Contacts of the helix formed by residues 313 - 326 (chain B) 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 LEU 313 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A GLU 4.7 1.8 - - - +
203A TYR* 4.3 16.4 - - + +
204A ILE* 4.2 18.4 - - + -
177B SER* 2.8 26.9 + - - +
179B PHE* 4.0 18.4 - - + -
311B ASP* 3.8 1.0 + - - -
312B LYS* 1.3 93.8 - - + +
314B ASP* 1.3 71.2 + - - +
317B GLY* 3.4 19.1 + - - -
318B ALA* 4.1 10.3 - - + +
345B LEU* 4.3 15.3 - - + -
356B ILE* 3.6 45.1 - - + -
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Residues in contact with ASP 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B PRO* 4.2 17.7 - - + +
177B SER* 4.0 12.3 - - - +
180B ILE* 3.9 12.0 - - + +
187B LYS* 3.0 32.0 + - - +
311B ASP* 2.9 28.6 + - - +
312B LYS 3.7 1.4 - - - -
313B LEU* 1.3 82.8 - - - +
315B ILE* 1.3 68.8 + - - +
316B GLU* 3.1 12.7 + - - +
317B GLY 2.6 26.6 + - - +
318B ALA* 2.9 7.4 + - - -
360B TYR* 4.1 1.6 - - - -
423B ASP* 5.3 1.7 - - - +
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Residues in contact with ILE 315 (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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192B ARG* 5.4 0.9 - - - +
311B ASP* 4.4 0.6 + - - -
314B ASP* 1.3 82.3 + - - +
316B GLU* 1.3 60.8 + - + +
318B ALA 4.4 0.9 - - - +
319B ILE* 2.9 40.7 + - + +
360B TYR* 3.3 33.7 - - + +
416B MET* 3.6 44.2 - - + +
419B TYR* 3.9 5.4 - - + +
420B TYR* 3.5 28.9 - - + +
423B ASP* 3.4 39.7 - - + +
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Residues in contact with GLU 316 (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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179B PHE* 3.2 18.0 - - - +
180B ILE* 3.0 8.3 - - + +
181B GLY* 2.8 29.4 + - - -
184B ASN* 2.4 32.6 + - - -
187B LYS* 3.4 26.0 + - - +
314B ASP* 3.0 6.6 + - - +
315B ILE* 1.3 77.2 - - + +
317B GLY* 1.3 56.2 + - - +
319B ILE* 3.6 6.0 - - - +
320B HIS* 3.1 26.9 + - - -
332B ILE* 5.5 0.2 - - - +
420B TYR* 4.3 19.0 + - + -
423B ASP* 4.2 6.3 - - - +
424B LYS* 5.8 1.9 - - - +
427B ILE* 5.1 0.5 - - - +
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Residues in contact with GLY 317 (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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179B PHE* 3.7 21.2 - - - +
313B LEU* 3.4 21.4 + - - -
314B ASP 2.6 14.5 + - - -
316B GLU* 1.3 71.1 - - - +
318B ALA* 1.3 62.3 + - - -
319B ILE 3.2 2.8 + - - -
320B HIS* 3.3 17.8 + - - +
321B CYS* 4.2 1.6 + - - -
345B LEU* 3.5 14.0 - - - +
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Residues in contact with ALA 318 (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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311B ASP* 5.2 0.4 - - - +
313B LEU* 4.1 6.0 - - + +
314B ASP 2.9 12.9 + - - +
315B ILE 4.3 0.2 - - - +
317B GLY* 1.3 69.6 - - - -
319B ILE* 1.3 65.9 + - - +
321B CYS* 3.0 16.3 + - - +
322B TYR 3.2 8.1 + - - -
356B ILE* 4.3 24.7 - - + -
357B VAL* 4.3 2.4 - - + +
360B TYR* 3.7 33.4 - - + -
416B MET* 4.0 13.4 - - + +
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Residues in contact with ILE 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B ILE* 2.9 23.3 + - + +
316B GLU 3.6 4.9 - - - +
318B ALA* 1.3 75.5 - - - +
320B HIS* 1.3 83.8 + - + +
322B TYR* 3.0 26.8 + - + +
323B TYR* 3.3 34.9 + - + +
332B ILE* 4.2 8.7 - - + -
416B MET* 3.4 37.1 - - + +
417B GLU* 4.4 4.3 - - - -
420B TYR* 3.7 36.8 - - + -
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Residues in contact with HIS 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B PHE* 5.9 0.6 - - + +
316B GLU 3.1 27.5 + - - -
317B GLY 3.5 10.3 - - - +
318B ALA 3.1 0.8 - - - -
319B ILE* 1.3 79.1 - - + +
321B CYS* 1.3 61.3 + - - +
323B TYR* 3.4 9.6 + - - +
324B ASP* 3.4 5.8 + - - +
330B CYS* 3.5 4.0 - - - -
332B ILE* 3.7 16.4 - - + +
333B CYS* 3.0 36.9 - - + +
342B GLU* 4.2 13.7 - - + +
345B LEU* 3.7 24.7 - - + -
346B HIS* 3.2 28.0 + - + +
700B ZN 2.1 29.7 - - - -
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Residues in contact with CYS 321 (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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317B GLY 4.8 2.5 - - - -
318B ALA 3.0 9.1 + - - +
320B HIS* 1.3 76.8 - - - +
322B TYR* 1.3 65.7 + - - +
324B ASP* 3.0 12.8 + - - +
325B ILE* 2.8 25.8 + - - +
345B LEU* 4.5 24.7 - - - -
348B LEU* 5.2 0.7 - - - -
353B SER* 4.0 19.5 - - - +
356B ILE* 3.9 36.8 - - + -
357B VAL* 3.6 16.4 - - + -
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Residues in contact with TYR 322 (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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318B ALA 3.2 7.5 + - - +
319B ILE* 3.0 18.0 + - + +
321B CYS* 1.3 77.3 - - - +
323B TYR* 1.3 78.1 + + - +
325B ILE* 3.0 10.0 + - + +
326B ILE* 3.0 68.8 + - + +
357B VAL* 3.8 4.7 - - + +
413B LEU* 3.6 33.4 - - + -
414B LYS* 4.0 11.0 - - - +
416B MET* 3.5 33.4 - - + -
417B GLU* 3.2 42.1 + - + -
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Residues in contact with TYR 323 (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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319B ILE* 3.3 45.9 + - + +
320B HIS 3.9 5.4 - - - +
321B CYS 3.2 0.6 - - - -
322B TYR* 1.3 89.5 - + - +
324B ASP* 1.3 63.4 + - - +
326B ILE* 3.9 13.0 - - + -
327B ASN 3.2 2.8 + - - -
328B GLN* 2.9 72.4 + - + +
330B CYS* 3.9 17.7 - - + -
331B PRO* 3.6 34.8 - - + +
332B ILE* 4.2 10.4 - - + +
417B GLU* 3.8 22.3 + - + +
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Residues in contact with ASP 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B HIS 3.4 5.6 + - - +
321B CYS* 3.0 10.7 + - - +
323B TYR* 1.3 77.6 - - - +
325B ILE* 1.3 65.1 + - - +
327B ASN* 3.3 13.8 + - - +
328B GLN 4.9 2.5 - - - +
330B CYS* 5.1 0.3 - - - +
345B LEU 3.5 7.4 - - - +
346B HIS* 2.8 55.2 + - - +
348B LEU 5.4 1.4 - - - +
350B LEU* 4.2 18.7 - - + +
353B SER* 4.3 14.2 + - - +
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Residues in contact with ILE 325 (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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64B ASP* 4.5 12.0 - - + +
67B HIS* 5.2 11.5 + - + +
68B LEU* 4.5 9.0 - - + -
321B CYS 2.8 21.0 + - - +
322B TYR* 3.0 8.3 + - + +
324B ASP* 1.3 78.4 - - - +
326B ILE* 1.3 61.1 + - + +
327B ASN* 3.1 9.2 + - - +
350B LEU* 4.8 8.5 - - + +
353B SER* 3.6 14.4 - - - +
354B LEU* 3.6 56.8 - - + +
357B VAL* 3.8 18.4 - - + -
413B LEU* 4.7 18.2 - - + -
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Residues in contact with ILE 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ASP* 3.5 38.7 - - + +
322B TYR* 3.0 68.5 + - + +
323B TYR* 3.9 15.7 - - + +
325B ILE* 1.3 76.0 - - + +
327B ASN* 1.3 67.6 + - - +
328B GLN* 3.2 27.9 + - + +
413B LEU* 4.8 2.9 - - + -
417B GLU* 5.1 2.5 - - - +
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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