Contacts of the helix formed by residues 234 - 255 (chain B) in PDB entry 1HXD
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 234 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B GLN* 2.4 35.9 + - - -
71B GLN* 4.7 6.8 + - - -
164B LEU* 5.5 0.3 - - - +
232B ASN 4.3 0.4 + - - -
233B LEU* 1.3 73.9 - - - +
235B ARG* 1.3 64.7 + - - +
236B ASN* 2.8 16.3 + - - +
237B THR* 3.2 24.3 + - - +
238B LEU* 2.9 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 4.6 3.1 - - - +
65B GLN* 2.3 63.4 + - - +
66B LEU* 3.3 5.7 - - - +
67B LEU* 3.6 27.8 - - + +
108B ILE* 6.3 0.2 - - - +
109B ALA 4.5 5.5 + - - -
110B GLU* 2.8 31.5 + - - +
128B GLY* 3.2 28.9 + - - -
129B ALA 5.0 3.7 - - - -
130B ASN 3.7 20.4 + - - -
131B LEU* 4.0 13.8 - - + +
209B MET* 3.9 24.9 - - + -
233B LEU 3.1 3.4 + - - +
234B ASP* 1.3 74.2 + - - +
236B ASN* 1.3 62.1 + - - +
238B LEU* 3.8 6.5 - - - +
239B ALA* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B GLN* 3.6 18.5 - - - +
66B LEU 3.9 15.5 + - - -
67B LEU* 4.2 6.7 - - - +
68B ASN* 2.7 36.1 + - - +
71B GLN* 3.6 24.0 + - + +
72B ILE* 2.8 29.0 - - + +
75B GLN* 4.9 1.2 - - - +
234B ASP* 2.8 7.2 + - - +
235B ARG* 1.3 80.0 - - - +
237B THR* 1.3 66.5 + - - +
239B ALA* 4.5 0.2 - - - -
240B ALA* 3.2 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B GLN* 4.7 4.7 + - - -
75B GLN* 3.8 22.2 + - - +
164B LEU* 4.7 13.2 - - + -
234B ASP* 3.0 29.9 + - - +
236B ASN* 1.3 80.5 - - - +
238B LEU* 1.3 60.7 + - - +
240B ALA* 3.6 1.0 - - - +
241B MET* 2.9 45.3 + - + +
244B ARG* 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LEU* 4.1 12.1 - - + -
160B VAL* 4.4 3.6 - - + -
161B LEU* 3.5 29.2 - - + -
164B LEU* 3.7 25.0 - - + +
207B ILE* 4.3 17.7 - - + -
209B MET* 3.8 32.5 - - + -
226B LEU* 5.1 2.7 - - + -
233B LEU* 4.9 5.6 - - + -
234B ASP 2.9 16.1 + - - +
235B ARG* 3.8 4.0 - - - +
237B THR* 1.3 76.7 - - - +
239B ALA* 1.3 66.2 + - - +
241B MET* 3.0 3.6 - - - +
242B LEU* 2.9 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 5.6 2.0 - - + -
72B ILE* 4.5 14.4 - - + -
108B ILE* 4.5 13.7 - - + -
131B LEU* 4.4 12.3 - - + -
133B LEU* 4.7 0.9 - - - -
235B ARG 3.0 17.9 + - - +
236B ASN* 3.8 5.2 - - - +
238B LEU* 1.3 76.8 - - - +
240B ALA* 1.3 52.2 + - - +
242B LEU* 2.7 30.3 + - - +
243B ILE* 2.8 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE* 4.3 16.0 - - + +
75B GLN* 4.2 29.8 - - + +
76B LEU* 3.4 13.5 - - + +
236B ASN 3.2 16.4 + - - +
237B THR 3.6 5.2 - - - +
239B ALA* 1.3 75.8 - - - +
241B MET* 1.3 67.5 + - - +
243B ILE* 3.3 1.4 + - - -
244B ARG* 2.8 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B VAL* 3.5 31.6 - - + +
163B LYS* 5.4 13.7 - - + -
164B LEU* 3.4 28.5 - - + -
237B THR* 2.9 29.4 - - + +
238B LEU* 3.0 7.9 - - - +
240B ALA* 1.3 79.5 - - - +
242B LEU* 1.3 58.9 + - - +
244B ARG* 3.5 33.4 - - - +
245B GLU* 3.0 41.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LEU* 3.8 23.1 - - + -
133B LEU* 4.4 10.3 - - + -
156B VAL* 5.4 0.7 - - + -
157B MET* 4.2 40.4 - - + +
160B VAL* 4.5 12.3 - - + -
161B LEU* 6.4 0.4 - - + -
207B ILE* 4.2 7.2 - - + -
238B LEU* 2.9 39.9 + - + +
239B ALA* 2.7 13.5 + - - +
241B MET* 1.3 75.4 - - - +
243B ILE* 1.3 68.3 + - - +
245B GLU* 4.7 2.5 - - - -
246B LEU* 2.8 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE* 5.5 4.9 - - + -
76B LEU* 3.9 16.4 - - + -
81B VAL* 5.5 2.5 - - + -
106B ALA* 4.0 21.8 - - + -
108B ILE* 5.2 7.0 - - + -
133B LEU* 3.0 32.5 - - + -
135B MET* 3.6 14.6 - - + +
239B ALA* 2.8 44.9 + - + +
240B ALA* 3.9 3.8 - - - +
242B LEU* 1.3 73.7 - - - +
244B ARG* 1.3 64.6 + - - +
246B LEU* 2.9 11.7 + - - -
247B ARG* 2.9 51.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLN* 3.9 30.8 + - - +
76B LEU* 3.7 18.4 - - + +
237B THR* 6.0 0.4 - - - +
240B ALA* 2.8 23.1 + - - +
241B MET* 3.5 54.5 + - - +
243B ILE* 1.3 78.0 - - - +
245B GLU* 1.3 73.1 + - + +
247B ARG* 3.8 8.8 + - - +
248B ALA* 3.6 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B VAL* 4.1 22.3 - - + +
160B VAL* 4.3 14.3 - - + +
163B LYS* 5.2 11.4 - - - +
241B MET* 3.0 25.8 + - - +
242B LEU* 4.1 2.5 - - - +
244B ARG* 1.3 93.6 + - + +
246B LEU* 1.3 63.8 + - - +
247B ARG 3.1 1.3 - - - -
248B ALA* 3.9 11.1 - - - +
249B ALA* 3.1 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 4.8 15.5 - - + -
135B MET* 3.9 27.1 - - + -
153B ILE* 4.2 38.8 - - + +
156B VAL* 4.1 26.2 - - + -
157B MET* 5.1 8.3 - - + +
203B ILE* 5.6 4.9 - - + -
242B LEU* 2.8 39.8 + - + +
243B ILE 3.9 0.4 - - - +
245B GLU* 1.3 76.8 - - - +
247B ARG* 1.3 63.0 + - - +
249B ALA* 3.3 3.7 + - + +
250B LEU* 2.8 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU* 3.2 27.7 - - - +
77B ASP* 3.6 18.0 + - - -
78B GLY 3.7 7.3 + - - -
79B GLY* 3.8 1.0 - - - -
80B SER* 3.1 38.6 + - - +
81B VAL* 4.3 2.0 - - - +
104B GLY* 3.1 32.5 + - - +
106B ALA 5.0 0.2 - - - +
135B MET* 3.6 13.9 - - + -
137B TRP* 3.3 18.5 - - + -
243B ILE* 2.9 39.3 + - - +
244B ARG* 3.8 8.0 - - - +
246B LEU* 1.3 78.7 - - - +
248B ALA* 1.3 63.1 + - - +
250B LEU 3.0 2.3 + - - -
251B GLU* 2.8 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ARG 3.6 13.5 + - - +
245B GLU* 3.9 15.5 - - - +
247B ARG* 1.3 79.7 - - - +
249B ALA* 1.3 64.1 + - - +
251B GLU* 3.0 10.6 + - - +
252B LEU* 2.9 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B VAL* 3.9 19.5 - - + +
156B VAL* 3.9 16.8 - - + -
245B GLU 3.1 13.8 + - - +
246B LEU* 3.3 11.6 + - + +
248B ALA* 1.3 77.8 - - - +
250B LEU* 1.4 53.4 - - + +
252B LEU* 3.3 2.2 + - - -
253B PHE* 2.8 24.6 + - - +
261B TYR* 2.5 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B MET* 4.0 13.9 - - - -
137B TRP* 3.0 56.1 + - + +
149B LEU* 3.4 31.0 - - + -
152B VAL* 4.0 17.7 - - + -
153B ILE* 4.2 6.7 - - + -
203B ILE* 4.6 9.4 - - + -
246B LEU* 2.8 26.6 + - + +
249B ALA* 1.4 70.3 - - + +
251B GLU* 1.3 69.4 + - - +
252B LEU 3.0 1.3 - - - -
253B PHE* 3.8 7.2 - - + +
254B GLU* 2.9 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B TRP* 3.5 13.4 - - + -
247B ARG 2.8 16.0 + - - +
248B ALA* 3.7 9.6 - - - +
250B LEU* 1.3 78.0 - - - +
252B LEU* 1.3 60.9 + - - +
254B GLU* 3.2 13.9 - - - +
255B GLN* 2.5 45.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ALA 2.9 12.6 + - - +
249B ALA* 3.6 4.5 - - - +
251B GLU* 1.3 78.9 - - - +
253B PHE* 1.3 62.6 + - - +
254B GLU 2.9 1.4 + - - -
255B GLN* 2.9 17.8 + - + +
256B GLU* 3.4 21.1 + - + +
257B GLY 3.9 0.2 + - - -
260B PRO* 3.5 32.1 - - + -
261B TYR* 2.8 39.3 - - + +
264B ARG* 5.6 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 4.3 7.4 - - + -
145B ALA* 3.2 30.1 - - + -
148B GLY* 3.6 13.0 - - - -
149B LEU* 3.0 53.2 - - + -
152B VAL* 3.6 22.2 - - + -
249B ALA 2.8 20.4 + - - +
250B LEU* 3.1 8.7 + - + +
252B LEU* 1.3 71.0 - - - +
254B GLU* 1.4 63.8 + - - +
255B GLN 3.2 0.2 - - - +
257B GLY* 2.8 37.4 + - - +
258B LEU* 3.7 29.2 - - + -
261B TYR* 3.9 7.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B SER* 4.9 2.3 + - - -
137B TRP* 3.6 23.6 + - - +
138B ARG 3.2 22.3 - - - +
139B LEU* 3.9 18.0 - - + +
140B GLU* 4.8 6.0 + - - +
250B LEU 2.9 9.3 + - - +
251B GLU* 3.2 22.3 - - - +
253B PHE* 1.4 80.7 - - - +
255B GLN* 1.3 70.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B GLU* 2.5 49.1 + - - +
252B LEU* 2.9 10.1 + - + +
253B PHE 3.2 0.7 - - - +
254B GLU* 1.3 91.5 + - - +
256B GLU* 1.3 55.6 + - + +
257B GLY* 2.3 22.1 + - - -
----------------------------------------------------------
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