Contacts of the helix formed by residues 243 - 259 (chain A) in PDB entry 1S9J
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 GLN 243 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A GLU* 4.6 0.2 - - - +
241A SER* 3.2 2.8 + - - +
242A VAL* 1.3 87.0 - - + +
244A SER* 1.3 64.9 + - - +
246A ILE* 3.0 19.1 + - - +
346A PRO* 3.1 37.0 + - + +
347A ALA* 5.6 0.4 - - - -
349A ARG* 3.0 42.3 + - - +
350A ALA 3.0 24.5 + - - +
351A ASP* 3.1 29.2 - - - +
352A LEU* 4.6 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A MET* 4.3 5.2 - - - -
230A MET* 5.3 0.2 - - - -
231A SER* 2.5 32.1 + - - -
233A GLU* 3.6 14.0 + - - -
234A ARG* 3.8 15.7 + - - +
240A TYR* 4.3 13.7 - - - -
241A SER 3.2 15.5 + - - -
243A GLN* 1.3 79.8 - - - +
245A ASP* 1.3 61.5 + - - +
247A TRP* 3.3 6.6 + - - +
248A SER* 3.3 23.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LEU* 4.1 23.1 - - + +
187A MET* 3.4 21.3 - - - +
188A HIS* 3.0 31.8 + - - +
189A ARG* 3.1 23.6 + - - -
190A ASP 4.4 1.0 + - - -
191A VAL* 4.2 9.4 + - + +
242A VAL* 3.2 12.9 + - - +
243A GLN 3.1 0.8 - - - -
244A SER* 1.3 76.3 - - - +
246A ILE* 1.3 65.4 + - + +
248A SER* 3.3 9.1 + - - -
249A MET* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LEU* 4.8 4.3 - - + -
242A VAL 4.5 4.0 - - - +
243A GLN* 3.0 25.7 + - - +
245A ASP* 1.3 75.8 - - + +
247A TRP* 1.3 66.7 + - - +
249A MET* 3.2 12.4 + - + +
250A GLY 3.0 18.4 + - - -
341A CYS* 3.7 37.2 - - - +
349A ARG* 3.8 6.1 - - - -
350A ALA 3.6 25.1 - - - +
351A ASP* 4.5 0.2 - - - -
352A LEU* 3.7 36.1 - - + +
355A LEU* 3.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A TYR 3.6 13.1 + - - -
230A MET 3.5 11.1 + - - -
231A SER* 3.6 24.5 - - - -
232A PRO* 3.6 29.8 - - + -
243A GLN 3.5 2.0 + - - -
244A SER 3.3 9.4 + - - +
246A ILE* 1.3 76.9 - - - +
248A SER* 1.3 66.0 + - - +
250A GLY 3.1 1.4 + - - -
251A LEU* 3.0 39.2 + - + +
263A ILE* 5.1 1.3 - - + -
317A ILE* 4.0 25.2 - - + +
322A PRO* 4.1 19.1 - - + -
323A PRO* 4.5 9.4 - - + -
341A CYS 3.4 12.0 + - - -
342A LEU* 3.3 48.6 - - + +
344A LYS* 4.3 7.2 - - + -
349A ARG* 3.6 25.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ARG 6.0 1.0 - - - -
190A ASP* 5.8 0.3 + - - -
191A VAL* 3.2 32.1 + - - +
229A TYR* 2.7 30.0 + - - +
230A MET* 4.6 2.4 - - - -
231A SER 4.8 0.2 + - - -
244A SER* 3.3 13.7 + - - -
245A ASP* 3.5 11.7 + - - -
246A ILE 3.2 0.4 - - - -
247A TRP* 1.3 79.3 - - - +
249A MET* 1.3 55.3 + - - +
251A LEU* 3.6 2.2 + - - +
252A SER* 2.7 35.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A SER* 4.6 4.3 - - - +
173A VAL* 3.4 37.5 - - + -
174A ILE* 4.1 16.2 - - + -
177A LEU* 5.0 5.6 - - + -
191A VAL* 4.0 13.7 - - + +
245A ASP 3.0 13.8 + - - +
246A ILE* 3.5 12.8 - - + +
248A SER* 1.3 73.4 - - - +
250A GLY* 1.3 66.6 + - - +
252A SER* 3.3 5.0 + - - -
253A LEU* 3.0 41.3 + - + +
337A PHE* 4.1 15.0 - - + -
341A CYS* 3.7 28.9 - - - -
355A LEU* 3.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ILE 3.0 10.9 + - - -
247A TRP 3.1 3.1 + - - -
249A MET* 1.3 77.0 - - - +
251A LEU* 1.3 60.2 + - - +
253A LEU* 3.3 12.3 + - - +
254A VAL* 3.2 27.5 + - - +
338A VAL* 4.5 4.4 - - - +
341A CYS* 3.8 23.5 - - - +
342A LEU* 3.9 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A SER 3.5 24.5 - - - +
229A TYR* 4.0 21.3 - - + -
247A TRP* 3.0 29.2 + - + +
248A SER 4.1 4.3 - - - +
250A GLY* 1.3 73.9 - - - +
252A SER* 1.3 64.9 + - - +
254A VAL* 3.4 3.6 + - + +
255A GLU* 3.1 22.3 + - - +
261A TYR* 4.0 12.1 - - + +
262A PRO* 3.6 20.6 - - + +
263A ILE* 3.8 17.3 - - + -
317A ILE* 5.9 1.1 - - + -
323A PRO* 3.5 31.9 - - + -
342A LEU* 3.6 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A VAL* 3.9 1.4 + - - +
192A LYS* 3.5 22.5 + - - -
193A PRO* 3.5 19.9 - - - +
196A ILE* 5.2 5.6 - - - -
229A TYR* 3.9 6.2 - - - -
248A SER 2.7 23.9 + - - -
249A MET* 3.3 7.2 + - - -
251A LEU* 1.3 79.4 - - - +
253A LEU* 1.3 56.6 + - - +
255A GLU* 3.3 6.5 + - - +
256A MET* 3.1 43.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LEU* 3.9 25.9 - - + +
169A VAL* 4.6 8.5 - - + -
170A SER* 3.3 28.9 - - - +
173A VAL* 6.4 0.4 - - + -
249A MET* 3.0 36.6 + - + +
250A GLY* 3.6 9.2 - - - +
251A LEU 3.3 0.4 - - - -
252A SER* 1.3 75.3 - - - +
254A VAL* 1.3 64.5 + - - +
256A MET* 3.9 17.0 - - + -
257A ALA* 3.1 25.8 + - - +
334A PHE* 4.4 9.1 - - + -
337A PHE* 3.7 24.2 - - + -
338A VAL* 4.3 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A GLY 3.2 15.5 + - - +
251A LEU* 3.8 7.4 - - + +
252A SER 3.3 0.2 - - - -
253A LEU* 1.3 75.2 - - - +
255A GLU* 1.3 64.0 + - - +
258A VAL* 3.1 31.2 + - + +
260A ARG 4.5 0.2 - - - +
262A PRO* 3.7 24.2 - - + -
323A PRO* 4.7 5.6 - - + +
324A LYS 4.3 12.8 - - - +
325A LEU* 3.9 27.4 - - + -
338A VAL* 4.2 14.8 - - + -
342A LEU* 4.1 20.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
152A ASP* 5.7 2.9 - - - +
155A LEU* 3.9 16.7 - - + +
193A PRO* 4.1 12.2 - - + +
227A ARG* 3.1 26.3 + - - -
229A TYR* 2.7 38.2 + - - -
251A LEU 3.1 12.4 + - - +
252A SER 3.5 8.5 - - - +
253A LEU 3.3 0.4 - - - -
254A VAL* 1.3 78.3 - - - +
256A MET* 1.3 58.3 + - + +
259A GLY* 3.0 26.3 + - - -
260A ARG* 3.5 27.6 + - - +
261A TYR* 3.7 8.4 - - - +
262A PRO* 3.8 7.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 3.8 38.8 - - + -
155A LEU* 3.3 28.0 - - + +
160A ARG* 3.9 1.0 - - - -
161A ILE* 3.1 36.6 + - + -
166A LEU* 3.7 28.9 - - + -
169A VAL* 4.6 4.9 - - + -
193A PRO* 4.5 14.1 - - + -
196A ILE* 5.0 5.6 - - + -
252A SER* 3.1 36.8 + - - +
253A LEU* 3.9 15.5 - - + +
255A GLU* 1.3 77.1 - - - +
257A ALA* 1.3 61.7 + - - +
259A GLY 4.1 0.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
160A ARG* 3.4 24.8 - - - +
161A ILE 4.1 5.1 - - - +
166A LEU* 3.6 18.1 - - + +
253A LEU 3.1 20.1 + - - +
254A VAL 3.9 3.1 - - - +
256A MET* 1.3 78.3 - - - +
258A VAL* 1.3 59.2 + - - +
325A LEU* 4.2 8.5 - - + -
330A PHE* 3.5 32.6 - - + -
334A PHE* 4.2 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ARG* 3.8 12.7 + - - +
254A VAL* 3.1 25.3 + - + +
255A GLU 4.4 0.9 - - - +
257A ALA* 1.3 77.5 - - - +
259A GLY* 1.3 59.3 + - - +
260A ARG* 4.5 13.5 - - + +
262A PRO* 6.3 2.0 - - + -
266A PRO* 4.9 15.3 - - + -
271A LEU* 5.5 1.6 - - + -
274A MET* 3.7 37.8 - - + +
275A PHE* 4.3 9.0 - - + -
325A LEU* 4.1 9.4 - - + -
326A PRO* 4.0 29.2 - - + -
330A PHE* 4.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LEU* 4.4 13.2 - - - +
159A GLY 3.4 26.8 - - - +
160A ARG* 4.0 3.8 - - - +
255A GLU 3.0 12.0 + - - -
256A MET 4.1 0.6 + - - -
257A ALA 3.5 2.0 - - - -
258A VAL* 1.3 78.3 - - - +
260A ARG* 1.3 60.1 + - - +
274A MET* 5.4 1.6 - - - -
----------------------------------------------------------
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