Contacts of the helix formed by residues 237 - 253 (chain A) in PDB entry 5HAN
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 237 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ALA* 3.3 6.0 - - - +
236A ASP* 1.3 78.7 - - + +
238A HIS* 1.3 65.5 + - - +
239A TYR* 3.0 34.5 + - - +
240A GLU* 3.0 26.8 + - + +
241A MET* 3.2 10.9 + - - +
94B ASN* 4.7 12.9 + - - +
96B ILE* 3.5 20.0 - - - +
97B ASP* 5.0 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ASP 3.6 4.9 + - - -
237A ASP* 1.3 74.3 + - - +
239A TYR* 1.3 91.9 + + + +
241A MET* 3.2 13.4 + - - +
242A LEU* 3.1 49.0 + - + +
275A THR* 2.9 44.0 + - + +
279A ALA* 5.6 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ASP* 3.0 22.6 + - - +
238A HIS* 1.3 98.0 - + + +
240A GLU* 1.3 59.9 + - - +
242A LEU* 3.8 15.4 - - + +
243A ALA* 3.0 28.1 + - - +
96B ILE* 4.2 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ALA* 3.5 17.0 - - + -
237A ASP* 3.0 19.7 + - + +
239A TYR* 1.3 75.7 - - - +
241A MET* 1.3 59.4 + - - +
243A ALA* 3.4 2.1 + - - +
244A ARG* 2.7 61.0 + - - +
94B ASN* 3.4 26.6 - - - +
95B VAL* 2.8 40.0 + - - +
96B ILE* 3.1 24.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ILE* 3.3 44.9 - - + +
234A THR* 4.4 1.1 - - - -
235A ALA* 3.8 18.4 - - + +
237A ASP 3.2 12.6 + - - +
238A HIS* 3.2 11.5 + - - +
240A GLU* 1.3 76.2 - - - +
242A LEU* 1.3 57.0 + - - +
244A ARG* 3.3 3.5 + - - +
245A GLY* 3.0 26.5 + - - -
263A VAL* 4.0 24.9 - - + -
272A ALA* 3.3 44.0 - - - +
275A THR* 3.9 21.3 - - + -
276A ALA* 4.4 1.8 - - + -
280A PHE* 4.2 2.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
238A HIS* 3.1 47.9 + - + +
239A TYR* 3.8 19.5 - - + +
241A MET* 1.3 76.8 - - - +
243A ALA* 1.3 56.5 + - - +
246A GLU* 2.9 53.5 + - - +
275A THR* 4.3 4.7 - - + -
279A ALA* 3.4 32.8 - - + -
280A PHE* 3.9 11.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A PHE* 5.0 0.4 - - - -
206A LYS* 6.0 0.3 - - - -
239A TYR 3.0 18.8 + - - +
240A GLU* 3.7 5.4 - - - +
241A MET 3.3 0.2 - - - -
242A LEU* 1.3 75.5 - - - +
244A ARG* 1.3 62.0 + - + +
246A GLU* 4.1 8.1 - - - +
247A PHE* 3.2 24.8 + - - +
95B VAL* 5.8 5.6 - - + -
96B ILE* 3.7 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A GLY* 3.8 13.9 - - - -
199A ASN* 3.5 10.3 - - - +
205A PHE* 3.5 38.0 - - + -
232A ASN* 4.0 9.9 + - - +
233A ILE* 4.0 24.5 - - + +
234A THR 3.8 10.7 + - - -
240A GLU* 2.7 43.5 + - - +
241A MET 3.7 4.0 - - - +
243A ALA* 1.3 77.3 - - - +
245A GLY* 1.3 62.3 + - - +
247A PHE* 3.7 0.2 - - - +
248A ILE* 3.1 29.1 + - - +
92B ASP* 2.9 32.5 + - - -
93B ARG 2.9 27.7 + - - -
95B VAL* 4.2 5.1 - - + +
101B MET* 3.6 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ILE* 4.1 3.4 - - - +
241A MET 3.0 12.5 + - - -
244A ARG* 1.3 76.3 - - - +
246A GLU* 1.3 60.0 + - - +
248A ILE 3.3 1.6 + - - -
249A LEU* 3.1 28.2 + - - +
261A PHE* 3.5 28.9 - - - -
280A PHE* 3.8 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LEU* 2.9 46.7 + - - +
243A ALA* 4.2 6.1 - - - +
245A GLY* 1.3 71.5 - - - +
247A PHE* 1.3 62.4 + - - +
249A LEU* 3.5 4.8 + - - +
250A GLU* 3.1 27.1 + - - +
280A PHE* 4.2 15.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A PHE* 3.9 17.5 - + + -
206A LYS* 3.7 65.5 - - + -
209A VAL* 3.7 18.8 - - + -
210A ARG* 3.8 25.4 - - + -
243A ALA 3.2 19.6 + - - +
244A ARG 3.7 3.4 - - - +
246A GLU* 1.3 72.9 - - - +
248A ILE* 1.3 64.0 + - - +
250A GLU* 3.5 8.0 + - + +
251A THR* 2.7 51.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A PHE* 3.6 24.0 - - + -
209A VAL* 3.8 20.2 - - + -
231A PHE* 3.5 48.5 - - + -
233A ILE* 4.0 13.2 - - + -
244A ARG 3.1 19.0 + - - +
245A GLY 3.7 3.8 - - - +
247A PHE* 1.3 76.2 - - - +
249A LEU* 1.3 57.2 - - - +
251A THR* 3.6 0.2 - - - -
252A PHE* 2.9 41.5 + - + +
259A ILE* 3.8 21.5 - - + -
261A PHE* 4.0 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A GLY 3.1 18.0 + - - +
246A GLU* 4.1 4.7 - - + +
247A PHE 3.4 0.2 - - - -
248A ILE* 1.3 75.4 - - - +
250A GLU* 1.3 63.1 + - - +
252A PHE* 3.5 0.6 + - - -
253A ALA* 3.0 19.8 + - - -
256A ALA* 3.7 27.5 - - + +
259A ILE* 4.2 9.0 - - + -
261A PHE* 3.8 12.6 - - + -
280A PHE* 4.0 26.7 - - + -
283A GLN* 3.6 40.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLU 3.1 18.0 + - - +
247A PHE* 3.9 9.5 - - + +
249A LEU* 1.3 78.1 - - - +
251A THR* 1.3 61.2 + - - +
253A ALA* 3.4 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A VAL* 4.1 17.3 - - + -
210A ARG* 4.2 20.2 - - + -
213A ALA* 4.0 23.0 - - + +
217A ARG* 4.9 4.0 + - - -
247A PHE* 2.7 45.1 + - - -
248A ILE 3.6 2.9 - - - -
250A GLU* 1.3 78.6 - - - +
252A PHE* 1.3 61.6 + - + +
253A ALA* 3.4 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A VAL* 3.8 11.0 - - + -
212A VAL* 4.0 5.4 - - + -
213A ALA* 3.4 42.2 - - + -
216A MET* 3.7 35.7 - - + -
217A ARG* 3.3 10.9 + - - -
231A PHE* 3.5 36.1 - + - -
248A ILE* 2.9 29.4 + - + +
251A THR* 1.3 78.0 - - - +
253A ALA* 1.3 61.0 + - - +
254A ASP 3.1 1.7 + - - -
255A ASN* 2.9 41.7 + - + +
256A ALA* 4.0 6.5 - - - +
259A ILE* 3.7 16.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
217A ARG* 4.1 4.5 - - - +
249A LEU 3.0 15.3 + - - -
250A GLU* 3.8 12.1 - - - +
251A THR 3.3 4.6 - - - +
252A PHE* 1.3 74.9 - - - +
254A ASP* 1.3 66.0 + - - +
256A ALA* 2.9 26.3 + - - +
----------------------------------------------------------
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