Contacts of the helix formed by residues 315 - 328 (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 GLU 315 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291T PHE* 3.6 29.3 - - + +
293T LYS* 5.8 4.9 - - - +
313T ASP 3.7 9.2 + - - +
314T LEU* 1.3 79.9 - - - +
316T GLY* 1.3 71.2 + - - +
318T ALA* 3.5 9.8 + - - +
319T LEU* 3.2 17.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 316 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288T ILE* 3.3 24.6 + - - +
289T MET* 3.8 11.9 - - - -
291T PHE* 3.5 22.5 - - - -
315T GLU* 1.3 75.9 - - - +
317T LYS* 1.3 64.1 + - - -
319T LEU* 3.0 4.3 + - - +
320T LEU 2.9 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 317 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165T LEU* 5.4 10.3 - - + -
216T HIS* 5.7 8.7 - - + +
289T MET* 3.3 34.7 - - + +
315T GLU 3.6 0.2 + - - -
316T GLY* 1.3 71.2 - - - -
318T ALA* 1.3 54.4 + - - +
320T LEU* 3.4 7.1 - - + +
321T LYS* 2.7 56.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 318 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314T LEU* 4.3 20.4 - - + -
315T GLU 3.5 9.4 + - - +
316T GLY 3.2 0.2 - - - -
317T LYS* 1.3 78.3 - - - +
319T LEU* 1.3 62.0 + - - +
321T LYS* 3.7 8.9 + - - +
322T VAL* 3.3 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 319 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288T ILE* 3.9 15.7 - - + -
296T ILE* 4.3 28.7 - - + -
307T LEU* 3.9 27.6 - - + -
311T GLU 4.1 2.5 - - - +
312T LYS 5.9 0.2 - - - -
314T LEU* 3.5 34.3 - - + +
315T GLU* 3.2 20.7 + - + +
316T GLY 3.0 8.4 + - - +
318T ALA* 1.3 75.8 - - - +
320T LEU* 1.3 56.2 + - - +
322T VAL* 3.2 2.5 + - + -
323T VAL* 2.8 55.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 320 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165T LEU* 5.8 4.3 - - + -
216T HIS* 5.4 10.8 - - + +
284T LEU* 4.2 1.6 - - + +
285T PHE* 3.7 59.0 - - + +
288T ILE* 3.7 29.3 - - + +
289T MET* 4.0 20.9 - - + -
316T GLY 2.9 12.4 + - - +
317T LYS* 3.4 12.3 - - + +
319T LEU* 1.3 76.4 - - - +
321T LYS* 1.3 66.1 + - + +
323T VAL* 3.0 1.2 + - - -
324T MET* 2.8 39.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 321 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215T LEU* 5.4 4.8 + - - +
216T HIS* 4.1 49.5 + - + +
218T TRP* 6.2 0.4 - - - -
317T LYS* 2.7 38.4 + - + +
318T ALA* 3.9 8.5 - - - +
320T LEU* 1.3 77.9 - - + +
322T VAL* 1.3 61.7 + - + +
324T MET* 3.6 4.2 + - - +
325T ARG* 3.1 44.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 322 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307T LEU* 4.5 10.3 - - + -
311T GLU* 3.6 33.2 - - + +
314T LEU* 3.6 21.3 - - + -
318T ALA 3.3 18.5 + - - +
319T LEU 3.2 3.8 + - - +
320T LEU 3.2 0.4 - - - -
321T LYS* 1.3 77.6 - - + +
323T VAL* 1.3 64.2 + - - +
325T ARG* 3.7 11.8 + - - +
326T LYS* 3.4 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 323 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284T LEU* 4.3 14.4 - - + -
288T ILE* 4.1 19.1 - - + -
300T LEU* 4.3 14.6 - - + -
305T ILE* 4.2 15.4 - - + +
307T LEU* 3.9 15.9 - - + -
319T LEU* 2.8 44.4 + - + +
320T LEU 3.0 2.9 + - - +
322T VAL* 1.3 73.4 - - - +
324T MET* 1.3 74.4 - - + +
326T LYS* 3.4 6.7 + - - +
327T PHE* 3.0 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 324 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218T TRP* 3.5 43.5 - - + +
281T ILE* 4.7 10.1 - - - -
284T LEU* 3.1 38.6 - - + -
285T PHE* 3.5 33.9 - - + -
320T LEU* 2.8 31.9 + - + +
321T LYS* 4.1 3.8 - - - +
323T VAL* 1.3 77.7 - - + +
325T ARG* 1.3 60.8 + - - +
327T PHE* 3.4 18.4 - - + -
328T LEU* 2.8 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 325 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215T LEU 4.9 3.8 + - - -
216T HIS 3.6 22.9 + - - +
217T GLY* 3.5 36.6 + - - +
321T LYS* 3.1 37.6 + - - +
322T VAL* 3.9 11.0 - - - +
323T VAL 3.3 0.2 - - - -
324T MET* 1.3 76.3 - - + +
326T LYS* 1.3 60.3 + - + +
329T PRO* 3.0 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 326 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305T ILE* 4.1 21.0 - - + +
306T VAL* 3.3 30.2 + - + +
307T LEU* 4.7 4.0 - - + +
308T LYS* 3.2 24.0 - - - +
311T GLU* 3.3 32.8 - - - -
322T VAL* 3.4 16.3 + - + +
323T VAL 3.4 8.0 + - - +
324T MET 3.2 0.4 - - - -
325T ARG* 1.3 80.4 - - + +
327T PHE* 1.3 63.7 + - - +
329T PRO* 4.0 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 327 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225T PHE* 4.2 16.4 - + - -
228T ARG* 3.3 46.3 + - - -
229T TYR* 5.8 0.4 - - - -
280T PRO* 4.9 4.9 - - + -
281T ILE* 4.1 15.3 - - + -
284T LEU* 3.7 17.0 - - + -
303T LEU* 4.1 22.9 - - + -
305T ILE* 3.6 28.0 - - + +
323T VAL* 3.0 17.6 + - + +
324T MET* 3.4 25.8 + - + +
326T LYS* 1.3 78.8 - - - +
328T LEU* 1.3 84.9 + - + +
329T PRO* 3.9 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 328 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218T TRP* 3.1 28.9 - - + -
219T ALA 3.1 15.0 + - - +
220T PHE* 3.9 27.1 - - + -
224T GLN* 4.7 10.1 - - + +
225T PHE* 3.9 24.7 - - + -
228T ARG* 4.1 11.4 - - - +
281T ILE* 4.1 15.3 - - + -
324T MET* 2.8 17.8 + - - +
327T PHE* 1.3 110.3 - - + +
329T PRO* 1.3 71.1 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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