Contacts of the helix formed by residues 314 - 326 (chain A) in PDB entry 2XAR
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 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A PRO* 4.1 25.6 - - + +
177A SER* 4.1 11.0 - - - -
180A ILE* 4.0 5.9 - - + +
187A LYS* 3.1 30.2 + - - +
311A ASP* 3.0 28.4 + - - +
312A LYS 3.6 1.4 - - - -
313A LEU* 1.3 79.6 - - - +
315A ILE* 1.3 69.0 + - - +
316A GLU* 3.1 12.7 + - - +
317A GLY 2.6 26.4 + - - +
318A ALA* 2.8 9.6 + - - -
360A TYR* 4.2 0.9 - - - -
423A ASP* 5.2 1.6 - - - +
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Residues in contact with ILE 315 (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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192A ARG* 5.3 1.8 - - - +
311A ASP* 4.4 0.2 + - - -
314A ASP* 1.3 79.5 + - - +
316A GLU* 1.3 60.0 + - + +
318A ALA 4.4 1.1 - - - +
319A ILE* 2.8 39.7 + - + +
360A TYR* 3.4 34.5 - - + +
416A MET* 3.6 36.3 - - + +
419A TYR* 3.8 15.9 - - + +
420A TYR* 3.5 27.4 - - + +
423A ASP* 3.4 39.9 - - + +
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Residues in contact with GLU 316 (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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179A PHE* 3.2 18.5 - - - +
180A ILE* 3.0 8.8 - - + +
181A GLY 3.0 27.5 + - - -
184A ASN* 2.6 29.8 + - - -
187A LYS* 3.2 29.4 + - - +
314A ASP* 3.0 6.6 + - - +
315A ILE* 1.3 76.5 - - + +
317A GLY* 1.3 57.4 + - - +
319A ILE* 3.7 6.4 - - - +
320A HIS* 3.1 25.5 + - - -
420A TYR* 4.4 18.1 + - + -
423A ASP* 3.8 8.3 - - - +
424A LYS* 5.6 1.9 - - - +
427A ILE* 4.7 1.2 - - - +
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Residues in contact with GLY 317 (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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179A PHE* 3.7 21.9 - - - +
313A LEU* 3.4 19.5 + - - -
314A ASP 2.6 14.6 + - - -
316A GLU* 1.3 73.7 - - - +
318A ALA* 1.3 62.4 + - - -
319A ILE 3.3 1.3 + - - -
320A HIS* 3.3 11.1 + - - +
321A CYS* 4.2 1.2 + - - -
345A LEU* 3.3 22.1 - - - +
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Residues in contact with ALA 318 (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 ASP* 5.2 0.7 - - - +
313A LEU* 4.1 6.0 - - + +
314A ASP 2.8 13.1 + - - +
315A ILE 4.3 0.7 - - - +
317A GLY* 1.3 70.0 - - - -
319A ILE* 1.3 66.9 + - - +
321A CYS* 2.9 16.5 + - - +
322A TYR 3.1 9.0 + - - -
356A ILE* 4.1 25.4 - - + -
357A VAL* 4.3 2.0 - - + +
360A TYR* 3.8 32.8 - - + -
416A MET* 4.0 13.3 - - + +
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Residues in contact with ILE 319 (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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315A ILE* 2.8 22.8 + - + +
316A GLU 3.7 3.8 - - - +
318A ALA* 1.3 76.7 - - - +
320A HIS* 1.3 83.1 + - + +
322A TYR* 3.0 26.5 + - + +
323A TYR* 3.3 33.9 + - + +
332A ILE* 4.0 8.7 - - + -
416A MET* 3.3 39.1 - - + +
417A GLU* 4.4 3.6 - - - -
420A TYR* 3.6 38.4 - - + -
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Residues in contact with HIS 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A GLU 3.1 27.9 + - - -
317A GLY* 3.3 9.8 + - - +
318A ALA 3.1 1.2 + - - -
319A ILE* 1.3 80.5 - - + +
321A CYS* 1.3 60.9 + - - +
323A TYR* 3.5 2.6 + - - +
324A ASP* 3.5 12.1 + - - +
330A CYS* 3.5 4.6 - - - -
332A ILE* 3.7 30.5 - - + +
333A CYS* 3.2 12.7 - - - -
342A GLU* 3.9 21.2 + - - -
345A LEU* 4.2 15.0 - - + -
346A HIS* 3.1 33.9 + + + +
700A ZN 2.1 31.5 - - - -
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Residues in contact with CYS 321 (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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317A GLY 4.8 2.7 - - - -
318A ALA* 2.9 11.4 + - - +
320A HIS* 1.3 76.6 - - - +
322A TYR* 1.3 65.4 + - - +
324A ASP* 3.1 11.7 + - - +
325A ILE* 2.9 27.1 + - - +
345A LEU* 4.2 24.5 - - - -
348A LEU* 4.9 0.7 - - - -
353A SER* 4.1 18.6 - - - +
356A ILE* 3.7 37.2 - - + -
357A VAL* 3.7 15.3 - - + -
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Residues in contact with TYR 322 (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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318A ALA 3.1 4.6 + - - -
319A ILE* 3.0 13.5 + - + +
321A CYS* 1.3 75.4 - - - +
323A TYR* 1.3 76.7 + + - +
325A ILE* 3.0 12.9 + - + +
326A ILE* 3.0 68.6 + - + +
357A VAL* 3.7 4.6 - - + +
413A LEU* 3.5 34.1 - - + -
414A LYS* 4.0 11.2 - - - +
416A MET* 3.3 43.5 - - + -
417A GLU* 3.3 41.3 + - + -
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Residues in contact with TYR 323 (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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319A ILE* 3.3 44.8 + - + +
320A HIS 3.5 2.9 + - - +
321A CYS 3.2 1.0 - - - -
322A TYR* 1.3 93.1 - + - +
324A ASP* 1.3 62.6 + - - +
326A ILE* 3.8 7.1 - - + -
327A ASN 3.2 2.3 + - - -
328A GLN* 2.9 77.2 + - + +
330A CYS* 3.9 17.9 - - + -
331A PRO* 3.6 32.2 - - + +
332A ILE* 3.8 16.2 - - + +
417A GLU* 3.5 24.6 + - + +
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Residues in contact with ASP 324 (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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320A HIS 3.5 6.0 + - - +
321A CYS* 3.1 10.0 + - - +
323A TYR* 1.3 75.7 - - - +
325A ILE* 1.3 66.5 + - - +
327A ASN* 3.3 13.7 + - - +
328A GLN 5.0 2.3 - - - +
330A CYS* 5.1 0.9 - - - +
345A LEU 3.9 5.4 - - - +
346A HIS* 2.8 54.7 + - - +
348A LEU 5.2 1.9 - - - +
350A LEU* 4.0 18.9 - - + +
353A SER* 4.2 15.4 + - - +
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Residues in contact with ILE 325 (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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64A ASP* 4.5 10.3 - - + +
67A HIS* 5.2 10.7 + - + -
68A LEU* 4.7 8.3 - - + -
321A CYS 2.9 18.8 + - - +
322A TYR* 3.0 8.5 + - + +
324A ASP* 1.3 74.3 - - - +
326A ILE* 1.3 65.5 + - + +
327A ASN* 3.0 13.0 + - - +
350A LEU* 4.6 8.3 - - + +
353A SER* 3.5 16.2 - - - -
354A LEU* 3.4 59.0 - - + +
357A VAL* 3.8 18.4 - - + -
413A LEU* 4.7 12.6 - - + -
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Residues in contact with ILE 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASP* 3.5 39.8 - - + +
322A TYR* 3.0 65.2 + - + +
323A TYR* 3.9 14.6 - - + +
325A ILE* 1.3 73.7 - - + +
327A ASN* 1.3 69.4 + - - +
328A GLN* 3.2 30.2 + - + +
413A LEU* 4.5 6.7 - - + -
417A GLU* 5.1 2.7 - - - +
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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