Contacts of the helix formed by residues 271 - 277 (chain T) in PDB entry 2P8Z
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 ARG 271 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172T GLU* 3.8 31.3 + - - +
175T TYR* 4.3 29.8 + - - -
176T GLN* 5.2 1.0 - - - +
246T GLY* 2.9 32.8 + - - +
247T ASP* 2.9 30.5 + - - +
248T SER 3.7 0.4 - - - -
249T PHE* 3.6 22.1 - - + -
261T ASP* 6.2 0.2 - - - +
269T LEU 3.5 4.6 + - - -
270T GLU* 1.3 73.7 - - - +
272T ALA* 1.3 66.6 + - - +
273T PHE* 3.8 16.6 - - + +
274T ASN* 2.9 37.7 + - - +
275T MET* 2.9 11.0 + - - +
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Residues in contact with ALA 272 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243T ARG 3.0 28.9 - - - +
244T LEU* 4.1 4.4 - - + +
246T GLY 5.9 0.2 - - - +
248T SER 2.7 20.3 + - - +
249T PHE* 4.3 2.2 - - - +
250T PHE 4.9 1.8 - - - +
257T TRP* 3.8 21.8 - - + -
270T GLU 3.5 2.5 + - - -
271T ARG* 1.3 71.4 - - - +
273T PHE* 1.3 61.7 + - - +
275T MET* 4.4 3.4 - - - -
276T PHE* 3.0 38.7 + - + +
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Residues in contact with PHE 273 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175T TYR* 4.6 12.1 - + + -
178T PHE* 5.3 10.3 - + - -
211T PHE* 5.0 9.0 - + - -
220T PHE* 4.3 14.6 - + - -
222T ILE* 3.7 22.7 - - + -
244T LEU* 3.2 31.1 + - - +
245T TRP* 3.8 32.0 - + + +
246T GLY 5.0 0.4 - - - +
271T ARG* 3.2 15.9 - - + +
272T ALA* 1.3 77.7 - - - +
274T ASN* 1.3 70.1 + - - +
277T ILE* 3.1 41.2 + - + +
278T LEU* 3.2 40.7 + - + -
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Residues in contact with ASN 274 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171T LYS* 4.0 22.4 - - + +
172T GLU* 3.8 22.8 + - - +
175T TYR* 4.7 5.4 - - - +
270T GLU* 3.5 23.7 + - + +
271T ARG* 2.9 32.0 + - - +
273T PHE* 1.3 87.0 - - - +
275T MET* 1.3 59.5 - - - +
278T LEU* 3.6 18.5 - - + +
279T ASP* 2.9 31.9 + - - +
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Residues in contact with MET 275 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250T PHE* 3.8 31.9 - - + +
252T PRO* 3.8 18.6 - - + -
270T GLU* 3.3 32.3 - - + +
271T ARG 2.9 13.8 + - - +
272T ALA* 4.1 4.5 - - - +
274T ASN* 1.3 79.3 - - - +
276T PHE* 1.3 97.3 + - + +
279T ASP* 3.6 17.9 - - - +
280T PRO* 4.0 2.9 - - - +
283T ARG* 5.0 2.8 + - - -
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Residues in contact with PHE 276 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229T TYR* 2.5 50.6 + + + -
233T PHE* 3.4 31.4 - + - -
244T LEU* 4.0 11.7 - - + -
250T PHE* 3.9 16.4 - + + -
257T TRP* 3.7 30.3 - + - -
272T ALA* 3.0 22.3 + - + +
275T MET* 1.3 115.5 - - + +
277T ILE* 1.3 60.9 + - - +
280T PRO* 3.4 10.9 - - - +
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Residues in contact with ILE 277 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220T PHE* 3.5 33.9 - - + -
222T ILE* 3.8 17.9 - - + -
225T PHE* 3.6 48.5 - - + -
229T TYR* 4.6 0.2 - - + -
244T LEU* 4.0 22.2 - - + +
273T PHE* 3.1 35.9 + - + +
276T PHE* 1.3 81.8 - - - +
278T LEU* 1.3 66.3 + - - +
279T ASP 3.6 0.4 - - - -
280T PRO* 3.5 6.5 - - - +
281T ILE* 3.4 19.8 - - + +
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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