Contacts of the helix formed by residues 221 - 234 (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 THR 221 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207T GLY* 4.5 13.0 - - - +
209T VAL 5.1 7.2 - - - +
210T ALA* 5.7 0.2 - - + -
220T PHE* 1.3 90.0 - - - +
222T ILE* 1.3 66.0 + - - +
223T ARG* 3.6 5.4 + - - +
224T GLN* 3.1 24.9 + - - +
225T PHE* 3.6 7.3 + - - -
333T ALA* 4.2 16.2 - - + +
336T GLU* 2.3 51.1 + - + +
337T MET* 4.5 13.9 - - + -
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Residues in contact with ILE 222 (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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204T PRO* 3.6 28.1 + - + +
205T ALA* 4.5 4.7 - - - +
207T GLY* 5.4 1.9 - - - +
211T PHE* 5.8 4.5 - - + -
220T PHE* 4.9 2.9 - - + -
221T THR* 1.3 72.7 - - - +
223T ARG* 1.3 58.7 + - - +
225T PHE* 2.9 9.1 + - - +
226T ALA* 2.8 25.9 + - - +
241T MET* 3.5 28.0 - - + +
244T LEU* 3.5 44.6 - - + +
245T TRP* 4.2 12.3 - - + -
273T PHE* 3.7 25.1 - - + -
277T ILE* 3.8 7.0 - - + -
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Residues in contact with ARG 223 (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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84T GLU* 3.7 4.4 + - - +
85T ASP* 2.8 37.3 + - - +
88T GLU* 1.7 55.9 + - - +
207T GLY* 5.8 5.4 - - - -
221T THR* 3.6 10.7 - - - +
222T ILE* 1.3 79.8 - - - +
224T GLN* 1.3 63.5 + - - +
226T ALA* 3.1 2.4 + - - +
227T THR* 2.9 41.9 + - - +
237T LYS* 3.4 15.6 - - - +
241T MET* 3.4 29.5 - - + +
336T GLU* 4.4 11.6 + - - +
340T LEU* 4.2 20.1 - - - +
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Residues in contact with GLN 224 (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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219T ALA 3.8 3.5 - - - +
220T PHE* 3.1 34.7 - - + +
221T THR* 3.1 11.0 + - - +
222T ILE 3.3 0.4 - - - -
223T ARG* 1.3 79.9 - - - +
225T PHE* 1.3 59.5 + - + +
227T THR* 3.4 8.3 + - - +
228T ARG* 3.1 28.4 + - - +
328T LEU* 4.7 8.9 - - + +
329T PRO* 5.0 2.0 + - - +
332T ASP* 4.4 25.9 + - - +
333T ALA* 4.8 2.3 - - - -
336T GLU* 3.0 29.5 + - - +
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Residues in contact with PHE 225 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220T PHE* 3.5 45.5 - + + -
221T THR 3.6 4.8 + - - -
222T ILE 2.9 8.5 + - - +
224T GLN* 1.3 76.3 - - + +
226T ALA* 1.3 61.4 + - - +
228T ARG* 3.2 17.7 + - - +
229T TYR* 2.8 67.4 + + + -
244T LEU* 4.0 5.2 - - + -
276T PHE 4.4 2.2 - - - -
277T ILE* 3.6 43.7 - - + -
280T PRO* 5.8 0.9 - - + -
281T ILE* 4.6 1.6 - - + -
327T PHE* 4.2 17.7 - + - -
328T LEU* 3.9 25.6 - - + -
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Residues in contact with ALA 226 (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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222T ILE 2.8 11.5 + - - +
223T ARG 3.1 8.7 + - - +
225T PHE* 1.3 73.8 - - - +
227T THR* 1.3 57.9 + - - +
229T TYR* 5.1 0.2 - - - -
230T ALA* 2.7 38.5 + - - +
237T LYS* 3.8 7.4 - - + +
240T MET* 4.0 5.0 - - + +
241T MET* 3.6 46.7 - - + +
244T LEU* 3.8 8.9 - - + +
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Residues in contact with THR 227 (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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84T GLU* 4.5 6.7 - - - +
223T ARG* 2.9 19.8 + - - -
224T GLN* 3.5 12.1 - - - +
226T ALA* 1.3 78.8 - - - +
228T ARG* 1.3 62.8 + - - +
230T ALA* 3.7 9.4 + - - +
231T LYS* 4.2 8.1 + - - +
237T LYS* 2.6 42.6 + - - +
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Residues in contact with ARG 228 (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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224T GLN 3.1 15.6 + - - +
225T PHE* 3.4 24.8 - - - +
227T THR* 1.3 80.6 - - - +
229T TYR* 1.3 82.7 + - + +
231T LYS* 4.9 1.6 + - - +
232T LYS* 3.7 29.6 + - - +
303T LEU* 4.0 18.8 + - - +
305T ILE* 5.5 0.4 - - - +
327T PHE* 3.3 52.2 + - - -
328T LEU* 4.1 8.1 - - - +
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Residues in contact with TYR 229 (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* 2.8 46.8 + + + +
226T ALA 4.5 0.2 - - - +
228T ARG* 1.3 97.5 - - + +
230T ALA* 1.3 59.9 + - - +
231T LYS 3.5 0.7 - - - -
232T LYS* 3.5 19.8 - - + +
233T PHE* 2.8 43.2 + + + +
240T MET* 3.5 20.0 - - + -
244T LEU* 4.0 15.5 - - + -
276T PHE* 2.5 53.7 + + + -
277T ILE* 4.6 0.2 - - + -
280T PRO* 4.1 9.2 - - - +
303T LEU* 5.6 5.2 - - + +
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Residues in contact with ALA 230 (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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226T ALA 2.7 24.6 + - - +
227T THR* 4.1 4.9 - - - +
228T ARG 3.6 0.8 - - - -
229T TYR* 1.3 71.2 - - - +
231T LYS* 1.3 57.1 + - + +
232T LYS 2.7 14.0 + - - -
233T PHE 3.1 7.3 + - - -
234T GLY* 3.1 9.2 + - - -
235T VAL 3.1 30.5 + - - +
236T ASP* 4.6 0.7 - - - -
237T LYS* 3.6 24.0 - - + +
240T MET* 3.9 6.9 - - - +
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Residues in contact with LYS 231 (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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227T THR 4.2 7.7 + - - +
228T ARG 4.9 1.8 + - - +
230T ALA* 1.3 77.6 - - + +
232T LYS* 1.3 58.4 + - - +
234T GLY* 4.4 4.2 + - - -
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Residues in contact with LYS 232 (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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228T ARG* 3.7 29.6 + - - +
229T TYR* 3.5 26.2 - - + +
230T ALA 2.7 3.6 + - - -
231T LYS* 1.3 79.8 - - - +
233T PHE* 1.3 60.9 + - + +
234T GLY 3.2 5.1 + - - -
302T LYS 5.0 8.7 + - - -
303T LEU* 6.3 0.2 - - - +
304T GLU* 5.6 10.5 - - - +
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Residues in contact with PHE 233 (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* 2.8 28.7 + + + +
230T ALA 4.2 1.6 - - - +
232T LYS* 1.3 79.5 - - + +
234T GLY* 1.3 63.3 + - - +
235T VAL* 3.4 13.5 - - + +
240T MET* 3.4 34.8 - - + -
250T PHE* 4.4 17.3 - + - -
257T TRP* 3.5 26.7 - + - -
276T PHE* 3.4 44.2 - + - -
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Residues in contact with GLY 234 (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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230T ALA 3.1 5.4 + - - -
231T LYS* 4.4 3.1 - - - -
232T LYS 3.2 4.2 - - - +
233T PHE* 1.3 79.5 - - - +
235T VAL* 1.3 61.0 + - - +
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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