Contacts of the helix formed by residues 280 - 292 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A LYS 4.0 1.8 + - - -
279A HIS* 1.3 70.1 - - - +
281A ILE* 1.3 63.0 + - - +
282A SER* 3.8 10.0 + - - -
283A HIS* 3.2 43.6 + - + +
284A TYR* 3.3 24.8 - - + -
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Residues in contact with ILE 281 (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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265A ILE* 4.0 12.3 - - + +
268A PHE* 3.7 27.6 - - + -
269A ILE* 4.0 12.8 - - + +
272A ASN* 3.6 25.4 - - - +
279A HIS* 2.9 18.6 + - + +
280A ASP* 1.3 71.7 - - - +
282A SER* 1.3 59.2 + - - +
283A HIS 3.1 0.3 + - - -
284A TYR* 3.3 5.2 + - - +
285A ILE* 2.9 41.2 + - + +
348A GLN* 4.4 10.1 - - - +
352A TYR* 2.9 45.1 - - + +
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Residues in contact with SER 282 (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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280A ASP* 3.3 8.7 + - - -
281A ILE* 1.3 81.9 - - - +
283A HIS* 1.3 59.6 + - - +
285A ILE* 3.9 6.8 - - - +
286A GLN* 3.3 25.6 + - - +
352A TYR* 4.7 11.5 + - - -
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Residues in contact with HIS 283 (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 GLN* 6.0 0.9 - - + +
195A GLU* 2.7 41.0 + - + -
280A ASP* 3.2 38.0 + - + +
281A ILE 3.1 0.6 - - - -
282A SER* 1.3 75.1 - - - +
284A TYR* 1.3 87.6 + + - +
286A GLN* 3.3 4.9 + - - +
287A TYR* 2.9 34.0 + + + +
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Residues in contact with TYR 284 (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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180A TYR* 2.9 33.4 - + - -
184A LEU* 4.2 2.2 - - + -
191A THR* 4.6 1.6 - - + +
195A GLU* 3.6 9.8 + - - -
264A ILE* 5.6 0.7 - - + -
265A ILE* 3.6 21.5 - - + -
268A PHE* 3.4 46.3 - + + -
279A HIS* 5.2 3.8 - - + -
280A ASP* 3.3 30.9 + - + -
281A ILE* 3.3 5.7 + - - +
283A HIS* 1.3 88.2 + + - +
285A ILE* 1.3 70.2 + - - +
287A TYR* 3.2 6.5 + + - +
288A LEU* 3.1 25.5 + - + +
329A PHE* 3.1 34.8 - - - -
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Residues in contact with ILE 285 (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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265A ILE* 3.5 24.7 - - + +
281A ILE* 2.9 37.0 + - + +
282A SER* 3.9 7.2 - - - +
284A TYR* 1.3 77.7 - - - +
286A GLN* 1.3 65.5 + - - +
288A LEU* 3.2 11.7 + - - +
289A ILE* 3.3 23.0 + - + +
295A LEU* 4.6 11.3 - - + +
298A ILE* 5.6 5.8 - - + -
349A LEU* 5.0 2.7 - - + -
352A TYR* 3.3 51.4 - - + -
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Residues in contact with GLN 286 (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 SER 3.3 16.3 + - - +
283A HIS* 3.7 3.8 - - - +
284A TYR 3.2 0.2 - - - -
285A ILE* 1.3 79.8 - - + +
287A TYR* 1.3 68.5 + - - +
289A ILE* 2.7 28.2 + - + +
290A GLN* 3.0 36.3 + - + +
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Residues in contact with TYR 287 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A TYR* 2.8 26.0 + - - -
180A TYR* 3.7 33.0 - + - -
195A GLU* 3.7 38.1 - - + -
198A PHE* 2.8 29.3 + - - +
199A LYS 4.1 11.2 - - - -
283A HIS* 2.9 29.5 + + + +
284A TYR* 3.2 8.5 + + - +
286A GLN* 1.3 71.8 - - - +
288A LEU* 1.3 67.6 + - + +
290A GLN* 3.7 11.4 + - - +
291A LEU* 3.2 44.2 + - + +
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Residues in contact with LEU 288 (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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180A TYR* 5.7 2.0 - - + -
261A MET* 3.5 46.2 - - + +
262A VAL* 5.0 3.4 - - + +
265A ILE* 3.3 33.9 - - + -
284A TYR* 3.1 11.7 + - + +
285A ILE* 3.4 7.2 - - - +
286A GLN 2.9 0.8 - - - -
287A TYR* 1.3 85.9 - - + +
289A ILE* 1.3 66.0 + - - +
291A LEU* 3.3 2.6 + - + -
292A GLY 3.1 5.4 + - - -
293A TYR* 2.9 47.9 + - + +
295A LEU* 4.6 16.2 - - + -
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Residues in contact with ILE 289 (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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285A ILE* 3.3 19.0 + - + +
286A GLN* 2.7 23.8 + - + +
288A LEU* 1.3 73.2 - - - +
290A GLN* 1.3 64.1 + - + +
292A GLY* 2.8 22.2 + - - -
293A TYR 4.5 7.7 - - - +
294A PRO 5.9 0.7 - - - +
295A LEU* 3.9 19.7 - - + +
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Residues in contact with GLN 290 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A LYS* 2.5 37.0 + - - +
200A ASP* 4.0 10.8 - - + +
201A ARG* 2.9 22.8 + - - +
286A GLN* 3.0 39.4 + - + +
287A TYR* 3.8 14.3 - - - +
289A ILE* 1.3 81.3 - - + +
291A LEU* 1.3 62.8 + - - +
292A GLY* 2.9 1.7 + - - -
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Residues in contact with LEU 291 (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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169A PHE* 3.1 28.1 - - - -
173A LEU* 3.2 4.9 - - + +
176A TYR* 3.2 36.8 - - + -
198A PHE* 3.6 25.8 - - + +
200A ASP* 4.3 14.6 - - - +
201A ARG* 3.5 7.8 - - - +
204A LEU* 4.2 15.7 - - + +
261A MET* 5.7 0.4 - - - -
287A TYR* 3.2 34.9 + - + +
288A LEU* 3.6 11.7 - - + +
290A GLN* 1.3 78.5 - - - +
292A GLY* 1.3 58.3 + - - +
293A TYR* 3.6 22.0 - - + -
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Residues in contact with GLY 292 (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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169A PHE* 4.4 6.7 - - - -
173A LEU* 3.5 15.9 - - - +
201A ARG* 4.5 12.2 + - - -
289A ILE 2.8 14.9 + - - -
290A GLN 2.9 2.4 + - - -
291A LEU* 1.3 80.6 - - - +
293A TYR* 1.3 69.0 + - - +
294A PRO* 3.3 5.2 - - - +
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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