Contacts of the helix formed by residues 230 - 244 (chain A) in PDB entry 3EA4
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A VAL* 4.5 1.8 - - + -
226A MET* 5.0 4.0 + - - +
227A ASP* 2.9 28.0 + - - +
229A GLU* 1.3 85.4 - - - +
231A ILE* 1.3 63.2 - - - +
232A PRO 3.4 0.7 - - - -
233A ARG* 3.2 29.1 + - - +
234A ILE* 2.9 44.3 + - + +
269A GLN* 5.0 2.3 - - - +
272A ARG* 5.4 3.9 + - - -
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Residues in contact with ILE 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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99A GLY* 3.5 34.3 - - - +
102A ILE* 3.9 8.3 - - + +
103A LEU* 3.7 38.8 - - + +
106A ALA* 4.8 0.4 - - + -
225A VAL* 4.1 22.7 - - + -
228A VAL* 3.2 15.0 + - + +
230A ASP* 1.3 76.4 - - - +
232A PRO* 1.4 71.8 - - + +
234A ILE* 4.8 3.6 - - - -
235A ILE* 3.0 34.2 + - + +
254A VAL* 5.1 5.8 - - + -
258A ILE* 3.9 18.8 - - + -
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Residues in contact with PRO 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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102A ILE* 4.0 19.1 - - + -
106A ALA* 4.9 3.0 - - + +
228A VAL 4.0 4.0 - - - +
229A GLU* 3.7 11.7 - - - +
230A ASP 3.6 2.9 - - - -
231A ILE* 1.4 95.6 - - + +
233A ARG* 1.3 60.1 + - - +
235A ILE* 4.1 1.2 - - - +
236A GLU* 3.2 24.6 + - - +
265A PRO* 4.1 15.3 - - + -
266A ASN 3.5 27.6 - - - +
267A TRP* 3.9 25.0 - - + -
269A GLN* 4.8 2.5 - - + +
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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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223A TYR* 4.9 4.2 - - - -
230A ASP* 3.2 38.9 + - - +
232A PRO* 1.3 76.5 - - - +
234A ILE* 1.3 78.0 + - - +
236A GLU* 3.2 8.0 + - - +
237A GLU* 2.7 63.0 + - - +
269A GLN* 3.6 30.0 + - + +
270A ALA 3.5 27.4 - - - +
271A MET* 4.3 5.4 - - + -
272A ARG* 3.8 45.4 - - - +
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Residues in contact with ILE 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A TYR* 3.6 43.2 - - + -
224A LEU 5.0 2.0 - - - +
225A VAL* 3.9 27.6 - - + -
226A MET 5.4 0.2 - - - +
230A ASP* 2.9 39.8 + - + +
231A ILE* 4.1 2.5 - - - +
233A ARG* 1.3 92.0 - - - +
235A ILE* 1.3 55.2 + - + +
237A GLU* 3.2 7.1 + - - +
238A ALA* 2.7 33.3 + - - +
252A VAL* 3.8 25.6 - - + -
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Residues in contact with ILE 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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103A LEU* 4.4 21.8 - - + +
106A ALA* 3.7 44.0 - - + +
107A LEU* 4.4 4.5 - - + -
110A GLN* 4.2 3.1 - - + +
190A VAL* 5.4 1.1 - - + -
192A ILE* 4.7 13.2 - - + -
231A ILE* 3.0 30.0 + - + +
232A PRO 4.1 1.1 - - - +
234A ILE* 1.3 77.0 - - + +
236A GLU* 1.3 62.1 + - - +
238A ALA* 3.3 4.2 + - + +
239A PHE* 3.1 44.4 + - + -
252A VAL* 4.6 22.2 - - + -
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Residues in contact with GLU 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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110A GLN* 3.8 24.9 + - - +
232A PRO 3.2 19.8 + - - +
233A ARG* 3.7 7.1 - - - +
235A ILE* 1.3 76.1 - - - +
237A GLU* 1.3 57.3 + - - +
239A PHE* 3.5 1.9 + - - +
240A PHE* 3.0 28.2 + - + +
267A TRP 4.9 7.3 - - - +
269A GLN 4.1 16.3 - - - +
271A MET* 3.9 28.3 - - + +
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Residues in contact with GLU 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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223A TYR* 2.6 42.5 + - + +
233A ARG* 2.7 54.4 + - - +
234A ILE* 3.6 3.4 - - - +
236A GLU* 1.3 71.7 - - - +
238A ALA* 1.3 61.7 + - - +
240A PHE* 3.7 0.5 - - - +
241A LEU* 2.8 34.8 + - - +
271A MET* 3.7 24.0 - - + -
272A ARG* 2.8 23.3 + - - +
273A LEU* 3.8 21.0 - - + +
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Residues in contact with ALA 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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190A VAL* 4.2 15.5 - - + -
223A TYR* 4.4 3.1 - - + -
234A ILE 2.7 20.5 + - - +
235A ILE* 3.3 7.2 + - + +
237A GLU* 1.3 72.5 - - - +
239A PHE* 1.3 57.4 + - - +
241A LEU* 4.8 0.2 - - - -
242A ALA* 3.0 31.2 + - - +
250A VAL* 3.6 30.6 - - + +
252A VAL* 3.9 17.9 - - + -
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Residues in contact with PHE 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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107A LEU* 3.7 20.6 - - + -
110A GLN* 3.4 37.2 - - + +
112A VAL* 3.5 33.7 - - + -
161A PRO* 3.8 29.4 - - + -
163A ILE* 3.7 20.0 - - + -
190A VAL* 3.8 25.6 - - + -
235A ILE* 3.1 32.4 + - + +
236A GLU 4.0 1.1 - - - +
238A ALA* 1.3 74.3 - - + +
240A PHE* 1.3 64.7 + - - +
242A ALA* 3.5 0.6 + - - -
243A THR* 2.9 34.4 + - + +
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Residues in contact with PHE 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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236A GLU* 3.0 19.0 + - + +
237A GLU 3.2 2.9 + - - +
239A PHE* 1.3 76.5 - - - +
241A LEU* 1.3 55.6 + - - +
243A THR* 3.7 3.7 + - - -
244A SER* 2.7 59.9 + - - -
271A MET* 3.9 23.8 - - + -
273A LEU* 4.0 17.7 - - + -
276A TYR* 3.8 20.9 - + - -
277A MET* 4.0 18.2 - - + -
280A MET* 3.7 31.0 - - + -
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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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220A LYS* 2.8 36.6 + - + -
221A HIS* 3.7 26.0 - - + -
223A TYR* 3.5 26.7 - - + +
237A GLU 2.8 18.4 + - - +
238A ALA* 4.0 2.5 - - - +
240A PHE* 1.3 76.7 - - + +
242A ALA* 1.3 61.8 + - - +
243A THR 3.4 0.5 + - - -
244A SER* 3.7 3.2 - - - +
250A VAL* 4.0 9.2 - - + -
273A LEU* 3.9 19.5 - - + -
276A TYR* 3.8 45.3 - - + -
697A NHE 3.8 11.7 - - + -
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Residues in contact with ALA 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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161A PRO* 5.3 0.7 - - + -
188A PRO* 3.2 11.3 - - - +
189A LEU 3.7 22.9 - - - +
190A VAL* 4.2 8.7 - - + -
238A ALA 3.0 18.8 + - - +
239A PHE 4.0 3.4 - - - +
241A LEU* 1.3 77.1 - - - +
243A THR* 1.3 63.3 + - + +
247A PRO* 3.2 3.8 - - - +
248A GLY 3.1 41.7 + - - +
250A VAL* 3.7 5.1 - - + +
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Residues in contact with THR 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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159A GLY 6.0 0.4 - - - +
161A PRO* 3.9 39.5 - - + -
188A PRO* 4.2 9.2 - - + -
239A PHE* 2.9 23.9 + - + +
240A PHE* 3.7 5.4 + - - -
242A ALA* 1.3 80.8 - - + +
244A SER* 1.3 66.4 + - - +
245A GLY 4.7 0.3 - - - +
247A PRO* 4.2 12.6 - - - +
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Residues in contact with SER 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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220A LYS* 2.9 20.1 + - - -
240A PHE* 2.7 42.1 + - - -
241A LEU* 3.7 0.5 - - - +
242A ALA 3.7 0.2 - - - -
243A THR* 1.3 78.9 + - - +
245A GLY* 1.3 68.7 + - - +
246A ARG 3.3 3.6 + - - -
276A TYR* 2.9 27.5 + - - -
280A MET* 4.7 5.8 - - - -
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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