Contacts of the helix formed by residues 247 - 263 (chain A) in PDB entry 1T2E
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 TYR 247 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A MET* 3.1 51.6 - - + +
31A ILE* 3.5 21.6 - - + +
35A VAL* 3.5 27.8 - - + -
245A ALA* 3.1 41.2 + - + -
246A PRO* 1.3 75.0 - - - +
248A VAL* 1.3 78.8 + - + +
250A PRO* 3.3 8.9 - - - +
251A ALA* 2.9 30.8 + - - +
336A NAI 4.3 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A VAL* 4.4 19.0 - - + +
39A LEU* 6.3 0.2 - - + -
245A ALA 5.1 0.2 + - - -
247A TYR* 1.3 103.4 - - + +
249A ALA* 1.3 64.6 + - - +
251A ALA* 3.3 2.8 + - - +
252A ALA* 3.1 22.0 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
167A LEU* 3.6 17.2 - - + +
170A SER* 4.6 8.7 - - - +
171A ARG* 5.1 5.6 - - + +
247A TYR 4.7 0.2 - - - +
248A VAL* 1.3 75.7 - - - +
250A PRO* 1.3 77.0 - - + +
252A ALA* 3.1 7.1 + - - +
253A ALA* 2.8 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE* 3.7 20.2 - - + -
163A LEU* 4.3 4.9 - - + -
167A LEU* 3.6 22.4 - - + -
171A ARG* 4.2 3.8 - - - +
246A PRO* 3.6 14.4 - - + +
247A TYR* 3.3 17.3 - - - +
249A ALA* 1.3 96.2 - - + +
251A ALA* 1.3 56.5 + - - +
253A ALA* 3.2 3.0 + - + +
254A ILE* 2.9 36.4 + - - +
336A NAI 3.5 29.6 - - + -
337A OXM 4.1 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE* 3.8 8.4 - - + +
35A VAL* 3.4 35.0 - - + -
36A MET* 3.7 23.1 - - + +
39A LEU* 4.1 2.0 - - + -
247A TYR 2.9 19.1 + - - +
248A VAL 3.6 0.4 - - - +
250A PRO* 1.3 75.8 - - - +
252A ALA* 1.3 57.3 + - - +
254A ILE* 3.2 2.3 + - - +
255A ILE* 2.8 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 3.7 19.4 - - + +
248A VAL* 3.1 18.6 + - + +
249A ALA* 3.7 7.4 - - - +
251A ALA* 1.3 73.1 - - - +
253A ALA* 1.3 60.7 + - - +
255A ILE* 3.3 1.9 + - - +
256A GLU* 2.8 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU* 3.8 16.2 - - + -
166A VAL* 3.5 29.0 - - + +
167A LEU* 3.9 14.1 - - + +
170A SER* 5.8 1.1 - - - +
249A ALA 2.8 17.6 + - - +
250A PRO 3.5 4.5 - - - +
252A ALA* 1.3 78.6 - - - +
254A ILE* 1.3 63.2 + - - +
256A GLU* 3.2 4.8 + - - +
257A MET* 3.1 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE* 3.5 29.8 - - + -
36A MET* 3.6 21.8 - - - -
95A ILE* 3.7 25.6 - - + -
136A ILE* 4.1 11.4 - - + +
138A VAL* 3.6 24.9 - - + -
163A LEU* 3.7 23.8 - - + -
250A PRO 2.9 24.9 + - - +
251A ALA* 3.6 3.8 - - - +
253A ALA* 1.3 76.1 - - - +
255A ILE* 1.3 51.7 + - - +
257A MET* 3.0 12.2 + - - +
258A ALA* 2.7 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A MET* 3.8 27.1 - - + -
39A LEU* 3.9 27.8 - - + -
40A ILE* 3.7 27.4 - - + -
43A LYS* 3.8 26.5 - - + -
45A LEU* 3.7 21.5 - - + -
95A ILE* 4.5 7.6 - - + -
251A ALA 2.8 23.2 + - - +
252A ALA* 3.8 3.6 - - - +
254A ILE* 1.3 76.1 - - - +
256A GLU* 1.3 57.3 + - - +
258A ALA* 4.3 4.9 - - + +
259A GLU* 2.7 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LYS* 6.4 0.9 - - - +
166A VAL* 3.8 17.7 - - + +
185A ARG* 2.7 34.2 + - - -
252A ALA 2.8 20.5 + - - +
253A ALA* 3.7 5.4 - - - +
255A ILE* 1.3 74.3 - - - +
257A MET* 1.3 63.1 + - - +
259A GLU* 3.7 10.4 - - - +
260A SER* 3.1 22.5 + - - -
265A LEU* 5.5 0.2 - - - +
267A LYS* 2.6 39.7 + - + +
269A LEU* 4.0 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A PHE* 5.2 0.6 - - - -
136A ILE* 3.7 26.7 - - + -
161A ILE* 3.4 24.9 - - + -
162A GLY 4.1 2.0 - - - +
163A LEU* 3.7 35.9 - - - -
164A GLY 5.4 0.2 - - - -
166A VAL* 4.1 20.9 - - + -
253A ALA 3.1 16.5 + - - +
254A ILE* 3.0 8.4 + - - +
256A GLU* 1.3 75.2 - - - +
258A ALA* 1.3 66.3 + - - +
260A SER* 3.2 12.0 + - - -
261A TYR* 3.2 11.4 + - - +
269A LEU* 3.9 5.8 - - + -
271A CYS* 3.7 18.6 - - - -
293A LEU* 3.7 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 5.8 2.5 - - + -
40A ILE* 6.4 0.2 - - + -
45A LEU* 5.3 2.7 - - + -
93A VAL* 4.5 10.3 - - + -
95A ILE* 4.3 15.0 - - + -
136A ILE* 3.9 19.4 - - + +
254A ILE 2.7 19.9 + - - +
255A ILE* 3.9 10.5 - - + +
257A MET* 1.3 72.0 - - - +
259A GLU* 1.3 59.2 + - - +
261A TYR* 3.3 9.5 + - - +
262A LEU* 2.9 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LYS* 4.1 24.5 + - - +
45A LEU* 3.9 22.5 - - + +
255A ILE* 2.7 22.6 + - + +
256A GLU* 3.7 8.3 - - - +
258A ALA* 1.3 71.7 - - - +
260A SER* 1.3 59.2 + - - +
262A LEU* 4.4 3.8 - - - -
263A LYS* 2.8 71.1 + - + +
265A LEU* 4.2 14.4 - - + +
267A LYS* 4.6 10.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A GLU 3.1 17.8 + - - -
257A MET 3.2 4.7 + - - -
259A GLU* 1.3 77.3 - - - +
261A TYR* 1.3 58.0 + - - +
264A ASP* 2.9 9.7 + - - -
265A LEU* 2.9 36.5 + - - +
266A LYS 3.5 1.7 + - - -
267A LYS* 3.2 26.3 + - - +
269A LEU* 4.0 14.8 - - - -
293A LEU* 2.6 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ASP* 4.2 7.3 + - + +
93A VAL* 3.8 26.0 - - + -
132A ASN 5.0 1.4 + - - -
134A PHE* 3.5 46.5 - + + +
159A LYS* 3.7 19.1 - - - -
257A MET 3.2 8.6 + - - +
258A ALA 3.4 7.0 - - - +
259A GLU 3.2 0.2 - - - -
260A SER* 1.3 81.0 - - - +
262A LEU* 1.3 76.3 + - + +
264A ASP 3.1 9.2 + - - -
293A LEU* 4.2 3.9 + - + +
294A GLY* 3.1 34.2 - - - +
295A ALA* 3.4 29.1 + - - -
296A ASN 4.5 0.2 - - - -
297A GLY* 3.6 17.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA* 3.5 24.5 - - + -
23A ILE* 3.7 31.2 - - + -
45A LEU* 4.0 24.7 - - + +
92A ASP* 5.0 2.9 - - + -
93A VAL* 3.9 22.9 - - + -
258A ALA* 2.9 28.6 + - + +
259A GLU* 3.9 4.7 - - - +
261A TYR* 1.3 84.9 - - + +
263A LYS* 1.3 66.5 + - + +
264A ASP* 3.7 0.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
43A LYS* 4.5 8.0 + - - +
45A LEU* 3.4 28.4 - - + +
259A GLU* 2.8 41.0 + - + +
262A LEU* 1.3 82.4 - - + +
264A ASP* 1.3 72.9 + - - +
265A LEU* 3.1 21.8 + - + +
----------------------------------------------------------
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