Contacts of the helix formed by residues 244 - 260 (chain A) in PDB entry 1T8U
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 ASP 244 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A ARG* 1.3 70.5 - - - +
245A PRO* 1.3 73.1 - - - +
246A VAL* 2.9 17.0 + - - +
247A THR* 3.2 18.9 + - + +
248A ARG* 2.9 20.6 + - - +
313A GLU* 2.9 15.7 + - - +
384A ARG* 2.7 42.0 + - - -
391A ASN* 5.4 0.9 + - - -
404A TRP* 3.2 33.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A ARG 2.8 5.8 - - - +
244A ASP* 1.3 90.0 - - - +
246A VAL* 1.3 56.1 + - + +
248A ARG* 3.8 4.8 + - + +
249A ALA* 3.1 28.8 + - - +
289A GLY* 3.6 19.1 - - - +
291A TYR* 3.8 17.7 - - + +
387A TYR* 3.6 37.8 + - + -
391A ASN* 3.4 25.6 - - - +
404A TRP* 3.6 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ASP* 2.9 11.9 + - - +
245A PRO* 1.3 75.0 - - - +
247A THR* 1.3 66.0 + - + +
249A ALA* 3.2 6.5 + - - +
250A ILE* 3.1 38.9 + - + +
380A VAL* 4.6 15.7 - - + -
383A LEU* 3.9 21.3 - - + -
384A ARG* 3.6 53.2 - - + +
387A TYR* 3.9 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A ARG* 2.9 34.0 + - - +
244A ASP* 3.2 25.2 + - + +
246A VAL* 1.3 78.5 - - + +
248A ARG* 1.3 57.8 + - - +
250A ILE* 4.5 9.2 - - + -
251A SER* 2.9 29.8 + - - -
313A GLU* 4.3 1.2 + - - -
372A HIS* 3.8 6.6 - - - +
384A ARG* 4.3 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A VAL* 4.0 11.0 - - + -
161A LYS* 2.9 40.6 + - - +
162A LYS* 4.0 5.9 - - + +
243A ARG* 3.8 17.5 - - - +
244A ASP 2.9 16.9 + - - +
245A PRO 3.8 3.1 + - - +
247A THR* 1.3 77.0 + - - +
249A ALA* 1.3 58.6 + - - +
251A SER* 3.2 3.8 + - - -
252A ASP* 2.8 76.2 + - - +
285A ALA* 2.7 34.2 + - - +
288A ILE* 3.7 26.9 - - - +
289A GLY* 4.2 6.4 - - - +
291A TYR* 3.4 24.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
245A PRO 3.1 18.9 + - - +
246A VAL* 3.2 7.2 + - - +
248A ARG* 1.3 89.0 - - - +
250A ILE* 1.3 57.5 + - - +
252A ASP* 3.2 3.3 + - - +
253A TYR* 2.8 29.1 + - - +
266A PHE* 3.9 18.5 - - + -
285A ALA* 3.6 23.1 - - + +
286A ILE* 5.0 3.4 - - + +
383A LEU* 5.2 2.2 - - + -
387A TYR* 4.4 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A VAL* 3.1 32.0 + - + +
247A THR* 3.9 9.0 - - + +
249A ALA* 1.3 75.0 - - - +
251A SER* 1.3 53.5 + - - +
253A TYR* 3.3 3.0 + - + +
254A THR* 2.7 39.8 + - - +
266A PHE* 3.7 27.8 - - + -
372A HIS* 3.5 33.2 - - + +
373A PRO* 4.5 6.1 - - + -
375A ILE* 3.5 36.3 - - + -
380A VAL* 5.0 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LYS* 3.2 24.5 - - - -
243A ARG* 3.4 13.0 + - - -
247A THR 2.9 19.0 + - - -
248A ARG 3.2 5.4 + - - -
250A ILE* 1.3 73.9 - - - +
252A ASP* 1.3 66.4 + - - +
254A THR* 3.2 4.2 + - - -
255A GLN* 3.0 24.4 + - - +
370A ARG* 5.0 1.2 + - - -
372A HIS* 3.7 11.2 - - - -
602B A3P 2.6 26.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LYS* 2.8 22.3 + - - -
162A LYS* 3.7 9.4 - - - +
248A ARG* 2.8 51.1 + - - +
249A ALA 3.3 6.1 - - - +
251A SER* 1.3 75.7 - - - +
253A TYR* 1.3 61.7 + - - +
255A GLN* 3.2 3.9 + - - +
256A THR 3.2 9.7 + - - -
284A SER* 4.9 2.0 + - - -
285A ALA* 3.9 11.5 + - + -
288A ILE* 3.7 15.2 - - - +
702A NA 2.2 49.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ALA 2.8 14.1 + - - +
250A ILE* 3.4 9.0 - - - +
252A ASP* 1.3 76.5 - - - +
254A THR* 1.3 61.0 + - - +
256A THR* 3.1 9.4 + - - -
257A LEU* 2.9 44.6 + - + +
263A ILE* 3.5 24.1 + - + +
264A PRO 2.5 30.5 + - - -
265A THR* 3.4 8.0 - - - -
266A PHE* 3.5 44.9 - + + -
269A LEU* 3.8 19.5 - - + -
283A TRP* 4.0 11.9 - + + -
285A ALA* 5.1 0.8 - - - +
373A PRO* 4.1 21.3 - - + -
702A NA 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ILE 2.7 27.8 + - - -
251A SER* 3.2 8.5 + - - -
253A TYR* 1.3 77.7 - - - +
255A GLN* 1.3 62.3 + - - +
257A LEU* 3.3 10.8 + - + +
258A SER* 3.1 22.5 + - - -
370A ARG* 3.9 23.8 - - + -
371A THR 3.5 23.3 - - - +
372A HIS* 3.8 8.3 - - + -
373A PRO* 3.3 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LYS* 3.9 24.6 - - - +
162A LYS* 2.8 33.8 + - - +
251A SER 3.0 11.6 + - - +
252A ASP* 3.5 10.3 - - - +
253A TYR 3.2 0.2 - - - -
254A THR* 1.3 73.8 - - - +
256A THR* 1.3 64.3 + - - +
258A SER* 2.5 23.2 + - - -
259A LYS* 3.4 34.2 + - + +
367A THR 5.0 0.2 - - - +
368A LYS* 5.4 0.7 + - - -
370A ARG* 3.1 34.6 + - - +
700A SO4 5.1 4.2 + - - -
702A NA 4.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ASP 3.2 0.8 + - - -
253A TYR* 3.1 11.4 + - - -
255A GLN* 1.3 75.6 - - - +
257A LEU* 1.3 55.3 + - - +
259A LYS* 2.9 12.5 + - + +
260A ARG* 2.7 35.8 + - + -
263A ILE* 3.9 23.8 - - + -
702A NA 2.2 31.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A TYR* 2.9 35.6 + - + +
254A THR* 3.5 15.3 - - + +
256A THR* 1.3 77.0 - - - +
258A SER* 1.3 61.4 + - - +
260A ARG 3.7 1.3 - - - -
261A PRO* 3.1 49.7 - - + +
263A ILE* 3.6 30.4 - - + +
373A PRO* 5.0 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A THR 3.1 12.5 + - - -
255A GLN 2.5 22.8 + - - -
257A LEU* 1.3 75.8 - - - +
259A LYS* 1.3 64.5 + - - +
261A PRO* 4.6 6.2 - - - +
370A ARG* 3.7 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A GLN* 3.4 42.8 - - - +
256A THR* 2.9 11.7 + - + +
258A SER* 1.3 84.7 - - - +
260A ARG* 1.3 63.9 + - + +
261A PRO* 3.8 5.2 - - - +
370A ARG* 5.5 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A THR* 2.7 16.4 + - + +
257A LEU* 3.2 5.0 - - - +
259A LYS* 1.3 79.3 - - + +
261A PRO* 1.3 63.5 - - - +
262A ASP* 3.0 30.3 + - + +
263A ILE* 3.3 39.8 + - + +
----------------------------------------------------------
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