Contacts of the helix formed by residues 277 - 290 (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 ILE 277 (chain T).
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Specific contacts
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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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Residues in contact with LEU 278 (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* 4.5 23.3 - - + +
174T LEU* 5.4 11.0 - - + -
175T TYR* 5.6 3.4 - - + +
178T PHE* 5.5 6.1 - - + -
220T PHE* 5.0 6.5 - - + -
273T PHE* 3.2 42.5 + - + +
274T ASN* 3.6 28.0 - - - +
277T ILE* 1.3 80.7 - - + +
279T ASP* 1.3 55.2 + - - +
281T ILE* 3.0 11.8 + - + +
282T PHE* 2.7 59.6 + - + -
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Residues in contact with ASP 279 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171T LYS* 3.9 20.3 + - - +
270T GLU* 5.4 2.8 - - - +
274T ASN 2.9 18.6 + - - +
275T MET* 3.6 12.5 - - - +
278T LEU* 1.3 75.1 - - - +
280T PRO* 1.3 63.1 - - + +
282T PHE* 3.6 8.0 - - - +
283T ARG* 2.6 78.3 + - - +
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Residues in contact with PRO 280 (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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225T PHE* 5.8 0.7 - - + -
229T TYR* 4.1 7.9 - - - +
275T MET 4.0 3.1 - - - +
276T PHE* 3.4 26.5 - - - +
277T ILE 3.5 13.9 - - - +
279T ASP* 1.3 96.8 - - + +
281T ILE* 1.3 59.8 + - - +
283T ARG* 3.5 19.8 + - + +
284T LEU* 3.1 30.3 + - - +
299T LEU* 5.1 3.6 - - + +
303T LEU* 4.3 24.9 - - + +
327T PHE* 4.9 8.3 - - + -
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Residues in contact with ILE 281 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164T LEU* 5.3 4.9 - - + -
218T TRP* 4.5 15.0 - - + -
220T PHE* 3.8 29.2 - - + -
225T PHE* 4.6 1.8 - - + -
277T ILE* 3.4 19.1 - - + +
278T LEU* 3.0 14.2 + - + +
280T PRO* 1.3 73.1 - - - +
282T PHE* 1.3 74.0 + - + +
284T LEU* 3.2 9.1 + - - +
285T PHE* 3.0 46.3 + - + -
324T MET* 4.7 5.2 - - - -
327T PHE* 4.1 20.4 - - + -
328T LEU* 4.1 15.7 - - + -
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Residues in contact with PHE 282 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164T LEU* 3.9 34.1 - - + -
169T VAL 4.8 7.2 - - - -
170T SER* 5.0 1.3 - - - -
171T LYS* 3.3 48.5 - - + -
174T LEU* 4.5 7.4 - - + -
278T LEU* 2.7 53.5 + - + +
279T ASP* 3.6 9.6 - - - +
281T ILE* 1.3 79.2 - - + +
283T ARG* 1.3 58.4 + - + +
285T PHE* 3.3 6.3 + - - +
286T THR* 2.9 36.8 + - - +
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Residues in contact with ARG 283 (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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275T MET 5.0 3.0 + - - -
279T ASP* 2.6 55.0 + - - +
280T PRO* 3.8 18.9 - - - +
282T PHE* 1.3 74.2 - - + +
284T LEU* 1.3 57.3 + - - +
286T THR* 4.0 4.8 - - - -
287T ALA* 3.0 32.9 + - - +
299T LEU* 3.4 29.0 - - + +
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Residues in contact with LEU 284 (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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280T PRO 3.1 17.2 + - - +
281T ILE* 3.2 7.8 + - - +
283T ARG* 1.3 77.1 - - - +
285T PHE* 1.3 64.7 + - + +
287T ALA* 4.0 0.3 - - - +
288T ILE* 3.0 38.2 + - + +
299T LEU* 3.8 18.4 - - + -
300T LEU* 3.8 29.2 - - + -
303T LEU* 3.4 29.2 - - + -
305T ILE* 5.7 0.4 - - + -
320T LEU* 4.4 0.4 - - + -
323T VAL* 4.3 11.4 - - + -
324T MET* 3.1 35.4 - - + -
327T PHE* 3.7 9.9 - - + -
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Residues in contact with PHE 285 (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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161T ASP* 5.4 7.6 - - + -
164T LEU* 3.7 30.3 - - + -
165T LEU* 4.6 21.5 - - + -
216T HIS* 5.6 4.3 - + - -
218T TRP* 3.9 27.6 - + - -
281T ILE* 3.0 27.8 + - + +
282T PHE* 3.6 9.4 - - - +
284T LEU* 1.3 77.8 - - - +
286T THR* 1.3 58.6 + - - +
289T MET* 2.9 39.7 + - + +
320T LEU* 3.7 36.6 - - + -
324T MET* 3.5 28.0 - - - -
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Residues in contact with THR 286 (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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282T PHE* 2.9 21.7 + - - +
283T ARG* 4.0 5.8 - - - -
285T PHE* 1.3 77.5 - - - +
287T ALA* 1.3 59.9 - - - +
289T MET* 5.1 1.1 - - - -
290T ASN* 2.7 47.0 + - - +
292T LYS* 3.8 19.8 - - - +
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Residues in contact with ALA 287 (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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283T ARG 3.0 18.8 + - - +
284T LEU* 4.1 1.8 - - - +
286T THR* 1.3 74.9 - - - +
288T ILE* 1.3 64.2 + - + +
290T ASN 3.6 0.3 + - - -
291T PHE 3.3 2.8 + - - -
292T LYS* 3.0 47.7 + - + +
295T GLU* 4.7 9.4 - - + +
296T ILE* 3.6 18.1 - - + +
299T LEU* 4.1 14.4 - - + -
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Residues in contact with ILE 288 (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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284T LEU* 3.0 27.6 + - + +
285T PHE 4.1 0.9 - - - +
287T ALA* 1.3 78.4 - - + +
289T MET* 1.3 62.2 + - - +
291T PHE* 3.3 12.8 + - - -
296T ILE* 3.7 27.3 - - + +
300T LEU* 4.9 0.2 - - + -
316T GLY* 3.3 38.2 + - - +
319T LEU* 3.9 14.6 - - + -
320T LEU* 3.7 36.8 - - + +
323T VAL* 4.1 28.0 - - + -
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Residues in contact with MET 289 (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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165T LEU* 5.0 22.0 - - + -
285T PHE* 2.9 23.8 + - + +
286T THR* 4.7 2.0 - - - +
288T ILE* 1.3 76.5 - - + +
290T ASN* 1.3 63.5 + - - +
291T PHE* 3.3 18.8 - - - -
316T GLY* 3.8 6.3 - - - -
317T LYS* 3.3 60.3 - - + +
320T LEU* 4.0 21.8 - - + -
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Residues in contact with ASN 290 (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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286T THR* 2.7 44.1 + - - +
287T ALA 3.6 0.2 + - - -
288T ILE 3.2 0.6 - - - -
289T MET* 1.3 82.9 - - - +
291T PHE* 1.3 74.5 + - - +
292T LYS* 3.2 22.0 + - + +
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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