Contacts of the helix formed by residues 230 - 249 (chain A) in PDB entry 1WBB
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 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A LEU* 3.8 14.6 - - + -
159A GLU* 3.2 19.7 - - - +
227A VAL* 3.1 13.3 + - - +
228A GLU 3.1 2.2 + - - -
229A ASN* 1.3 79.6 - - + +
231A PRO* 1.3 59.6 - - - +
233A GLY 3.3 0.7 + - - -
234A LEU* 2.9 31.2 + - - +
260A MET* 3.8 27.1 - - + -
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Residues in contact with PRO 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLU* 4.2 2.0 - - - +
206A ILE* 3.8 26.9 - - + -
210A ARG* 4.2 12.6 - - - +
229A ASN 3.2 13.5 - - - +
230A ALA* 1.3 82.2 - - - +
232A ARG* 1.3 67.4 + - - +
234A LEU* 3.1 3.0 + - + +
235A CYS* 2.9 31.9 + - - -
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Residues in contact with ARG 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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137A TRP* 3.2 32.2 + - - +
139A ASP* 2.7 56.9 + - - +
141A LYS* 3.4 26.1 - - - +
142A GLY* 3.5 13.7 - - - +
143A PHE 3.3 33.4 - - - +
144A GLY* 3.4 9.1 - - - -
159A GLU* 3.1 25.5 + - + +
231A PRO* 1.3 80.0 - - - +
233A GLY* 1.3 60.0 + - - +
235A CYS* 3.7 4.5 + - - +
236A ALA 3.8 1.2 + - - -
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Residues in contact with GLY 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A GLY* 4.1 4.3 - - - -
145A TYR 4.5 1.3 - - - -
146A ALA* 4.6 2.1 - - - +
157A LEU* 3.6 23.6 - - - +
158A SER 3.9 16.2 - - - -
159A GLU* 3.3 7.3 + - - +
230A ALA 3.3 2.2 + - - -
231A PRO 3.2 0.4 - - - -
232A ARG* 1.3 75.4 - - - +
234A LEU* 1.3 60.5 + - - +
235A CYS 3.1 1.8 - - - -
236A ALA* 3.2 5.4 + - - +
237A ALA* 2.9 27.2 + - - +
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Residues in contact with LEU 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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157A LEU* 3.6 18.3 - - + +
206A ILE* 3.8 10.3 - - + -
209A ALA* 3.3 11.8 - - + +
210A ARG* 3.5 37.5 - - + +
213A LEU* 3.8 15.5 - - + +
222A LEU* 3.5 26.9 - - + -
227A VAL* 3.2 29.6 - - + +
230A ALA 2.9 25.8 + - - +
231A PRO* 3.6 5.2 - - + +
233A GLY* 1.3 75.6 - - - +
235A CYS* 1.3 56.5 + - - +
237A ALA* 3.6 2.9 - - - +
238A GLY 2.8 24.3 + - - -
258A ILE* 5.5 0.9 - - + -
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Residues in contact with CYS 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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137A TRP* 3.9 25.4 - - + +
203A GLU 4.1 0.2 - - - +
204A PHE* 3.1 42.7 - - + +
206A ILE* 3.8 28.7 - - - -
209A ALA* 4.6 4.4 - - - +
231A PRO* 2.9 24.9 + - - +
232A ARG 3.7 7.9 - - - +
233A GLY 3.1 0.2 - - - -
234A LEU* 1.3 76.1 - - - +
236A ALA* 1.3 61.0 + - - +
238A GLY* 3.3 9.5 + - - -
239A CYS 3.3 9.5 + - - -
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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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135A ALA* 3.2 39.1 - - + +
136A ILE* 4.4 1.3 - - - +
137A TRP* 4.6 2.2 - - + +
144A GLY* 4.0 21.8 - - - +
146A ALA* 4.1 6.5 - - - +
204A PHE* 4.0 16.1 - - + -
232A ARG 3.8 2.9 + - - +
233A GLY 3.2 7.5 + - - +
235A CYS* 1.3 76.4 - - - +
237A ALA* 1.3 60.7 + - - +
239A CYS 3.5 0.5 + - - -
240A LEU* 3.0 24.9 + - - +
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Residues in contact with ALA 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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146A ALA* 3.8 15.2 - - + +
155A PHE* 3.8 6.8 - - + -
157A LEU* 4.2 2.0 - - + -
213A LEU* 4.2 9.5 - - + +
233A GLY 2.9 16.2 + - - +
234A LEU* 3.6 11.2 - - - +
235A CYS 3.2 0.2 - - - -
236A ALA* 1.3 75.2 - - - +
238A GLY* 1.3 64.7 + - - +
240A LEU* 3.6 3.1 - - - +
241A LEU* 3.1 25.5 + - - +
258A ILE* 3.8 28.7 - - + -
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Residues in contact with GLY 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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203A GLU 4.8 0.4 - - - -
209A ALA* 3.5 30.9 - - - +
212A GLN* 5.6 2.5 - - - +
213A LEU* 4.6 4.0 - - - +
234A LEU 2.8 10.3 + - - -
235A CYS 3.3 1.8 + - - -
236A ALA 3.2 0.2 - - - -
237A ALA* 1.3 74.6 - - - +
239A CYS* 1.3 59.7 + - - +
241A LEU* 3.8 4.2 - - - +
242A GLN* 2.9 40.1 + - - +
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Residues in contact with CYS 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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135A ALA* 4.5 0.9 - - + -
179A LEU* 3.8 19.1 - - - -
199A ARG* 4.0 7.4 - - - -
203A GLU* 3.4 39.2 + - - +
204A PHE* 3.5 40.8 - - + -
235A CYS 3.3 5.2 + - - +
236A ALA 3.7 7.6 - - - +
238A GLY* 1.3 73.9 - - - +
240A LEU* 1.3 65.1 + - - +
242A GLN* 3.0 8.3 + - - +
243A TYR* 2.8 23.4 + - - +
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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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133A LEU* 3.3 38.6 - - + +
134A ALA 3.5 24.0 - - - +
135A ALA* 3.6 1.5 - - + +
146A ALA* 3.8 14.6 - - + -
147A THR 3.6 24.9 - - - -
148A LEU* 3.7 8.3 - - + -
155A PHE* 3.6 26.2 - - + -
179A LEU* 3.8 8.0 - - + +
236A ALA 3.0 14.9 + - - +
237A ALA 3.6 5.4 - - - +
239A CYS* 1.3 78.3 - - - +
241A LEU* 1.3 57.9 + - - +
243A TYR* 3.1 4.3 + - - +
244A ALA* 2.8 29.3 + - - +
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Residues in contact with LEU 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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148A LEU* 6.2 0.9 - - + -
155A PHE* 4.5 17.9 - - + -
212A GLN* 3.5 40.8 - - + +
213A LEU* 3.9 13.7 - - + -
216A GLN* 3.9 31.2 - - + -
237A ALA 3.1 15.6 + - - +
238A GLY 3.8 2.9 - - - +
240A LEU* 1.3 75.7 - - - +
242A GLN* 1.3 66.7 + - - +
244A ALA* 3.2 9.8 + - + +
245A LYS* 2.9 41.0 + - + +
252A LEU* 5.1 1.8 - - + -
255A ILE* 4.9 11.7 - - + -
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Residues in contact with GLN 242 (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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202A TRP* 4.8 12.9 - - - -
203A GLU* 3.7 28.0 + - - +
208A THR* 4.2 23.4 - - - +
209A ALA 5.2 2.0 - - - +
212A GLN* 4.3 28.5 - - + +
238A GLY* 2.9 31.3 + - - +
239A CYS* 3.5 7.2 - - - +
241A LEU* 1.3 77.5 - - - +
243A TYR* 1.3 59.7 + - - +
245A LYS* 3.8 7.7 - - + +
246A ASP* 3.1 23.6 + - - +
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Residues in contact with TYR 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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89A SER* 4.2 0.2 + - - -
115A THR* 3.5 14.7 - - + +
118A THR* 4.4 0.9 - - + -
133A LEU* 3.9 16.4 - - + -
177A GLU* 2.7 38.8 + - - -
179A LEU* 3.6 40.2 - - + -
197A ARG* 3.5 12.7 + - - -
199A ARG* 3.6 36.8 - - - +
203A GLU* 5.5 2.6 + - - +
239A CYS* 2.8 8.1 + - - +
240A LEU 3.4 8.1 - - - +
242A GLN* 1.3 73.6 - - - +
244A ALA* 1.3 64.0 + - - +
246A ASP* 3.3 11.3 + - + +
247A THR* 3.1 47.0 + - + +
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Residues in contact with ALA 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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118A THR* 4.9 0.4 - - - -
133A LEU* 4.6 6.7 - - + -
148A LEU* 4.1 24.9 - - + -
150A ILE* 4.5 8.5 - - + -
240A LEU 2.8 15.8 + - - +
241A LEU* 3.2 12.1 + - + +
243A TYR* 1.3 77.0 - - - +
245A LYS* 1.3 60.7 + - - +
247A THR* 2.9 20.2 + - - -
248A GLN* 3.2 16.6 + - - +
252A LEU* 4.1 12.7 - - + +
255A ILE* 5.2 0.9 - - + -
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Residues in contact with LYS 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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212A GLN* 2.8 36.0 + - - +
215A LEU* 4.5 13.7 - - - +
216A GLN* 5.0 10.3 + - - +
241A LEU* 2.9 36.9 + - + +
242A GLN* 3.8 6.5 - - + +
244A ALA* 1.3 76.1 - - - +
246A ASP* 1.3 58.3 + - - +
249A ARG* 2.8 32.1 + - - +
250A THR 5.1 4.2 - - - +
252A LEU* 4.0 21.1 - - + -
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Residues in contact with ASP 246 (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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24A HIS* 4.7 2.9 - - - -
113A ILE* 3.4 26.2 - - - +
199A ARG* 5.8 2.1 + - - -
242A GLN 3.1 17.6 + - - +
243A TYR* 3.7 12.7 - - + +
244A ALA 3.3 0.4 - - - -
245A LYS* 1.3 75.3 - - - +
247A THR* 1.3 64.0 + - - +
249A ARG* 3.1 45.1 + - - -
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Residues in contact with THR 247 (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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112A ARG* 3.3 6.8 - - - +
113A ILE* 2.9 43.5 + - + +
115A THR* 3.8 26.9 - - + -
118A THR* 3.6 10.2 - - - +
243A TYR* 3.1 32.5 + - + +
244A ALA* 2.9 20.4 + - - -
246A ASP* 1.3 80.2 - - - +
248A GLN* 1.3 81.3 + - - +
249A ARG* 4.3 0.2 - - - +
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Residues in contact with GLN 248 (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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111A VAL 3.3 12.1 - - - +
112A ARG* 4.5 12.3 - - - +
113A ILE 4.2 3.6 + - - -
118A THR* 3.6 24.4 + - - +
120A SER* 5.1 1.7 + - - -
150A ILE* 3.6 20.6 - - + -
244A ALA 3.2 15.9 + - - +
247A THR* 1.3 104.4 + - - +
249A ARG* 1.3 71.3 + - - +
250A THR* 3.2 16.2 + - - +
252A LEU* 3.7 24.5 - - + -
357A LEU* 4.2 18.4 - - + +
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Residues in contact with ARG 249 (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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23A GLN* 5.6 7.3 + - - +
24A HIS* 3.7 20.8 + - - -
110A VAL* 3.0 47.8 + - - +
111A VAL* 3.7 15.5 - - - +
112A ARG* 4.4 2.2 - - - +
113A ILE* 4.7 0.2 - - - +
245A LYS 2.8 23.4 + - - +
246A ASP* 3.1 44.0 + - - +
247A THR 4.3 1.3 - - - +
248A GLN* 1.3 75.0 - - - +
250A THR* 1.3 64.0 + - - +
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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