Contacts of the helix formed by residues 228 - 245 (chain A) in PDB entry 1I4A
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 SER 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A GLU* 4.9 2.4 + - - -
227A THR* 1.3 78.7 + - - +
229A GLY* 1.3 70.1 + - - +
231A PHE* 3.7 10.0 + - - +
232A GLU* 3.0 23.2 + - - -
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Residues in contact with GLY 229 (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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228A SER* 1.3 77.7 - - - +
230A SER* 1.3 65.9 + - - -
231A PHE 4.2 0.2 - - - -
232A GLU* 3.0 15.9 + - - +
233A ASP* 3.1 19.1 + - - +
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Residues in contact with SER 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A GLU* 2.4 34.8 + - - +
109A ILE* 4.5 2.6 - - - +
147A PHE* 3.4 37.5 - - - -
229A GLY* 1.3 68.5 - - - -
231A PHE* 1.3 65.1 + - - +
233A ASP* 3.2 15.3 + - - +
234A ALA* 2.9 19.9 + - - +
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Residues in contact with PHE 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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146A MET* 3.7 30.5 - - + -
147A PHE* 3.9 19.1 - - + +
150A VAL* 3.5 31.4 - - + -
189A GLU* 3.5 63.0 - - + -
192A PHE* 4.5 1.6 - - + -
193A LEU* 4.7 2.5 - - + -
227A THR* 3.8 13.7 - - + -
228A SER 3.7 7.4 - - - +
229A GLY 3.1 0.2 - - - -
230A SER* 1.3 78.3 - - - +
232A GLU* 1.3 62.9 + - - +
234A ALA* 3.2 2.5 + - - +
235A LEU* 3.1 57.0 + - + +
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Residues in contact with GLU 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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223A ILE* 3.8 9.8 - - + +
224A LYS* 3.4 30.8 - - - +
227A THR* 3.2 33.7 - - - +
228A SER* 3.0 31.0 + - - -
229A GLY 3.0 11.5 + - - +
231A PHE* 1.3 77.1 - - - +
233A ASP* 1.3 67.5 + - - +
235A LEU* 3.3 5.3 + - - +
236A LEU* 3.0 31.4 + - + +
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Residues in contact with ASP 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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109A ILE* 3.6 17.6 - - + +
229A GLY 3.1 16.0 + - - +
230A SER* 3.2 16.0 + - - +
232A GLU* 1.3 84.0 - - - +
234A ALA* 1.3 57.5 + - - +
236A LEU* 3.5 11.1 + - - +
237A ALA* 2.9 30.0 + - - +
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Residues in contact with ALA 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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109A ILE* 3.8 16.0 - - + +
113A ALA* 4.8 0.6 - - - +
147A PHE* 4.1 16.8 - - + -
150A VAL* 3.9 26.0 - - + -
151A LEU* 5.3 1.6 - - + -
154A LEU* 5.6 2.4 - - + +
230A SER 2.9 16.3 + - - +
231A PHE 3.2 5.1 + - - +
233A ASP* 1.3 74.9 - - - +
235A LEU* 1.3 67.3 + - + +
237A ALA* 3.2 2.6 + - - +
238A ILE* 3.0 29.8 + - - +
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Residues in contact with LEU 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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150A VAL* 4.1 13.7 - - + -
192A PHE* 3.8 22.2 - - + +
193A LEU* 5.4 3.6 - - - +
196A LEU* 4.0 20.8 - - + +
197A CYS* 6.1 0.4 - - - -
223A ILE* 3.8 17.7 - - + -
227A THR* 4.1 13.5 - - + +
231A PHE* 3.1 59.3 + - + +
232A GLU 3.7 6.3 - - - +
234A ALA* 1.3 76.1 - - - +
236A LEU* 1.3 61.9 + - - +
238A ILE* 3.2 10.4 + - + +
239A VAL* 3.0 28.8 + - - +
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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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220A GLU* 4.1 20.0 - - + +
223A ILE* 3.3 39.3 - - + -
224A LYS* 4.0 28.7 - - + -
232A GLU* 3.0 28.5 + - + +
233A ASP* 3.7 9.6 - - - +
235A LEU* 1.3 77.3 - - - +
237A ALA* 1.3 56.6 + - - +
239A VAL* 3.2 4.3 + - - +
240A LYS* 2.8 56.3 + - + +
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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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109A ILE* 3.3 26.0 - - + -
113A ALA* 3.7 12.1 - - + -
233A ASP 2.9 18.5 + - - +
234A ALA 3.5 3.6 - - - +
236A LEU* 1.3 75.5 - - - +
238A ILE* 1.3 57.3 + - - +
240A LYS* 3.8 0.3 - - - +
241A CYS* 2.8 35.9 + - - +
248A TYR* 3.9 27.8 - - + +
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Residues in contact with ILE 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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113A ALA* 4.1 20.4 - - + +
150A VAL* 4.3 6.3 - - + -
154A LEU* 4.2 19.1 - - + -
159A ARG* 3.8 10.3 - - - +
196A LEU* 3.4 37.0 - - + +
197A CYS* 4.0 27.8 - - - -
204A LEU* 4.6 2.9 - - + -
208A PHE* 5.9 0.2 - - + -
234A ALA 3.0 20.3 + - - +
235A LEU* 3.2 11.4 + - + +
237A ALA* 1.3 75.6 - - - +
239A VAL* 1.3 64.7 + - - +
241A CYS* 3.3 3.4 + - - +
242A MET* 3.0 39.8 + - + +
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Residues in contact with VAL 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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196A LEU* 3.8 10.1 - - + -
208A PHE* 3.8 28.5 - - + -
219A ILE* 4.0 13.0 - - + -
220A GLU* 3.6 32.8 - - + +
223A ILE* 3.7 22.9 - - + -
235A LEU 3.0 18.0 + - - +
236A LEU* 3.6 6.7 - - - +
238A ILE* 1.3 76.3 - - - +
240A LYS* 1.3 62.9 + - - +
242A MET* 3.1 4.9 + - - +
243A ARG* 3.0 31.4 + - - +
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Residues in contact with LYS 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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220A GLU* 3.4 31.9 - - - +
224A LYS* 5.1 8.6 - - - +
236A LEU* 2.8 43.5 + - + +
237A ALA 3.9 2.5 - - - +
239A VAL* 1.3 74.9 - - - +
241A CYS* 1.3 57.6 + - - +
243A ARG* 4.6 3.8 - - - +
244A ASN* 2.8 37.1 + - - +
247A ALA* 6.4 0.2 - - + -
248A TYR* 4.1 28.5 - - + +
251A GLU* 2.7 39.8 + - - +
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Residues in contact with CYS 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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113A ALA* 3.8 16.8 - - - +
114A SER* 3.8 27.1 - - - -
201A ARG* 5.0 1.9 + - - -
237A ALA 2.8 27.1 + - - +
238A ILE 3.9 2.7 - - - +
240A LYS* 1.3 73.9 - - - +
242A MET* 1.3 62.6 + - + +
243A ARG 4.7 0.2 - - - -
245A LYS* 3.7 40.2 + - + +
248A TYR* 3.5 34.1 - - - -
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Residues in contact with MET 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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113A ALA 5.9 2.5 - - - +
159A ARG* 3.5 48.5 - - - +
201A ARG* 2.9 71.5 + - + +
204A LEU* 4.1 19.5 - - + -
205A LEU* 3.9 15.4 - - + +
208A PHE* 4.5 4.7 - - + -
238A ILE* 3.0 27.6 + - + +
239A VAL* 3.1 7.4 + - - +
241A CYS* 1.3 79.0 - - + +
243A ARG* 1.3 58.2 + - - +
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Residues in contact with ARG 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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201A ARG* 3.9 10.7 + - - +
205A LEU* 3.9 20.4 - - + +
208A PHE* 3.9 25.8 + - + +
212A LYS* 5.4 0.4 - - - +
218A ASP* 2.7 40.6 + - - -
219A ILE* 3.6 18.4 - - - +
220A GLU* 2.8 38.9 + - - +
239A VAL* 3.0 19.2 + - - +
240A LYS* 4.1 3.1 - - - +
242A MET* 1.3 79.6 - - - +
244A ASN* 1.3 64.9 + - + +
245A LYS 4.1 0.2 - - - -
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Residues in contact with ASN 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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240A LYS* 2.8 16.0 + - - +
243A ARG* 1.3 80.7 - - + +
245A LYS* 1.3 63.1 + - - +
246A SER* 3.7 6.8 + - - -
247A ALA* 3.0 31.1 + - + +
248A TYR 3.2 7.8 + - - -
281A ASP* 4.1 4.5 - - - +
285A ASN* 2.9 31.1 + - - +
288A ARG* 3.9 7.3 - - - +
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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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113A ALA 5.1 0.4 + - - -
114A SER* 2.8 30.7 + - - +
116A THR* 5.8 4.4 - - - +
240A LYS 3.5 1.6 + - - -
241A CYS* 3.7 41.0 + - - +
244A ASN* 1.3 72.9 + - - +
246A SER* 1.3 63.7 + - - +
248A TYR* 3.0 13.3 + - - +
249A PHE* 3.1 31.7 + - + -
274A ARG* 3.2 33.4 - - - +
278A ASP* 4.5 0.9 - - - +
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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
------------------------------------------------------------
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