Contacts of the helix formed by residues 237 - 255 (chain A) in PDB entry 1O1L
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 237 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A VAL 3.2 3.3 - - - +
236A ASP* 1.3 94.5 - - - +
238A VAL* 1.3 63.8 + - - +
239A ASN 3.0 1.3 + - - -
240A PHE* 3.2 30.6 + - + +
241A LYS* 4.2 7.2 + - - +
279A THR* 4.0 18.1 - - + +
282A TYR* 4.1 18.6 - - + -
37B TRP* 3.9 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ASP* 3.1 19.1 + - - +
237A PRO* 1.3 78.1 - - - +
239A ASN* 1.3 79.4 + - - +
240A PHE 3.3 0.7 + - - -
241A LYS* 3.3 27.0 + - + +
242A LEU* 3.9 16.1 + - + +
99B ASP* 4.7 1.1 - - - +
101B GLU* 3.8 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A MET* 4.4 1.2 - - - +
180A THR* 4.7 2.6 + - - -
181A THR* 3.3 25.8 + - + +
184A TYR* 3.4 18.5 + - - -
235A VAL* 3.9 12.1 - - + -
236A ASP* 2.9 25.0 + - - +
237A PRO 3.0 1.2 - - - -
238A VAL* 1.3 80.7 - - - +
240A PHE* 1.3 66.0 + - - +
242A LEU* 3.2 15.3 + - - +
243A LEU 3.1 17.7 + - - -
285A HEM 3.6 17.4 - - + +
99B ASP* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A HIS* 4.0 18.8 - + + -
235A VAL* 3.9 17.0 - - + -
236A ASP 4.1 0.9 - - - -
237A PRO* 3.2 18.7 + - + +
239A ASN* 1.3 78.3 - - - +
241A LYS* 1.3 63.1 + - + +
243A LEU* 3.4 3.5 + - - +
244A SER* 3.0 27.8 + - - -
275A SER* 3.4 24.9 + - - +
278A LEU* 3.8 26.2 - - + -
279A THR* 3.5 28.0 - - + -
282A TYR* 3.8 20.0 - - - -
285A HEM 3.4 48.2 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A PRO 4.5 8.1 - - - +
238A VAL* 3.3 20.0 + - + +
239A ASN 3.3 0.6 - - - -
240A PHE* 1.3 78.8 - - + +
242A LEU* 1.3 64.8 + - + +
244A SER* 3.5 7.2 + - - -
245A HIS* 3.2 23.2 + - - +
275A SER* 5.4 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A MET* 4.1 7.9 - - - -
178A PHE* 4.0 46.2 - - + -
180A THR* 4.9 5.4 - - - +
181A THR* 3.8 24.0 - - + -
238A VAL* 3.9 20.2 - - + +
239A ASN* 3.2 18.1 + - - +
241A LYS* 1.3 78.3 - - + +
243A LEU* 1.3 65.2 + - - +
245A HIS* 3.4 4.9 + - + +
246A CYS* 3.1 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ALA* 4.5 19.1 - - + +
171A TRP* 3.9 41.5 - - + +
174A MET* 3.5 23.7 - - + -
204A VAL* 4.4 3.4 - - + -
239A ASN 3.1 8.4 + - - +
240A PHE 3.4 5.6 + - - +
242A LEU* 1.3 79.3 - - - +
244A SER* 1.3 58.4 + - - +
246A CYS* 3.1 4.5 + - - +
247A LEU* 2.8 38.8 + - + +
285A HEM 3.7 52.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
240A PHE 3.0 18.6 + - - -
241A LYS* 3.6 8.9 - - - -
242A LEU 3.2 0.2 - - - -
243A LEU* 1.3 78.2 - - - +
245A HIS* 1.3 56.3 + - - +
247A LEU* 3.4 8.2 + - - +
248A LEU* 3.0 33.2 + - - +
268A ASP* 5.6 4.7 - - - -
271A LEU* 3.6 33.8 + - - +
272A ALA* 5.4 0.6 - - - -
275A SER* 3.6 14.6 + - - -
285A HEM 5.4 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A PHE* 4.1 21.1 - + + -
241A LYS 3.2 14.2 + - - +
242A LEU* 3.7 5.6 - - + +
244A SER* 1.3 77.7 - - - +
246A CYS* 1.3 58.9 + - - +
248A LEU* 3.2 12.4 + - - +
249A VAL* 2.9 45.5 + - + +
108D ASN* 3.4 54.1 + - + +
111D VAL* 4.3 2.2 - - + -
112D CYS* 4.2 7.0 - - - -
127D GLN* 4.2 4.5 - - - -
131D GLN* 2.7 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ALA* 3.6 19.7 - - - +
173A ARG* 4.0 5.7 - - + -
174A MET* 3.5 33.2 - - + +
178A PHE* 3.8 18.6 - - - -
242A LEU 3.1 13.2 + - - +
243A LEU* 3.1 8.6 + - - +
245A HIS* 1.3 82.3 - - - +
247A LEU* 1.3 58.9 + - - +
249A VAL* 3.5 6.9 + - - +
250A THR* 2.9 29.4 + - - -
127D GLN* 3.9 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A TRP* 5.6 7.4 - - + -
166A TYR* 4.9 3.1 - - + +
167A GLY* 4.9 9.9 - - - +
170A ALA* 3.5 24.2 - - + -
171A TRP* 6.3 0.4 - - + -
204A VAL* 5.3 3.4 - - + -
208A LEU* 3.9 31.0 - - + -
243A LEU* 2.8 44.1 + - + +
244A SER* 3.6 6.5 - - - +
246A CYS* 1.3 69.2 - - - +
248A LEU* 1.3 62.0 + - - +
250A THR* 3.2 5.0 + - - -
251A LEU* 2.9 41.0 + - + +
271A LEU* 4.1 22.4 - - + -
285A HEM 4.8 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A SER 3.0 17.9 + - - +
245A HIS* 3.4 13.9 - - - +
247A LEU* 1.3 77.2 - - - +
249A VAL* 1.3 56.2 + - - +
251A LEU* 3.3 6.8 + - + +
252A ALA* 2.9 29.8 + - - +
259A PHE* 3.9 19.7 - - + -
264A HIS* 4.1 23.3 - - + +
267A LEU* 3.7 32.5 - - + -
268A ASP* 3.4 32.3 - - + +
271A LEU* 4.2 11.2 - - + -
35D TYR* 5.4 2.0 - - - +
112D CYS* 4.2 13.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ARG* 4.0 12.6 - - - +
245A HIS* 2.9 44.8 + - + +
246A CYS 3.9 4.0 - - - +
248A LEU* 1.3 75.5 - - - +
250A THR* 1.3 62.4 + - - +
252A ALA* 3.3 7.3 + - - +
253A ALA* 3.0 22.9 + - - +
111D VAL* 3.8 13.2 - - + -
112D CYS* 4.0 10.3 - - - -
115D ALA* 3.6 18.8 - - + +
122D PHE* 4.1 5.8 - - + -
127D GLN* 3.6 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A TYR* 3.5 40.6 - - + +
169A GLU* 3.8 24.5 - - - +
170A ALA* 3.5 10.3 + - - -
173A ARG* 3.3 19.1 + - - +
246A CYS 2.9 16.1 + - - -
247A LEU* 3.5 11.2 - - + -
249A VAL* 1.3 77.8 - - - +
251A LEU* 1.3 63.5 + - + +
253A ALA* 3.3 7.0 + - - +
254A HIS* 3.2 27.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
155A ALA* 5.8 1.8 - - + -
156A TRP* 4.6 19.7 - - + -
159A VAL* 3.9 27.4 - - + -
166A TYR* 4.3 17.7 - - + -
247A LEU* 2.9 33.8 + - + +
248A LEU* 3.7 8.7 - - + +
250A THR* 1.3 73.6 - - + +
252A ALA* 1.3 57.8 + - - +
254A HIS* 3.1 3.5 + - - -
255A LEU* 2.8 44.7 + - + +
259A PHE* 4.5 10.8 - - + -
267A LEU* 3.7 31.6 - - + -
271A LEU* 5.7 3.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
248A LEU 2.9 17.2 + - - +
249A VAL* 3.6 6.7 - - - +
251A LEU* 1.3 76.6 - - - +
253A ALA* 1.3 61.4 + - - +
254A HIS 3.4 0.9 + - - -
255A LEU 3.7 6.2 + - - -
256A PRO* 4.2 1.2 - - - +
259A PHE* 3.6 36.9 - - + -
112D CYS* 3.8 18.8 - - - +
115D ALA* 3.7 3.5 - - + +
116D HIS* 3.5 27.1 - - - +
119D GLY* 5.4 0.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
169A GLU* 4.7 0.2 - - - +
173A ARG* 4.2 17.9 - - - +
249A VAL 3.0 17.0 + - - +
250A THR 3.8 4.7 - - - +
251A LEU 3.2 0.6 - - - -
252A ALA* 1.3 75.4 - - - +
254A HIS* 1.3 67.2 + - + +
256A PRO* 5.0 3.4 - - - +
115D ALA* 3.4 18.6 + - + +
119D GLY* 3.5 34.5 - - - +
120D LYS* 4.1 3.1 + - - +
122D PHE 5.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LYS* 5.5 1.2 + - - -
165A GLU* 4.8 6.3 - - - -
166A TYR* 3.4 59.0 + + + +
169A GLU* 2.8 35.7 + - - -
250A THR* 3.2 24.8 + - + +
251A LEU* 3.1 3.6 + - - +
253A ALA* 1.3 83.3 + - + +
255A LEU* 1.3 66.9 + - + +
256A PRO* 3.3 12.7 - - - +
120D LYS* 6.4 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ALA* 4.0 26.5 - - + +
158A LYS* 3.3 33.0 - - + +
159A VAL* 4.3 15.3 - - + +
166A TYR* 5.5 3.1 - - + +
251A LEU* 2.8 28.7 + - + +
252A ALA 3.7 4.2 + - - -
253A ALA 3.7 0.2 - - - -
254A HIS* 1.3 87.7 - - + +
256A PRO* 1.3 66.7 - - - +
257A ALA 3.2 2.7 - - - -
258A GLU* 3.0 37.5 - - + +
259A PHE* 3.0 27.3 + - + +
267A LEU* 6.1 0.7 - - + -
----------------------------------------------------------
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