - - +
360A PHE 3.4 0.6 - - - -
361A LYS* 1.3 78.2 - - - +
363A PHE* 1.3 62.6 + - - +
365A ASP* 3.8 9.1 - - - +
366A LYS* 3.0 27.2 + - - +
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Residues in contact with PHE 363 (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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194A SER* 3.8 9.9 - - - -
197A GLY 4.0 2.0 - - - -
198A PHE* 3.7 51.8 - + + -
201A ILE* 3.5 21.8 - - + +
359A LEU 5.6 0.4 + - - -
360A PHE* 3.3 8.8 + + - +
362A ASP* 1.3 77.5 - - - +
364A ILE* 1.3 74.3 + - + +
366A LYS* 3.8 0.2 - - - +
367A TRP* 3.2 51.7 + + - +
385A MET* 3.4 37.5 - - + -
386A LEU* 4.4 10.8 - - + -
389A LEU* 3.8 24.2 - - + -
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Residues in contact with ILE 364 (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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255A PRO* 3.4 33.4 - - + +
258A MET* 4.1 7.4 - - + -
259A TYR* 3.5 34.3 - - + +
360A PHE* 2.9 37.2 + - + +
363A PHE* 1.3 89.1 - - + +
365A ASP* 1.3 59.4 + - - +
368A THR* 2.7 48.7 + - - +
386A LEU* 4.0 15.3 - - + -
480A LEU* 4.9 9.6 - - + -
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Residues in contact with ASP 365 (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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259A TYR* 2.7 31.1 + - - -
361A LYS* 2.7 33.5 + - - +
362A ASP* 3.8 11.1 + - - +
364A ILE* 1.3 72.0 - - - +
366A LYS* 1.3 65.1 + - - +
368A THR* 4.0 3.2 - - - -
369A TYR* 3.0 25.8 + - - +
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Residues in contact with LYS 366 (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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197A GLY* 5.8 0.9 - - - -
201A ILE* 3.7 25.1 - - + -
362A ASP 3.0 17.6 + - - +
363A PHE 3.8 2.9 - - - +
365A ASP* 1.3 79.0 - - - +
367A TRP* 1.3 87.0 + - + +
369A TYR* 3.4 5.8 + - - +
370A ILE* 3.2 48.9 + - + +
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Residues in contact with TRP 367 (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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183A GLN* 5.2 9.6 - - + -
185A LEU* 4.5 15.9 - - + -
197A GLY* 5.4 4.4 - - - -
201A ILE* 5.0 0.4 - - - +
363A PHE* 3.2 54.8 + + - +
366A LYS* 1.3 103.0 - - + +
368A THR* 1.3 59.7 + - - +
369A TYR 3.2 1.8 - - - -
370A ILE* 3.6 30.7 - - + -
371A LYS* 3.0 25.5 + - - +
378A ILE* 5.4 2.5 - - + -
381A LEU* 4.9 3.8 - - + -
382A ALA* 3.7 33.1 - - + +
385A MET* 3.8 33.9 - - + +
386A LEU* 3.8 23.7 - - + +
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Residues in contact with THR 368 (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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364A ILE* 2.7 38.9 + - - +
365A ASP* 4.0 3.6 - - - -
367A TRP* 1.3 75.6 - - - +
369A TYR* 1.3 61.6 + - - +
371A LYS* 3.5 11.5 - - - +
372A THR* 2.9 41.1 + - - +
386A LEU* 3.8 15.6 - - - +
480A LEU* 6.1 0.9 - - - +
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Residues in contact with TYR 369 (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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365A ASP 3.0 18.6 + - - +
366A LYS* 3.5 7.0 - - - +
368A THR* 1.3 75.9 - - - +
370A ILE* 1.3 61.8 + - + +
372A THR* 3.0 6.7 + - - -
373A THR* 2.8 66.3 + - + +
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Residues in contact with ILE 370 (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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366A LYS* 3.2 37.6 + - + +
367A TRP* 3.6 35.9 - - + +
369A TYR* 1.3 82.8 - - + +
371A LYS* 1.3 61.8 + - - +
373A THR* 3.6 7.6 - - - +
374A SER* 2.7 43.0 + - - +
378A ILE* 3.8 17.7 - - + -
382A ALA* 4.2 9.4 - - + -
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Residues in contact with LYS 371 (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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367A TRP 3.0 20.4 + - - +
368A THR* 3.5 12.1 - - - +
369A TYR 3.1 0.2 - - - -
370A ILE* 1.3 80.9 - - - +
372A THR* 1.3 69.5 + - - +
373A THR 3.5 0.3 + - - -
374A SER 3.6 5.4 + - - +
379A LYS* 3.6 36.2 - - + +
382A ALA* 3.7 12.3 - - + +
383A LYS* 3.4 41.8 - - + +
386A LEU* 4.6 14.5 - - + +
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Residues in contact with THR 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A THR* 2.9 23.3 + - - +
369A TYR* 3.0 6.8 + - - -
371A LYS* 1.3 84.2 - - - +
373A THR* 1.3 63.8 + - + +
374A SER 3.4 2.7 + - - +
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Residues in contact with THR 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A TYR* 2.8 64.7 + - + +
370A ILE* 3.6 10.9 + - - +
372A THR* 1.3 79.3 - - + +
374A SER* 1.3 59.7 + - - +
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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