Contacts of the helix formed by residues 282 - 293 (chain A) in PDB entry 2P18
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 ASN 282 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275A VAL* 3.8 6.3 - - - -
281A GLY* 1.3 74.1 - - - +
283A ALA* 1.3 59.6 + - - +
284A HIS* 3.4 16.4 + - - +
285A ALA* 3.0 25.4 + - - +
286A LEU* 2.8 26.0 + - - +
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Residues in contact with ALA 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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183A CYS* 4.0 8.5 - - + -
187A GLU* 5.7 4.7 - - - +
269A VAL* 3.5 32.5 - - + +
275A VAL* 3.7 20.4 - - + +
282A ASN* 1.3 76.0 - - - +
284A HIS* 1.3 59.8 + - + +
286A LEU* 3.3 1.2 + - - +
287A MET* 2.9 26.7 + - - +
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Residues in contact with HIS 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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179A GLU* 3.7 13.9 - - + +
180A LYS* 3.8 43.0 + - + +
183A CYS* 3.7 25.0 - - + +
282A ASN* 3.3 15.1 + - - +
283A ALA* 1.3 79.5 - - + +
285A ALA* 1.3 62.9 + - - +
287A MET* 3.2 3.6 + - - +
288A MET* 3.0 30.0 + - + +
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Residues in contact with ALA 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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280A GLN 3.3 20.8 - - - +
281A GLY* 4.0 2.7 - - - -
282A ASN* 3.0 25.5 + - - +
284A HIS* 1.3 74.1 - - - +
286A LEU* 1.3 57.3 + - - +
288A MET* 3.2 23.4 + - + +
289A TYR* 2.8 28.6 + - - +
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Residues in contact with LEU 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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269A VAL* 3.8 22.9 - - + -
274A PHE* 4.2 6.7 - - + -
275A VAL* 3.8 34.8 - - + +
278A MET* 3.6 44.6 - - + -
280A GLN* 3.9 18.5 + - + +
281A GLY 4.8 2.2 - - - +
282A ASN 2.8 16.1 + - - +
283A ALA* 3.6 5.2 - - - +
285A ALA* 1.3 75.0 - - - +
287A MET* 1.3 60.9 + - - +
289A TYR* 3.2 5.8 + - + +
290A LEU* 2.9 37.6 + - + +
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Residues in contact with MET 287 (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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171A ILE* 4.0 12.6 - - - -
174A PHE* 4.3 7.0 - - + -
179A GLU* 3.8 26.0 - - + +
182A MET* 4.0 9.4 - - + -
183A CYS* 3.6 24.0 - - - +
186A MET* 3.9 17.0 - - + -
266A PHE* 3.7 47.1 - - + +
269A VAL* 4.0 14.8 - - + +
283A ALA 2.9 17.3 + - - +
284A HIS 3.2 4.9 + - - +
286A LEU* 1.3 75.8 - - - +
288A MET* 1.3 57.8 + - - +
290A LEU* 3.3 3.0 + - - +
291A TYR* 2.9 31.8 + - - +
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Residues in contact with MET 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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174A PHE* 6.1 0.2 - - - -
179A GLU* 3.6 35.4 - - + +
284A HIS* 3.0 14.8 + - + +
285A ALA* 3.4 26.7 - - + +
286A LEU 3.2 0.2 - - - -
287A MET* 1.3 74.0 - - - +
289A TYR* 1.3 64.4 + - - +
291A TYR* 3.4 5.8 + - - +
292A ASN* 3.1 40.9 + - - +
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Residues in contact with TYR 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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219A PHE* 6.3 0.2 - + - -
223A THR* 4.6 10.0 - - + +
278A MET* 4.0 16.4 - - + +
280A GLN* 3.3 50.5 + - + -
285A ALA 2.8 14.2 + - - +
286A LEU* 3.4 13.0 - - + +
288A MET* 1.3 76.9 - - - +
290A LEU* 1.3 67.0 - - + +
292A ASN* 4.1 2.9 - - - +
293A ALA* 2.2 40.4 - - + +
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Residues in contact with LEU 290 (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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219A PHE* 3.6 23.7 - - + -
223A THR* 4.0 18.8 - - + -
265A LEU* 3.6 37.9 - - + +
266A PHE* 3.6 21.7 - - + +
269A VAL* 3.7 19.5 - - + -
274A PHE* 5.0 1.3 - - + -
278A MET* 4.4 9.0 - - + -
286A LEU* 2.9 26.1 + - + +
287A MET* 3.8 3.8 - - - +
289A TYR* 1.3 85.3 - - + +
291A TYR* 1.3 62.6 + - - +
293A ALA* 3.0 23.3 - - - +
304A SPD 3.6 9.2 - - - -
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Residues in contact with TYR 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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171A ILE* 4.0 5.2 - - + -
172A GLY 4.1 4.3 - - - -
173A ALA* 3.5 9.4 - - + +
174A PHE* 2.8 79.5 + + + +
266A PHE* 4.1 5.6 - - - -
287A MET 2.9 17.8 + - - +
288A MET* 3.7 7.6 - - - +
290A LEU* 1.3 78.3 - - - +
292A ASN* 1.3 74.7 + - - +
293A ALA 3.9 4.9 - - - -
304A SPD 3.9 36.5 + - - -
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Residues in contact with ASN 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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288A MET* 3.1 27.3 + - - +
289A TYR* 4.2 2.7 - - - +
291A TYR* 1.3 93.9 - - - +
293A ALA* 1.3 55.0 + - + +
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Residues in contact with ALA 293 (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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219A PHE* 4.0 17.3 - - + -
289A TYR* 2.2 39.9 - - + +
290A LEU* 3.0 20.2 - - - +
291A TYR 3.9 6.3 - - - -
292A ASN* 1.3 74.8 + - + +
304A SPD 3.9 17.1 + - - -
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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