Contacts of the helix formed by residues 284 - 292 (chain A) in PDB entry 1PTG
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 LEU 284 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A THR* 4.1 13.0 - - + -
253A ASN* 3.9 37.2 + - + +
256A ILE* 4.3 7.4 - - + -
257A ALA* 3.6 17.0 - - - +
260A ILE* 3.7 17.9 - - + -
271A VAL* 3.7 25.4 - - + -
273A GLN* 3.7 27.1 - - + +
283A LEU* 1.3 73.5 - - - +
285A TYR* 1.3 65.5 + - - +
287A GLU* 3.2 2.4 + - - +
288A VAL* 3.0 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A TRP* 3.9 27.0 - + - -
29A PRO* 4.0 21.3 - - + +
61A HIS* 3.0 39.9 - + - +
273A GLN* 3.6 17.4 + - - +
276A ILE* 3.5 25.8 - - + -
277A ASN 2.5 31.3 + - - -
278A GLU* 3.3 19.1 - - - +
283A LEU* 3.4 27.7 - - + +
284A LEU* 1.3 80.5 - - - +
286A GLN* 1.3 68.3 + - - +
288A VAL* 3.7 3.2 + - - +
289A ILE* 3.1 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU 6.1 0.7 - - - +
8A GLU* 3.2 12.6 + - - +
10A TRP* 4.0 30.1 - - + +
282A PRO 4.9 1.7 - - - +
283A LEU* 3.4 33.2 + - + +
284A LEU 3.2 0.4 - - - -
285A TYR* 1.3 82.5 - - + +
287A GLU* 1.3 59.6 + - - +
289A ILE* 3.3 9.9 + - + +
290A ARG* 2.9 75.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ALA* 3.5 30.7 - - + +
260A ILE* 4.2 17.4 - - + +
261A LYS* 2.9 51.7 + - + +
282A PRO 4.0 7.9 - - - +
283A LEU 3.3 12.0 + - - +
284A LEU 3.2 7.7 + - - +
286A GLN* 1.3 77.8 - - - +
288A VAL* 1.3 64.8 + - - +
290A ARG* 3.1 29.1 + - - +
291A ALA* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER* 3.2 44.0 - - - -
28A ILE 4.1 4.0 - - - +
29A PRO* 4.0 18.2 - - + -
260A ILE* 3.7 14.4 - - + -
268A VAL* 4.4 3.1 - - + -
269A GLY 4.3 5.2 - - - +
271A VAL* 3.8 21.1 - - + -
284A LEU* 3.0 36.6 + - + +
285A TYR* 3.9 6.5 - - - +
287A GLU* 1.3 76.4 - - - +
289A ILE* 1.3 63.3 + - - +
291A ALA* 3.5 9.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 3.5 29.4 - - + +
10A TRP* 4.1 18.6 - - + +
13A TRP* 3.6 56.1 - - + +
27A SER 4.4 1.1 - - - -
29A PRO* 3.9 10.1 - - + -
61A HIS 4.4 1.3 - - - +
62A GLY* 3.8 15.7 - - - -
285A TYR 3.1 20.3 + - - +
286A GLN* 3.6 6.5 - - - +
287A GLU 3.2 0.2 - - - -
288A VAL* 1.3 76.9 - - - +
290A ARG* 1.3 57.7 + - + +
292A ASN* 3.0 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 4.3 9.8 - - + +
8A GLU* 3.1 35.1 + - - +
261A LYS* 3.9 10.9 - - - +
286A GLN* 2.9 55.6 + - + +
287A GLU* 3.1 37.4 + - - +
289A ILE* 1.3 72.0 - - + +
291A ALA* 1.3 51.6 + - - +
292A ASN 2.7 16.3 + - - -
293A LYS* 2.8 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG* 4.6 0.2 + - - -
27A SER* 4.3 6.2 + - - +
260A ILE* 4.5 2.7 - - + -
265A PRO* 4.0 15.2 - - + +
266A ALA 3.5 12.8 - - - +
267A ARG 4.8 0.9 - - - +
268A VAL* 3.6 31.2 - - + -
287A GLU 3.1 12.0 + - - +
288A VAL 3.7 9.4 - - - +
289A ILE 3.3 1.0 - - - -
290A ARG* 1.3 72.9 - - - +
292A ASN* 1.3 56.9 + - - +
293A LYS* 3.2 15.5 - - - +
294A SER* 3.2 16.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 4.1 14.8 - - + -
13A TRP* 3.6 12.1 - - - -
17A ILE* 4.3 4.9 - - + +
25A ARG* 4.5 1.7 + - - +
26A ILE* 3.4 8.0 - - - +
27A SER* 2.8 54.5 + - - -
288A VAL 3.6 0.6 + - - -
289A ILE 3.0 22.1 + - - +
290A ARG 2.7 1.2 + - - -
291A ALA* 1.3 75.6 - - - +
293A LYS* 1.3 65.6 + - - +
294A SER* 3.0 4.5 - - - -
295A LEU* 2.9 44.2 + - + +
296A ILE* 3.9 5.9 + - - +
----------------------------------------------------------
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