Contacts of the helix formed by residues 245 - 263 (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 PRO 245 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLN 5.2 0.7 - - - +
46A VAL 4.0 9.9 - - - +
47A TRP 4.6 12.3 - - - +
49A MET 3.5 24.9 - - - +
50A THR* 4.6 7.2 - - + -
235A LEU 3.9 19.9 - - - +
236A SER* 4.5 16.8 - - - -
237A SER 5.0 3.1 - - - +
239A GLY* 5.4 0.7 - - - -
243A ASN 4.6 0.7 - - - +
244A SER* 1.3 85.2 - - - +
246A TYR* 1.3 56.0 + - - +
248A TYR* 4.2 1.9 - - + +
249A ALA* 2.9 30.5 + - - +
274A ASP* 3.4 24.1 - - - +
275A TYR* 3.8 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLU* 4.3 7.6 - - - -
242A TRP* 4.9 18.4 - + - -
244A SER* 2.8 13.0 + - - +
245A PRO* 1.3 76.9 - - - +
247A TYR* 1.3 54.8 + - - +
249A ALA* 3.2 1.6 + - - +
250A SER* 2.8 34.9 + - - -
275A TYR* 3.4 51.3 - + + +
279A LYS* 2.9 36.2 + - - +
280A TRP* 3.1 31.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A TRP* 3.2 63.2 - + + -
243A ASN* 3.9 16.4 - - - +
244A SER* 2.9 11.5 + - - +
246A TYR* 1.3 78.8 - - - +
248A TYR* 1.3 74.5 + + - +
250A SER* 2.5 22.7 + - - -
251A TYR* 3.0 50.9 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A VAL 4.7 1.6 + - - -
203A SER* 5.3 1.2 - - - -
204A TYR* 3.5 42.9 + + + -
235A LEU* 3.3 50.5 - - + +
237A SER* 3.9 14.2 + - - -
243A ASN* 3.3 43.5 + - - -
244A SER 3.3 6.7 + - - -
245A PRO 4.2 3.6 - - - +
246A TYR 3.3 0.2 - - - -
247A TYR* 1.3 91.0 - + - +
249A ALA* 1.3 52.8 + - - +
251A TYR* 3.0 8.4 + + - +
252A ILE* 2.8 48.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A THR 6.0 0.7 - - - -
245A PRO 2.9 23.3 + - - +
246A TYR 3.2 4.0 + - - +
248A TYR* 1.3 76.2 - - - +
250A SER* 1.3 58.2 + - - +
251A TYR 3.1 0.2 - - - -
252A ILE* 4.5 4.7 - - - +
253A ASN* 3.0 54.0 + - - +
274A ASP* 4.3 10.3 - - + -
275A TYR* 4.0 21.1 - - + -
280A TRP* 3.9 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A TRP* 5.7 2.6 - - - -
246A TYR* 2.8 12.7 + - - -
247A TYR* 2.5 28.6 + - - -
249A ALA* 1.3 75.1 - - - +
251A TYR* 1.3 71.1 + - - +
254A PRO* 3.6 17.1 - - - +
280A TRP* 3.3 41.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A TYR* 3.2 28.7 + + + +
247A TYR* 3.0 69.9 + + - -
248A TYR* 3.0 6.5 + + - +
250A SER* 1.3 88.8 - - - +
252A ILE* 1.3 63.4 - - - +
253A ASN 3.2 1.5 + - - -
254A PRO* 3.3 2.9 - - - +
255A GLU* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A TYR* 3.5 29.4 - - + -
207A LYS* 3.9 23.3 - - + -
208A VAL* 4.9 6.1 - - + -
211A ILE* 3.6 21.1 - - + -
233A THR* 3.5 30.9 - - - +
235A LEU* 4.3 7.4 - - + +
248A TYR* 2.8 37.0 + - + +
249A ALA* 4.7 2.9 - - - -
251A TYR* 1.3 72.3 - - - +
253A ASN* 1.3 60.3 + - - +
255A GLU* 4.1 5.4 - - - -
256A ILE* 2.9 38.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A THR* 3.8 18.9 + - - +
249A ALA* 3.0 30.3 + - - +
252A ILE* 1.3 77.5 - - - +
254A PRO* 1.3 70.0 - - + +
256A ILE 3.2 1.6 + - - -
257A ALA* 2.8 25.6 + - - +
273A GLN* 3.9 16.5 + - - +
274A ASP 3.6 20.6 + - - +
275A TYR 3.8 1.6 + - - -
280A TRP* 3.4 28.1 - - + +
284A LEU* 3.9 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ALA 3.8 1.8 - - - +
250A SER 3.6 20.9 - - - +
251A TYR 3.3 10.5 - - - +
253A ASN* 1.3 93.2 - - + +
255A GLU* 1.3 63.2 + - - +
257A ALA* 3.0 12.1 + - + +
258A ASN* 3.0 17.1 + - - +
280A TRP* 3.6 26.7 - - + -
281A SER 5.1 0.2 - - - +
282A PRO* 3.9 29.7 - - + +
283A LEU 5.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A TYR* 4.1 12.7 + - - +
208A VAL* 4.0 14.3 - - + +
212A LYS* 3.0 29.3 + - - -
251A TYR 3.0 20.7 + - - +
252A ILE* 3.7 5.2 - - - +
254A PRO* 1.3 80.7 - - - +
256A ILE* 1.3 78.8 + - + +
258A ASN* 3.6 4.2 + - - +
259A TYR* 3.2 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A VAL* 4.6 4.7 - - + -
211A ILE* 3.7 29.6 - - + -
212A LYS* 4.2 20.9 - - + -
215A MET* 3.5 33.7 - - + -
233A THR* 4.7 5.2 - - + -
252A ILE* 2.9 32.4 + - + +
253A ASN 4.0 1.6 - - - +
255A GLU* 1.3 87.2 - - + +
257A ALA* 1.3 68.1 + - - +
259A TYR* 3.4 5.3 + - + +
260A ILE* 3.2 19.5 + - + +
284A LEU* 4.3 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ASN 2.8 18.2 + - - +
254A PRO* 3.0 4.7 + - + +
256A ILE* 1.3 74.4 - - - +
258A ASN* 1.3 63.7 + - - +
260A ILE* 3.0 9.2 + - - +
261A LYS* 3.0 16.5 + - - -
282A PRO* 3.8 15.9 - - + -
283A LEU 3.8 9.0 - - - +
284A LEU* 3.6 35.8 - - - +
287A GLU* 3.5 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A PRO 3.0 12.3 + - - +
255A GLU* 3.9 4.3 - - - +
257A ALA* 1.3 78.0 - - - +
259A TYR* 1.3 65.7 + - - +
261A LYS* 2.8 31.7 + - - +
262A GLN* 2.9 30.9 + - - +
282A PRO* 4.6 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A LYS* 4.0 51.2 + - + +
215A MET* 4.0 18.6 - - - -
216A ASP* 2.6 36.0 + - - -
219A MET* 3.7 21.1 - - + -
255A GLU* 3.2 14.1 + - - +
256A ILE* 3.5 13.7 - - + +
258A ASN* 1.3 78.7 + - - +
260A ILE* 1.3 60.7 + - - +
262A GLN* 4.5 1.9 - - - +
263A LYS* 3.2 57.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A MET* 3.7 21.8 - - + -
219A MET* 5.2 0.7 - - - -
256A ILE 3.2 15.9 - - - +
257A ALA 3.0 6.1 + - - +
259A TYR* 1.3 75.9 - - - +
261A LYS* 1.3 67.9 + - - +
263A LYS* 4.7 0.4 - - - -
264A ASN* 3.2 3.3 + - - -
265A PRO* 3.1 49.2 - - + +
268A VAL* 3.7 22.0 - - + -
284A LEU* 3.7 24.2 - - + -
287A GLU* 4.2 20.4 - - + +
288A VAL* 3.7 19.3 - - + +
291A ALA* 4.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ALA 3.0 11.5 + - - +
258A ASN* 2.8 26.6 + - - +
260A ILE* 1.3 79.7 - - - +
262A GLN* 1.3 62.2 + - + +
264A ASN* 3.6 10.4 + - - +
282A PRO* 4.8 11.3 + - + +
287A GLU* 2.9 41.5 + - - +
290A ARG* 3.9 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ASN* 2.9 30.9 + - - +
259A TYR* 4.6 2.7 - - - +
261A LYS* 1.3 71.6 - - + +
263A LYS* 1.3 70.2 + - + +
264A ASN* 3.1 7.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ASP* 3.7 8.9 + - - -
219A MET* 3.9 28.7 - - + +
259A TYR* 3.2 64.2 + - + +
261A LYS 3.5 0.2 - - - -
262A GLN* 1.3 82.9 - - + +
264A ASN* 1.3 68.6 + - - +
265A PRO* 3.2 5.2 - - + +
----------------------------------------------------------
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