Contacts of the helix formed by residues 308 - 315 (chain B) in PDB entry 1PE0
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 GLY 308 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU* 4.0 9.3 - - - +
273B PRO 3.6 17.7 - - - -
274B GLY* 3.7 3.6 - - - -
279B ALA* 4.3 5.8 - - - -
282B LEU* 5.3 0.7 - - - -
304B ALA* 3.8 9.5 - - - +
305B ILE 2.9 13.8 + - - -
307B ALA* 1.3 78.5 - - - +
309B PRO* 1.3 63.6 - - - +
311B ALA* 2.9 24.4 + - - +
312B LEU 4.1 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ALA* 3.6 26.9 - - + +
305B ILE 3.6 9.0 - - - +
306B CYS 3.3 17.9 - - - +
307B ALA 3.3 1.1 - - - -
308B GLY* 1.3 87.9 - - - +
310B THR* 1.3 54.7 + - - +
311B ALA 3.0 0.9 - - - -
312B LEU* 2.9 30.8 + - + +
313B LEU 3.4 0.7 + - - -
324B THR 3.6 19.7 - - - +
325B THR* 3.7 13.0 - - + -
333B MET* 3.2 27.8 - - + +
354B THR* 3.9 8.1 - - + -
355B SER 4.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ALA* 3.8 11.6 - - - +
283B SER* 3.7 4.3 + - - -
307B ALA* 2.5 24.3 + - + +
309B PRO* 1.3 77.5 - - + +
311B ALA* 1.3 58.2 + - - +
313B LEU* 3.3 6.9 + - - +
314B ALA* 3.1 26.2 + - - +
325B THR* 5.5 0.4 - - + -
329B ALA* 4.2 26.5 - - + +
332B LYS* 3.9 44.0 + - + +
333B MET* 3.8 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU* 4.0 17.7 - - + -
279B ALA 4.6 1.6 - - - +
282B LEU* 4.1 23.3 - - + +
283B SER* 3.3 20.9 - - - +
288B VAL* 5.5 0.2 - - + -
292B LEU* 4.8 1.8 - - + -
308B GLY 2.9 13.9 + - - +
310B THR* 1.3 77.8 + - - +
312B LEU* 1.3 66.5 + - - +
314B ALA* 3.3 1.2 + - - +
315B HIS* 3.1 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU* 4.0 14.1 - - + -
292B LEU* 4.3 6.3 - - + -
302B ILE* 3.7 28.7 - - + +
304B ALA* 4.2 12.6 - - + -
309B PRO* 2.9 28.4 + - + +
311B ALA* 1.3 78.3 - - - +
313B LEU* 1.3 55.1 + - - +
315B HIS 3.4 0.9 + - - -
316B GLU 3.0 7.6 + - - -
317B ILE* 2.7 54.8 + - + +
323B VAL* 5.4 0.9 - - + -
333B MET* 4.6 4.7 - - + -
339B TYR* 3.3 13.0 - - + +
352B ILE* 4.4 24.7 - - + -
353B LEU 5.8 0.2 - - - +
354B THR* 4.4 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B PRO 3.4 1.4 + - - -
310B THR* 3.3 10.7 + - - +
311B ALA 3.2 0.2 - - - -
312B LEU* 1.3 80.8 - - - +
314B ALA* 1.3 63.3 + - - +
316B GLU* 3.0 17.8 + - - +
319B PHE* 4.0 5.5 - - + -
332B LYS* 3.1 34.1 - - + +
333B MET* 3.5 21.8 - - - +
335B ASN* 4.3 9.4 - - + +
338B HIS* 3.9 28.5 - - + -
339B TYR* 3.3 26.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B SER* 3.6 40.1 - - - +
289B LYS* 3.6 12.3 + - - -
310B THR 3.1 12.3 + - - +
311B ALA 3.3 4.0 + - - +
313B LEU* 1.3 77.7 - - - +
315B HIS* 1.3 59.7 + - + +
316B GLU* 3.3 4.6 - - - +
332B LYS* 5.9 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B LEU 2.9 26.7 - - - -
283B SER* 3.0 25.3 + - - -
284B GLU 4.7 0.2 - - - -
285B SER 3.1 19.2 + - - -
288B VAL* 3.7 5.6 - - + -
289B LYS* 2.9 61.1 + - + +
292B LEU* 3.6 14.3 - - - +
293B LYS* 3.1 21.9 + - - -
311B ALA* 3.1 16.8 + - + +
314B ALA* 1.3 76.1 - - - +
316B GLU* 1.3 71.5 + - - +
317B ILE* 3.3 15.6 + - + +
----------------------------------------------------------
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