Contacts of the helix formed by residues 234 - 256 (chain A) in PDB entry 1BIB
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLN* 2.3 38.5 + - - +
71A GLN* 5.1 1.2 - - - +
75A GLN* 4.8 0.7 + - - -
232A ASN 3.8 1.2 + - - -
233A LEU* 1.3 71.1 - - - +
235A ARG* 1.3 65.6 + - - +
236A ASN* 3.2 8.2 + - - +
237A THR* 2.5 47.0 + - - +
238A LEU* 2.9 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLN* 3.4 42.5 + - + +
66A LEU 4.4 5.2 - - - -
67A LEU* 4.4 13.9 - - + +
110A GLU* 3.2 39.8 + - - +
128A GLY 2.4 30.9 + - - -
130A ASN 3.5 11.3 + - - -
131A LEU* 4.6 9.4 - - + +
209A MET* 3.5 44.6 - - + +
210A ALA* 4.9 4.2 - - - +
233A LEU 3.2 7.0 + - - +
234A ASP* 1.3 71.6 - - - +
236A ASN* 1.4 56.5 + - - +
238A LEU* 3.6 7.0 - - - +
239A ALA* 2.8 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLN* 2.6 33.1 - - - +
66A LEU 3.3 11.1 + - - -
67A LEU* 3.3 6.7 - - - +
68A ASN* 2.7 28.1 + - - -
71A GLN* 3.3 37.5 + - + +
72A ILE* 3.3 24.9 - - + +
75A GLN* 4.2 5.5 + - - +
234A ASP* 3.2 5.6 + - - +
235A ARG* 1.4 73.3 - - - +
237A THR* 1.3 65.7 + - - +
239A ALA* 3.4 2.3 - - - +
240A ALA* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLN* 3.6 23.0 + - - +
164A LEU* 3.9 26.5 - - + -
234A ASP* 2.5 36.3 + - - +
236A ASN* 1.3 72.4 - - - +
238A LEU* 1.4 53.7 - - - +
240A ALA* 2.7 10.4 + - - +
241A MET* 2.7 42.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU* 4.1 8.5 - - + -
160A VAL* 3.7 20.9 - - + -
161A LEU* 4.5 17.9 - - + -
164A LEU* 3.8 13.8 - - + +
207A ILE* 4.6 7.2 - - + -
209A MET* 4.2 21.3 - - + -
226A LEU* 4.7 2.0 - - + -
233A LEU* 4.4 25.8 - - + -
234A ASP 2.9 11.4 + - - +
235A ARG* 3.6 9.6 - - - +
237A THR* 1.4 72.6 - - - +
239A ALA* 1.3 74.4 + - - +
240A ALA 3.1 0.2 + - - -
241A MET* 4.5 0.7 - - - +
242A LEU* 2.9 50.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 4.7 6.3 - - + -
72A ILE* 3.9 22.9 - - + -
108A ILE* 4.7 11.2 - - + -
131A LEU* 4.3 7.4 - - + +
133A LEU* 4.2 3.9 - - - +
235A ARG 2.8 22.6 + - - +
236A ASN 3.4 8.1 - - - +
238A LEU* 1.3 80.7 - - - +
240A ALA* 1.3 60.3 + - - +
242A LEU* 3.3 10.0 + - - +
243A ILE* 3.1 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 4.3 13.9 - - + +
75A GLN* 4.0 34.1 - - + +
76A LEU* 3.8 11.9 - - + +
236A ASN 3.1 11.6 + - - +
237A THR 2.7 16.0 + - - +
239A ALA* 1.3 73.9 - - - +
241A MET* 1.3 63.1 + - - +
243A ILE* 3.3 5.6 + - - +
244A ARG* 3.0 28.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
160A VAL* 3.6 25.6 - - + -
163A LYS* 3.7 31.6 - - + +
164A LEU* 3.4 42.4 - - + -
237A THR* 2.7 24.8 + - + +
238A LEU* 4.0 2.5 - - - +
240A ALA* 1.3 71.2 - - - +
242A LEU* 1.3 55.2 + - - +
244A ARG* 2.8 35.1 + - - +
245A GLU* 2.6 42.3 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
131A LEU* 4.4 8.1 - - + -
133A LEU* 3.8 26.2 - - + -
156A VAL* 5.3 1.8 - - + -
157A MET* 4.2 26.5 - - + +
160A VAL* 3.8 27.4 - - + -
161A LEU* 6.1 0.9 - - + -
207A ILE* 4.4 12.1 - - + -
238A LEU* 2.9 39.4 + - + +
239A ALA* 3.4 6.1 - - - +
241A MET* 1.3 71.5 - - - +
243A ILE* 1.3 69.3 + - - +
245A GLU* 4.3 4.0 - - - -
246A LEU* 2.7 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 5.7 0.2 - - + -
76A LEU* 4.2 17.3 - - + -
81A VAL* 4.3 4.5 - - + -
106A ALA* 3.9 22.0 - - + -
108A ILE* 3.9 21.1 - - + -
133A LEU* 3.7 21.8 - - + -
135A MET* 3.6 12.2 - - + +
239A ALA 3.1 21.4 + - - +
240A ALA* 3.3 6.7 + - - +
241A MET 3.2 0.2 - - - -
242A LEU* 1.3 76.6 - - - +
244A ARG* 1.3 62.0 + - - +
246A LEU* 5.0 0.2 - - - -
247A ARG* 2.8 67.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
75A GLN* 3.6 29.4 + - - +
76A LEU* 4.3 12.1 - - + +
240A ALA* 3.0 19.6 + - - +
241A MET* 2.8 44.8 + - - +
243A ILE* 1.3 81.8 - - - +
245A GLU* 1.3 72.2 + - - +
246A LEU 3.1 1.2 + - - -
247A ARG* 3.2 7.0 + - - +
248A ALA* 3.1 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A VAL* 4.1 11.4 - - + +
159A GLU* 5.4 4.2 - - - +
160A VAL* 3.5 28.6 + - + +
163A LYS* 2.5 33.3 + - - +
241A MET* 2.6 29.0 + - + +
242A LEU 3.9 2.0 - - - +
244A ARG* 1.3 84.2 + - + +
246A LEU* 1.3 57.3 + - - +
248A ALA* 3.3 10.7 + - - +
249A ALA* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LEU* 4.1 25.4 - - + -
135A MET* 3.4 23.6 - - + -
152A VAL* 6.2 0.2 - - + -
153A ILE* 4.6 28.5 - - + +
156A VAL* 3.8 29.4 - - + -
157A MET* 5.3 6.3 - - + +
203A ILE* 6.1 4.3 - - + -
242A LEU* 2.7 37.5 + - + +
245A GLU* 1.3 68.1 - - - +
247A ARG* 1.3 58.0 - - - +
248A ALA 3.0 1.1 - - - -
249A ALA* 3.0 5.3 + - + +
250A LEU* 2.7 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU* 4.7 9.5 - - - +
77A ASP 4.2 7.1 + - - -
78A GLY 3.3 22.2 + - - -
79A GLY* 3.4 22.8 - - - -
80A SER 3.6 1.2 + - - -
81A VAL* 3.4 26.3 - - - +
104A GLY* 2.9 32.7 + - - -
135A MET* 3.5 14.1 - - + -
137A TRP* 4.2 17.6 - - + -
243A ILE* 2.8 38.4 + - - +
244A ARG* 4.0 5.6 - - - +
246A LEU* 1.3 76.0 - - - +
248A ALA* 1.3 61.4 + - - +
250A LEU 3.9 0.6 - - - +
251A GLU* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ARG 3.1 12.6 + - - +
245A GLU* 3.3 18.2 - - - +
246A LEU 3.0 0.4 - - - -
247A ARG* 1.3 76.8 - - - +
249A ALA* 1.3 56.0 + - - +
251A GLU* 2.9 12.1 + - - +
252A LEU* 2.8 34.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
152A VAL* 4.0 8.3 - - + -
156A VAL* 3.6 26.7 - - + -
245A GLU 2.9 10.3 + - - +
246A LEU* 3.4 10.5 - - + +
248A ALA* 1.3 79.9 - - - +
250A LEU* 1.3 61.4 + - + +
252A LEU* 2.8 4.4 + - - +
253A PHE* 2.7 27.9 + - - +
261A TYR* 3.0 23.0 + - + +
264A ARG* 5.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A MET* 5.2 2.7 - - - -
137A TRP* 3.6 54.6 + - + -
149A LEU* 3.8 31.2 - - + -
152A VAL* 4.3 13.5 - - + -
153A ILE* 5.1 6.5 - - + -
203A ILE* 3.7 26.5 - - + -
246A LEU* 2.7 27.3 + - + +
249A ALA* 1.3 79.7 - - + +
251A GLU* 1.3 62.3 + - - +
253A PHE* 3.7 7.5 - - + +
254A GLU* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A TRP* 4.1 14.2 - - + -
247A ARG* 3.0 16.3 + - - +
248A ALA* 2.9 14.3 + - - +
250A LEU* 1.3 76.5 - - - +
252A LEU* 1.3 73.3 + - - +
254A GLU* 3.4 15.1 + - + +
255A GLN* 3.6 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ALA 2.8 12.7 + - - +
249A ALA* 2.8 7.4 + - - +
251A GLU* 1.3 84.5 - - - +
253A PHE* 1.3 62.8 + - - +
255A GLN* 3.1 16.9 + - + +
256A GLU* 3.3 37.7 + - + +
260A PRO* 3.7 27.1 - - + -
261A TYR* 3.6 15.9 - - + +
264A ARG* 4.9 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 4.5 5.6 - - + -
144A ALA 3.7 23.3 - - - -
145A ALA* 4.1 4.0 - - - -
148A GLY* 4.0 4.7 - - - -
149A LEU* 3.6 46.2 - - + -
152A VAL* 3.6 20.0 - - + -
249A ALA 2.7 18.5 + - - +
250A LEU* 3.7 12.3 - - + +
252A LEU* 1.3 69.0 - - - +
254A GLU* 1.3 61.0 + - - +
255A GLN 2.9 8.2 + - - -
257A GLY* 2.9 55.9 + - - -
258A LEU* 3.3 27.8 - - + -
261A TYR* 4.0 6.9 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A TRP* 3.6 27.4 + - - +
138A ARG 3.8 4.9 - - - +
139A LEU* 3.6 22.7 - - + +
140A GLU* 3.2 37.5 + - - +
250A LEU 3.0 18.0 + - - +
251A GLU* 3.8 10.1 - - - +
252A LEU 3.3 0.4 - - - -
253A PHE* 1.3 77.8 - - - +
255A GLN* 1.3 58.6 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
251A GLU* 3.6 26.0 + - - +
252A LEU* 3.6 10.8 - - + +
253A PHE 2.9 0.6 - - - -
254A GLU* 1.3 81.8 - - + +
256A GLU* 1.3 76.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A LEU* 3.3 24.6 + - + +
253A PHE 3.2 0.6 + - - -
254A GLU 3.8 0.2 - - - -
255A GLN* 1.3 92.7 - - + +
257A GLY* 1.3 69.5 + - - +
258A LEU 3.7 0.5 + - - -
259A ALA* 3.7 10.6 - - - +
260A PRO* 3.2 38.2 - - + +
----------------------------------------------------------
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