Contacts of the helix formed by residues 229 - 245 (chain A) in PDB entry 1B70
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 ALA 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A GLY 4.0 2.2 - - - +
228A ILE* 1.3 76.9 - - - +
230A MET* 1.3 66.1 + - - +
231A ALA* 3.4 2.2 - - + +
232A HIS* 2.9 31.2 - - + +
233A LEU 3.8 2.4 + - - -
285A MET* 3.5 11.8 - - - +
313A PHE* 3.8 2.4 - - - -
413B ARG 3.4 16.8 - - - +
414B LEU 2.9 16.4 - - - +
415B LEU 3.6 1.1 - - - +
416B GLY* 3.6 19.5 - - - +
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Residues in contact with MET 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ALA* 1.3 69.9 - - - +
231A ALA* 1.3 68.3 + - - +
232A HIS 2.9 2.5 - - - -
233A LEU* 2.8 41.7 + - + +
234A LYS* 2.9 15.6 + - + +
253A PHE* 5.7 2.9 - - + -
263A PRO* 4.2 29.2 - - + +
265A ALA* 4.6 16.6 - - + -
284A GLY* 4.0 16.8 - - - -
285A MET* 3.4 23.1 - - + +
414B LEU 2.9 7.3 + - - -
415B LEU* 3.1 22.1 + - + +
469B TYR* 4.9 8.5 - - + -
472B ILE* 4.3 24.9 - - + -
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Residues in contact with ALA 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ALA* 3.4 2.6 - - + -
230A MET* 1.3 75.8 - - - +
232A HIS* 1.3 57.9 + - + +
234A LYS* 3.3 3.2 + - - +
235A GLY 2.8 24.9 + - - -
415B LEU 2.9 14.0 + - - +
416B GLY* 4.1 15.5 - - - +
472B ILE* 3.8 6.3 - - + +
473B PRO* 3.2 29.6 - - + +
475B ALA* 3.2 26.4 + - + -
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Residues in contact with HIS 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A GLY 3.9 10.3 + - - -
228A ILE* 3.7 8.9 - - + +
229A ALA* 2.9 43.0 + - + +
230A MET 2.9 0.2 - - - -
231A ALA* 1.3 77.2 - - + +
233A LEU* 1.3 60.5 + - - +
235A GLY 3.4 0.3 + - - -
236A ALA* 2.8 29.5 + - - +
313A PHE* 3.5 17.4 - - + -
475B ALA* 3.4 19.8 - - + +
476B LEU* 3.6 12.7 + - - +
477B PRO* 3.4 43.5 - - + +
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Residues in contact with LEU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A MET* 2.8 41.5 + - + +
232A HIS* 1.3 79.6 - - - +
234A LYS* 1.3 60.2 + - + +
236A ALA* 2.9 4.3 + - - +
237A ILE* 2.8 43.5 + - + +
253A PHE* 4.1 12.8 - - + -
265A ALA* 6.0 0.2 - - + -
283A ALA* 3.6 22.0 - - + -
284A GLY* 3.6 25.1 - - - +
313A PHE* 3.5 41.1 - - + -
315A PHE* 4.3 6.5 - - + -
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Residues in contact with LYS 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A MET* 2.9 13.1 + - + +
231A ALA 3.3 9.6 - - - +
233A LEU* 1.3 77.7 - - + +
235A GLY* 1.3 57.4 + - - +
237A ILE* 3.4 2.4 + - - +
238A TYR* 2.9 28.6 + - - +
251A VAL* 4.8 5.0 - - - +
253A PHE* 3.8 45.9 - - + -
469B TYR 2.9 21.4 + - - +
470B GLU* 3.4 17.6 + - - +
472B ILE* 2.8 46.7 + - + +
473B PRO 4.0 0.4 - - - +
474B LEU* 3.7 22.7 - - + +
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Residues in contact with GLY 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A ALA 2.8 14.9 + - - -
234A LYS* 1.3 69.0 - - - +
236A ALA* 1.3 66.3 + - - +
238A TYR* 3.1 5.0 + - - +
239A GLU* 2.8 28.6 + - - +
474B LEU* 3.8 16.5 - - - +
475B ALA 3.4 17.7 - - - -
476B LEU* 3.8 9.9 - - - -
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Residues in contact with ALA 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A PHE* 4.8 5.7 - - + -
117A LEU* 4.6 8.7 - - - +
119A TYR* 3.9 22.9 - - + +
232A HIS 2.8 15.4 + - - +
233A LEU* 3.0 14.8 - - + +
235A GLY* 1.3 78.6 - - - +
237A ILE* 1.3 71.7 + - + +
239A GLU* 3.1 6.1 + - - +
240A LEU* 3.1 18.4 + - - +
313A PHE* 4.1 6.5 - - + -
315A PHE* 5.1 2.9 - - + -
476B LEU* 4.0 7.3 - - + +
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Residues in contact with ILE 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A PHE* 4.9 1.1 - - + -
233A LEU* 2.8 20.3 + - + +
236A ALA* 1.3 75.6 - - + +
238A TYR* 1.3 65.3 + - - +
240A LEU* 3.0 27.3 + - + +
241A ALA* 2.9 19.6 + - - +
251A VAL* 3.7 15.0 - - + -
253A PHE* 3.4 41.5 - - + -
267A PHE* 4.2 31.4 - - + -
268A ALA 5.6 0.4 - - - +
269A VAL* 6.4 1.3 - - + -
315A PHE* 4.1 33.7 - - + -
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Residues in contact with TYR 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A LYS 2.9 19.8 + - - +
235A GLY* 3.4 6.1 - - - +
237A ILE* 1.3 78.0 - - - +
239A GLU* 1.3 82.6 + - + +
241A ALA* 3.2 3.6 + - + +
242A GLN* 3.1 58.9 + - + +
247A PRO 5.5 0.2 + - - -
249A SER 5.1 3.8 - - - -
250A LYS* 5.5 3.4 - - + -
251A VAL* 3.6 25.8 - - + -
474B LEU* 3.4 28.3 - - + -
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Residues in contact with GLU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ILE* 5.5 1.1 - - - -
117A LEU* 3.7 26.5 - - + +
235A GLY 2.8 17.2 + - - +
236A ALA 3.4 8.5 - - - +
238A TYR* 1.3 92.2 - - + +
240A LEU* 1.3 58.1 + - - +
242A GLN* 3.3 11.5 + - - +
243A ALA* 2.8 32.0 + - - +
476B LEU* 4.5 20.8 - - + +
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Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU* 4.3 8.5 - - + -
113A ILE* 4.1 23.3 - - + -
114A PHE* 3.8 32.8 - - + -
117A LEU* 5.5 0.6 - - - +
236A ALA 3.1 12.3 + - - +
237A ILE* 3.0 26.9 + - + +
239A GLU* 1.3 77.3 - - - +
241A ALA* 1.3 61.8 + - - +
243A ALA* 3.2 5.7 + - - +
244A LEU* 3.0 43.4 + - + +
267A PHE* 5.3 5.4 - - + -
280A LEU* 5.5 8.7 - - + -
317A LEU* 4.3 16.6 - - + -
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Residues in contact with ALA 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A ILE 2.9 6.2 + - - +
238A TYR* 3.4 9.9 - - + +
240A LEU* 1.3 74.0 - - - +
242A GLN* 1.3 69.7 + - + +
244A LEU* 2.7 17.3 + - - +
245A PHE* 2.8 15.2 + - - +
249A SER* 3.6 17.8 + - - +
250A LYS* 4.6 2.5 - - - +
251A VAL* 3.7 19.7 - - + -
269A VAL* 3.6 27.1 - - + -
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Residues in contact with GLN 242 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A TYR* 3.1 49.0 + - + +
239A GLU* 3.4 16.6 - - - +
241A ALA* 1.3 77.6 - - - +
243A ALA* 1.3 62.8 + - - +
244A LEU 4.0 0.2 - - - -
245A PHE 2.3 24.2 - - - +
246A GLY 4.7 1.9 - - - -
247A PRO* 2.7 45.9 + - - +
249A SER* 3.2 28.9 + - - -
250A LYS* 5.3 0.2 - - - +
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Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A GLU* 5.2 2.3 - - - +
113A ILE* 3.1 42.4 - - + +
239A GLU* 2.8 15.8 + - - +
240A LEU 3.3 6.7 - - - +
241A ALA 3.1 0.2 - - - -
242A GLN* 1.3 78.9 - - - +
244A LEU* 1.3 58.2 + - - +
326A ARG* 5.3 0.3 + - - -
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Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A MET* 4.8 3.6 - - + -
109A GLU* 4.0 18.2 - - + +
110A LEU* 4.9 2.2 - - + -
113A ILE* 4.0 15.5 - - + -
240A LEU* 3.0 29.5 + - + +
241A ALA* 2.7 14.7 + - - +
243A ALA* 1.3 75.6 - - - +
245A PHE* 1.3 78.4 + - + +
280A LEU* 5.6 4.9 - - + -
322A LEU* 3.9 35.2 - - + -
326A ARG* 2.6 50.7 + - - +
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Residues in contact with PHE 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A ALA* 2.8 13.1 + - - +
242A GLN* 2.3 35.0 - - - +
244A LEU* 1.3 101.3 - - + +
246A GLY* 1.3 65.9 + - - +
249A SER* 3.9 2.7 - - - -
269A VAL* 3.8 30.5 - - + -
270A TRP 3.8 14.1 - - - -
271A TRP* 3.9 22.9 - + + -
272A PRO* 3.7 18.8 - - + -
273A GLU* 5.7 3.6 - - + -
278A LEU* 4.3 17.0 - - + -
322A LEU* 4.5 10.3 - - + -
325A LEU* 4.4 9.0 - - + -
326A ARG* 3.5 24.2 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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