Contacts of the helix formed by residues 280 - 292 (chain B) in PDB entry 1XAI
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 280 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278B LYS 3.9 2.2 + - - -
279B HIS* 1.3 67.9 - - - +
281B ILE* 1.3 66.1 + - - +
282B SER* 3.6 10.2 + - - -
283B HIS* 3.0 46.4 + - + +
284B TYR* 3.2 25.3 - - + -
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Residues in contact with ILE 281 (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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265B ILE* 4.1 11.2 - - + +
268B PHE* 3.7 28.0 - - + -
269B ILE* 4.0 12.1 - - + +
272B ASN* 3.6 24.7 - - - +
279B HIS* 2.9 18.9 + - + +
280B ASP* 1.3 72.9 - - - +
282B SER* 1.3 63.6 + - - +
283B HIS 3.1 0.5 + - - -
284B TYR* 3.3 4.5 + - - +
285B ILE* 2.9 35.6 + - + +
348B GLN* 4.4 9.2 - - - +
352B TYR* 2.9 45.5 - - + +
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Residues in contact with SER 282 (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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280B ASP* 3.3 8.0 + - - -
281B ILE* 1.3 79.6 - - - +
283B HIS* 1.3 59.5 + - - +
285B ILE* 4.0 7.5 - - - +
286B GLN* 3.3 26.0 + - - +
352B TYR* 4.8 11.3 + - - -
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Residues in contact with HIS 283 (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 GLN* 6.2 0.4 - - + -
195B GLU* 2.7 42.6 + - - -
280B ASP* 3.0 38.0 + - + +
281B ILE 3.1 0.2 - - - -
282B SER* 1.3 74.7 - - - +
284B TYR* 1.3 85.2 + + - +
286B GLN* 3.3 5.9 + - - +
287B TYR* 2.9 35.2 + + + +
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Residues in contact with TYR 284 (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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180B TYR* 2.9 33.0 - + - -
184B LEU* 4.1 1.5 - - + +
191B THR* 4.5 1.8 - - + +
195B GLU* 3.6 10.7 + - - -
264B ILE* 5.7 0.7 - - + -
265B ILE* 3.6 21.1 - - + -
268B PHE* 3.4 46.7 - + + -
279B HIS* 5.2 3.6 - - + -
280B ASP* 3.2 30.2 + - + -
281B ILE* 3.3 6.3 + - + +
283B HIS* 1.3 89.9 - + - +
285B ILE* 1.3 69.3 + - - +
287B TYR* 3.2 6.8 + + - +
288B LEU* 3.1 26.3 + - + +
329B PHE* 3.1 33.3 - - - -
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Residues in contact with ILE 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ILE* 3.5 24.0 - - + +
281B ILE* 2.9 32.9 + - + +
282B SER* 4.0 6.5 - - - +
284B TYR* 1.3 77.9 - - - +
286B GLN* 1.3 66.5 + - - +
288B LEU* 3.2 10.9 + - - +
289B ILE* 3.3 23.3 + - + +
295B LEU* 4.5 11.7 - - + +
298B ILE* 5.3 7.0 - - + -
349B LEU* 4.9 2.9 - - + -
352B TYR* 3.4 50.3 - - + -
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Residues in contact with GLN 286 (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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282B SER 3.3 17.1 + - - +
283B HIS* 3.7 4.3 - - - +
284B TYR 3.2 0.6 - - - -
285B ILE* 1.3 80.8 - - - +
287B TYR* 1.3 55.8 + - - +
289B ILE* 2.7 38.0 + - + +
290B GLN* 3.0 36.3 + - + +
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Residues in contact with TYR 287 (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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176B TYR* 2.7 26.7 + + - -
180B TYR* 3.7 31.6 - + - -
195B GLU* 3.7 39.8 - - + -
198B PHE* 2.8 29.2 + - - +
199B LYS* 4.2 11.0 - - - -
283B HIS* 2.9 30.1 + + + +
284B TYR* 3.2 8.0 + + - +
286B GLN* 1.3 71.7 - - - +
288B LEU* 1.3 67.3 + - + +
290B GLN* 3.8 11.5 - - - +
291B LEU* 3.1 49.4 + - + +
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Residues in contact with LEU 288 (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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180B TYR* 5.7 1.8 - - + -
261B MET* 3.2 50.3 - - + +
262B VAL* 5.0 3.8 - - + +
265B ILE* 3.3 32.8 - - + -
284B TYR* 3.1 14.9 + - + +
285B ILE* 3.5 6.7 - - - +
286B GLN 3.0 1.4 - - - -
287B TYR* 1.3 80.4 - - + +
289B ILE* 1.3 66.8 + - - +
291B LEU* 3.3 5.9 + - + -
292B GLY 3.1 5.4 + - - -
293B TYR* 2.9 45.7 + - + -
295B LEU* 4.6 18.4 - - + -
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Residues in contact with ILE 289 (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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285B ILE* 3.3 22.4 + - + +
286B GLN* 2.7 22.2 + - + +
288B LEU* 1.3 72.3 - - - +
290B GLN* 1.3 63.4 + - + +
292B GLY* 2.8 21.7 + - - -
293B TYR 4.5 8.7 - - - +
294B PRO 6.0 0.2 - - - +
295B LEU* 4.0 17.7 - - + -
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Residues in contact with GLN 290 (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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199B LYS* 2.5 36.2 + - - +
200B ASP* 4.0 10.6 - - + +
201B ARG* 2.9 22.4 + - - +
286B GLN* 3.0 38.4 + - + +
287B TYR* 3.8 16.0 - - - +
289B ILE* 1.3 81.4 - - + +
291B LEU* 1.3 63.3 + - - +
292B GLY* 2.9 1.6 + - - -
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Residues in contact with LEU 291 (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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169B PHE* 3.1 29.5 - - - -
173B LEU* 3.3 3.7 - - + +
176B TYR* 3.4 29.2 - - + -
198B PHE* 3.6 27.4 - - + +
200B ASP* 4.3 13.5 - - - +
201B ARG* 3.5 8.8 - - - +
204B LEU* 4.2 16.9 - - + +
261B MET* 5.5 0.4 - - - -
287B TYR* 3.1 39.6 + - + +
288B LEU* 3.3 10.7 + - + +
290B GLN* 1.3 77.6 - - - +
292B GLY* 1.3 56.5 + - - +
293B TYR* 3.6 24.7 - - + -
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Residues in contact with GLY 292 (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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169B PHE* 4.4 5.9 - - - -
173B LEU* 3.6 13.0 - - - +
201B ARG* 4.5 13.0 + - - -
288B LEU 3.1 0.6 + - - -
289B ILE 2.8 15.8 + - - -
290B GLN 2.9 2.4 + - - -
291B LEU* 1.3 80.4 - - - +
293B TYR* 1.3 67.6 + - - +
294B PRO* 3.3 7.3 - - - +
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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