Contacts of the helix formed by residues 363 - 376 (chain A) in PDB entry 1XV9
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 ASP 363 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A HIS* 4.0 2.5 - - - -
361A GLN 3.7 2.2 + - - -
362A MET* 1.3 75.0 - - - +
364A LYS* 1.3 59.5 + - - +
365A THR* 3.1 11.5 + - - +
366A GLU* 2.8 43.1 + - - +
367A LEU* 2.9 24.8 + - - +
403A TYR* 2.9 28.4 + - - +
407A LYS* 5.3 0.7 + - - -
408A TYR* 2.8 27.4 + - - +
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Residues in contact with LYS 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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236A LEU* 3.6 16.8 - - + +
239A GLU* 3.5 20.9 - - + +
240A LEU* 4.3 16.3 - - + +
243A GLU* 3.1 33.5 + - - +
315A HIS* 3.4 28.4 + - + +
363A ASP* 1.3 73.5 - - - +
365A THR* 1.3 55.8 + - - +
367A LEU* 3.6 6.7 - - + +
368A GLY 3.0 19.6 + - - -
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Residues in contact with THR 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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232A VAL* 3.1 32.4 - - + +
235A ILE* 4.0 3.0 - - - +
236A LEU* 3.1 42.7 - - - +
363A ASP* 3.0 9.9 + - - +
364A LYS* 1.3 74.8 - - - +
366A GLU* 1.3 69.2 + - - +
368A GLY* 3.3 2.4 + - - -
369A CYS* 3.0 26.9 + - - -
403A TYR* 3.2 33.0 + - + -
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Residues in contact with GLU 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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362A MET* 2.9 31.7 - - + +
363A ASP* 2.8 25.7 + - - +
365A THR* 1.3 73.1 - - - +
367A LEU* 1.3 68.5 + - - +
369A CYS* 3.3 4.0 + - - +
370A LEU* 3.1 22.5 + - - +
400A LEU* 4.4 11.7 - - + +
403A TYR* 4.2 11.2 - - + -
404A CYS* 4.2 3.7 - - - -
408A TYR* 3.4 10.9 - - - -
414A ARG* 2.6 49.0 + - - -
418A LEU* 3.7 21.7 - - + +
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Residues in contact with LEU 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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239A GLU* 3.4 18.8 - - - +
311A ALA* 3.6 18.6 - - + +
312A SER* 4.8 11.4 - - - +
315A HIS* 3.3 38.4 - - + +
357A MET* 4.7 3.6 - - + -
362A MET* 3.1 34.8 - - + +
363A ASP 2.9 9.5 + - - +
364A LYS* 3.6 11.0 - - + +
366A GLU* 1.3 76.0 - - - +
368A GLY* 1.3 53.5 + - - +
370A LEU* 2.8 29.4 + - + +
371A ARG* 2.8 23.5 + - + +
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Residues in contact with GLY 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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235A ILE* 3.5 24.5 - - - +
239A GLU* 3.0 23.4 + - - -
282A TRP* 4.2 3.9 - - - -
364A LYS 3.0 6.9 + - - -
365A THR 3.3 0.6 + - - -
366A GLU 3.3 0.4 - - - -
367A LEU* 1.3 79.2 - - - +
369A CYS* 1.3 55.4 + - - +
371A ARG* 3.4 3.5 + - - +
372A ALA* 2.9 30.3 + - - +
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Residues in contact with CYS 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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232A VAL* 5.1 5.6 - - - -
235A ILE* 3.8 21.0 - - - +
365A THR* 3.0 25.4 + - - -
366A GLU 3.7 3.1 - - - +
367A LEU 3.2 0.2 - - - -
368A GLY* 1.3 74.0 - - - +
370A LEU* 1.3 59.0 + - - +
372A ALA* 3.4 7.1 - - - +
373A ILE* 2.9 34.3 + - - +
396A VAL* 3.8 7.7 - - + +
399A SER* 5.2 0.7 - - - -
400A LEU* 3.3 54.7 - - + -
403A TYR* 5.8 0.4 - - - -
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Residues in contact with LEU 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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311A ALA* 6.4 2.7 - - + -
362A MET* 5.1 11.7 - - - -
366A GLU 3.1 11.9 + - - +
367A LEU* 2.8 13.3 + - + +
369A CYS* 1.3 75.9 - - - +
371A ARG* 1.3 62.5 + - + +
372A ALA 2.9 5.7 + - - -
373A ILE* 3.1 34.3 + - + +
374A VAL* 3.1 18.5 + - + +
400A LEU* 3.9 14.1 - - + -
418A LEU* 3.3 31.4 - - + +
419A LEU* 4.0 12.8 - - + -
421A ARG* 5.4 4.9 - - + -
422A LEU* 4.3 21.0 - - + +
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Residues in contact with ARG 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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239A GLU* 3.9 14.0 + - - +
242A VAL* 4.4 12.5 - - - +
279A LEU* 3.4 27.3 - - - +
282A TRP* 3.0 65.1 - - + +
308A LEU* 3.4 57.7 + - - +
309A LEU* 3.9 5.9 - - - +
311A ALA* 4.7 8.3 - - + +
312A SER* 3.8 26.9 + - - +
367A LEU* 2.8 37.3 + - + +
368A GLY 3.9 2.0 - - - +
370A LEU* 1.3 71.8 - - + +
372A ALA* 1.3 58.8 + - - +
374A VAL* 4.1 3.6 - - - -
375A LEU 3.5 4.3 + - - -
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Residues in contact with ALA 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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235A ILE* 5.4 4.3 - - + -
282A TRP* 3.7 11.9 - - + -
286A ILE* 4.5 19.1 - - + -
368A GLY 2.9 17.7 + - - +
369A CYS* 3.4 8.5 - - - +
370A LEU 2.9 0.2 - - - -
371A ARG* 1.3 76.1 - - - +
373A ILE* 1.3 57.4 + - - +
374A VAL 3.1 1.6 - - - -
375A LEU* 2.7 31.6 + - - +
376A PHE* 2.9 13.3 + - + -
396A VAL* 4.7 14.4 - - + -
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Residues in contact with ILE 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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369A CYS 2.9 28.5 + - - +
370A LEU* 3.1 25.3 + - + +
372A ALA* 1.3 75.6 - - - +
374A VAL* 1.3 62.2 + - + +
376A PHE* 3.1 28.7 - - - +
377A ASN* 3.9 1.4 + - - -
393A ARG* 4.0 24.8 - - + +
396A VAL* 3.7 17.3 - - + -
397A TYR* 4.0 28.3 - - + +
400A LEU* 4.0 14.8 - - + -
419A LEU* 4.2 6.5 - - + -
422A LEU* 5.2 12.6 - - + -
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Residues in contact with VAL 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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300A LEU 5.0 2.8 - - - +
303A ALA 5.3 2.4 - - - +
304A GLY* 4.1 18.1 - - - +
307A GLU* 4.2 19.5 - - + +
308A LEU* 3.3 28.5 - - + -
370A LEU 3.1 18.7 + - - +
371A ARG* 4.0 2.2 - - - +
372A ALA 3.1 0.8 - - - -
373A ILE* 1.3 74.0 - - - +
375A LEU* 1.3 67.4 + - - +
376A PHE 3.2 0.5 + - - -
377A ASN* 3.5 17.7 + - - +
422A LEU* 4.9 12.8 - - + -
425A LEU* 4.2 24.9 - - + -
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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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282A TRP* 3.5 28.3 - - + -
283A ALA* 4.2 9.4 - - - -
286A ILE* 4.4 15.5 - - + -
289A PHE* 4.0 31.0 - - + -
300A LEU* 3.1 45.1 - - - +
301A LEU* 3.4 33.0 - - + -
308A LEU* 4.3 7.0 - - + -
371A ARG 3.5 9.0 + - - +
372A ALA 2.7 17.6 + - - +
374A VAL* 1.3 77.6 - - - +
376A PHE* 1.3 61.5 + - + -
377A ASN 3.3 0.3 + - - -
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Residues in contact with PHE 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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230A MET* 4.2 14.8 - - + -
286A ILE* 4.2 20.2 - - + -
287A PRO 4.1 14.1 - - - -
289A PHE* 4.4 14.1 - + + -
292A LEU* 4.3 13.5 - - + -
300A LEU* 4.6 3.4 - - + -
372A ALA* 2.9 18.2 + - + +
373A ILE* 3.1 15.0 + - - +
374A VAL 3.1 0.4 - - - -
375A LEU* 1.3 84.4 - - + +
377A ASN* 1.3 58.6 + - - +
378A PRO* 3.1 13.1 - - - +
389A VAL* 4.0 15.9 - - + +
392A LEU* 3.6 46.9 - - + -
393A ARG* 3.2 30.5 - - + -
396A VAL* 4.3 13.5 - - + -
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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