Contacts of the helix formed by residues 230 - 248 (chain A) in PDB entry 1EG4
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 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A PHE 4.3 0.2 - - - -
229A CYS* 1.3 73.7 - - - +
231A GLN* 1.3 64.1 + - - +
232A ARG* 3.8 15.4 + - - +
233A ARG* 3.1 35.1 + - - +
234A LEU* 3.0 18.7 + - - +
267A PHE* 3.5 8.3 - - - -
274A PRO 3.5 20.6 - - - +
275A GLU* 4.4 6.7 - - + +
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Residues in contact with GLN 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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230A ASP* 1.3 75.7 - - - +
232A ARG* 1.3 63.9 + - - +
234A LEU 3.5 0.2 + - - -
235A GLY* 2.9 19.2 + - - -
260A GLU* 5.2 5.2 - - - +
263A VAL* 3.5 21.1 - - + +
264A ARG* 4.7 13.5 - - - +
267A PHE* 3.5 49.1 - - + +
273A LYS 5.5 0.6 + - - -
274A PRO* 4.5 1.7 + - - +
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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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230A ASP* 3.3 14.9 + - - +
231A GLN* 1.3 78.2 - - - +
233A ARG* 1.4 101.1 + - - +
235A GLY* 3.1 3.6 + - - -
236A LEU* 3.1 48.9 + - + +
260A GLU* 6.1 0.2 - - - -
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Residues in contact with ARG 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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222A VAL* 3.0 49.8 + - - +
223A ALA 3.6 10.7 + - - -
224A SER* 3.8 23.7 - - - +
228A PHE 3.9 16.6 - - - -
229A CYS* 3.7 12.1 - - - -
230A ASP* 3.1 24.1 + - - +
232A ARG* 1.4 103.9 - - - +
234A LEU* 1.3 66.6 + - - +
236A LEU* 3.2 29.4 - - + +
237A LEU 3.4 4.2 + - - -
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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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219A PHE* 5.5 0.9 - - + -
229A CYS* 3.5 15.1 - - - -
230A ASP 3.0 18.3 + - - +
231A GLN 3.9 4.0 - - - +
233A ARG* 1.3 77.2 - - - +
235A GLY* 1.3 63.7 + - - +
237A LEU* 3.1 12.2 + - + +
238A LEU* 3.0 40.0 + - + +
263A VAL* 4.2 11.7 - - + -
266A CYS* 3.6 37.7 - - + -
267A PHE* 3.8 16.6 - - + -
276A ILE* 4.6 2.9 - - + -
281A PHE* 3.9 31.0 - - + -
284A TRP* 4.7 0.9 - - + -
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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 GLN 2.9 13.8 + - - -
232A ARG 3.1 5.3 + - - -
234A LEU* 1.3 76.9 - - - +
236A LEU* 1.3 52.4 + - - +
238A LEU 4.6 0.2 - - - -
239A HIS* 2.7 38.7 + - - +
259A ILE* 3.7 9.6 - - - +
260A GLU* 5.6 2.2 - - - -
263A VAL* 3.6 21.2 - - - +
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Residues in contact with LEU 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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195A ARG* 5.4 5.5 + - - +
197A LEU* 4.0 16.9 - - + +
222A VAL* 4.0 14.1 - - + +
232A ARG* 3.1 43.5 + - + +
233A ARG* 3.2 21.1 - - + +
235A GLY* 1.3 75.7 - - - +
237A LEU* 1.3 62.3 + - - +
239A HIS* 3.8 4.4 - - + +
240A ASP* 3.1 24.3 + - - +
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Residues in contact with LEU 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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197A LEU* 4.9 2.9 - - + -
201A THR* 4.3 13.0 - - - +
218A LEU* 3.7 50.7 - - + +
219A PHE* 4.0 7.0 - - + +
222A VAL* 3.9 22.8 - - + +
233A ARG 3.4 1.4 + - - -
234A LEU* 3.1 12.7 + - + +
236A LEU* 1.3 77.0 - - - +
238A LEU* 1.3 66.7 + - + +
240A ASP* 3.3 3.4 + - - +
241A SER* 2.9 44.7 + - - +
281A PHE* 3.8 31.6 - - + -
292A MET* 5.6 3.1 - - + -
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Residues in contact with LEU 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 LEU* 3.0 32.1 + - + +
235A GLY 4.1 0.4 - - - +
237A LEU* 1.3 78.3 - - + +
239A HIS* 1.3 68.7 + - - +
241A SER* 3.8 3.2 - - - -
242A ILE* 3.0 28.1 + - - +
259A ILE* 3.9 19.2 - - + +
262A SER* 4.0 14.4 - - - -
263A VAL* 3.8 35.2 - - + +
281A PHE* 5.0 3.4 - - + -
284A TRP* 4.2 15.7 - - + -
291A SER* 4.4 3.8 - - - +
292A MET* 3.8 34.3 - - + +
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Residues in contact with HIS 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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195A ARG* 4.3 19.7 + - - -
235A GLY 2.7 24.9 + - - +
236A LEU* 3.8 5.8 - - + +
238A LEU* 1.3 75.9 - - - +
240A ASP* 1.3 64.0 + - - +
242A ILE* 3.3 5.8 - - - +
243A GLN* 3.0 45.9 + - + +
257A SER 4.7 11.7 + - - -
259A ILE* 3.5 19.5 + - + +
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Residues in contact with ASP 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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186A TYR* 2.8 31.1 + - + -
195A ARG* 2.7 45.9 + - - -
197A LEU* 3.4 9.0 - - + +
198A SER* 3.0 29.7 + - - -
201A THR* 3.6 20.0 - - + +
236A LEU 3.1 17.0 + - - +
237A LEU 4.0 1.8 - - - +
239A HIS* 1.3 76.3 - - - +
241A SER* 1.3 68.4 + - - +
243A GLN* 3.4 8.2 + - - +
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Residues in contact with SER 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A THR* 3.5 19.7 - - - +
205A SER* 4.9 2.4 + - - -
218A LEU* 4.9 1.6 - - - +
237A LEU* 2.9 28.0 + - - +
238A LEU 3.8 1.3 - - - -
240A ASP* 1.3 78.1 - - - +
242A ILE* 1.3 56.7 + - - +
243A GLN 3.1 5.4 + - - -
244A ILE* 3.1 25.5 + - - +
245A PRO* 3.4 3.6 - - - +
292A MET* 3.5 37.3 - - - +
294A TRP* 3.6 11.5 - - - -
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Residues in contact with ILE 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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238A LEU 3.0 15.4 + - - +
239A HIS* 3.3 18.6 - - - +
241A SER* 1.3 72.4 - - - +
243A GLN* 1.3 74.2 + - - +
244A ILE 3.2 0.8 + - - -
245A PRO* 3.2 8.8 - - + +
246A ARG* 3.1 23.3 + - + +
251A VAL* 3.7 17.9 - - + -
254A PHE* 3.6 36.6 - - + +
256A GLY 3.8 12.1 - - - +
257A SER* 4.4 11.2 - - - +
259A ILE* 3.7 15.9 - - + -
291A SER* 3.7 25.6 - - - +
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Residues in contact with GLN 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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185A VAL* 3.6 30.6 - - + +
186A TYR* 3.7 18.8 - - + -
239A HIS* 3.0 50.0 + - + +
240A ASP* 3.5 8.7 - - - +
241A SER 3.1 0.8 + - - -
242A ILE* 1.3 94.8 - - - +
244A ILE* 1.3 56.7 + - - +
246A ARG* 3.4 34.3 + - - +
247A GLN* 2.9 30.5 + - - +
257A SER* 5.2 1.8 + - - -
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Residues in contact with ILE 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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112A LEU* 3.7 33.9 - - + -
181A TRP* 4.2 23.6 + - + +
185A VAL* 4.3 9.1 - - + +
186A TYR* 3.8 21.5 - - + +
201A THR* 4.1 9.6 - - + +
202A GLY* 4.2 6.5 - - - -
205A SER* 4.0 21.3 - - - +
206A LEU* 4.7 2.5 - - + -
241A SER 3.1 11.3 + - - +
243A GLN* 1.3 78.2 - - - +
245A PRO* 1.3 71.4 - - + +
247A GLN* 3.4 10.2 + - - +
248A LEU* 3.6 13.0 + - - +
294A TRP* 4.0 18.2 - - + -
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Residues in contact with PRO 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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108A THR* 3.9 16.8 - - + -
241A SER 3.4 8.1 - - - +
242A ILE* 3.2 19.7 - - + +
244A ILE* 1.3 95.4 - - + +
246A ARG* 1.3 64.8 + - - +
248A LEU* 3.0 15.8 + - + +
250A GLU* 3.1 19.8 + - + -
251A VAL* 4.3 1.6 - - + -
254A PHE* 3.8 31.9 - - + -
294A TRP* 3.5 30.7 - - + +
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Residues in contact with ARG 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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185A VAL 5.3 2.6 + - - -
188A THR* 4.4 14.5 + - - +
242A ILE* 3.1 20.0 + - - +
243A GLN* 3.4 31.8 + - - +
245A PRO* 1.3 77.0 - - - +
247A GLN* 1.3 56.7 + - - +
249A GLY* 3.0 21.1 + - - -
251A VAL* 3.7 29.5 + - + +
257A SER* 4.1 24.1 - - - +
6P TYR* 4.1 22.3 + - - -
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Residues in contact with GLN 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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88A MET* 5.7 0.2 - - - +
92A TYR* 2.6 46.5 + - - -
181A TRP* 4.0 11.8 - - - +
184A ASN* 3.6 44.3 + - + +
185A VAL* 3.8 17.5 - - + -
243A GLN 2.9 18.0 + - - +
244A ILE 3.7 4.9 + - - +
245A PRO 3.2 0.2 - - - -
246A ARG* 1.3 75.6 - - - +
248A LEU* 1.3 64.8 + - - +
249A GLY 3.4 0.7 + - - -
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Residues in contact with LEU 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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92A TYR* 3.7 36.1 - - + +
95A LEU* 3.8 18.0 - - + +
108A THR* 4.2 13.5 - - + -
111A LYS* 3.8 31.9 + - + +
112A LEU* 3.6 37.7 - - + +
115A LEU* 5.2 3.6 - - + -
181A TRP* 6.0 0.2 - - - +
244A ILE 3.9 10.1 - - - +
245A PRO 3.0 9.0 + - - +
247A GLN* 1.3 76.3 - - - +
249A GLY* 1.3 60.9 + - - +
250A GLU* 3.5 13.7 + - + +
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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