Contacts of the helix formed by residues 227 - 247 (chain A) in PDB entry 4K71
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 GLU 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A LYS 4.9 4.9 - - - +
226A ALA* 1.3 77.9 - - - +
228A PHE* 1.3 66.8 + - - +
229A ALA* 4.3 9.4 - - + +
230A GLU* 2.9 21.6 + - + +
231A VAL* 3.0 11.8 + - - +
270A SER 4.7 1.4 + - - +
332A TYR* 3.6 5.5 + - - -
336A ARG* 5.4 2.3 + - - -
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Residues in contact with PHE 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A VAL* 4.8 9.2 - - + -
227A GLU* 1.3 71.4 - - - +
229A ALA* 1.3 60.7 + - - +
231A VAL* 3.1 6.4 + - + +
232A SER* 2.8 50.8 + - - -
325A VAL* 4.0 20.0 - - + -
328A GLY* 3.5 26.9 - - - -
329A MET* 3.6 35.2 - - + -
332A TYR* 3.5 48.0 + + + -
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Residues in contact with ALA 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A GLU* 3.2 7.0 - - + +
228A PHE* 1.3 80.7 - - - +
230A GLU* 1.3 57.3 + - - +
232A SER* 3.5 7.0 + - - -
233A LYS* 3.1 27.0 + - - +
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Residues in contact with GLU 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ALA* 4.3 9.0 - - + -
227A GLU* 2.9 18.0 + - + +
229A ALA* 1.3 75.4 - - - +
231A VAL* 1.3 67.0 + - - +
233A LYS* 3.4 7.9 + - - +
234A LEU* 3.1 32.3 + - + +
263A TYR* 2.8 39.8 + - - -
267A ASN* 5.5 0.4 - - - +
270A SER* 3.7 38.1 + - - +
271A ILE* 4.1 14.6 - - + +
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Residues in contact with VAL 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A VAL* 4.4 11.0 - - + +
219A LEU* 4.3 15.7 - - + +
220A SER* 3.8 22.2 - - - +
223A PHE* 4.5 11.2 - - + +
226A ALA* 3.8 19.7 - - + -
227A GLU 3.0 12.2 + - - +
228A PHE* 3.6 10.8 - - + +
230A GLU* 1.3 76.6 - - - +
232A SER* 1.3 56.5 + - - +
234A LEU* 3.4 10.3 + - + +
235A VAL* 2.9 43.3 + - + +
332A TYR* 4.2 17.0 - - + -
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Residues in contact with SER 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A VAL* 5.5 4.3 - - - +
228A PHE* 2.8 49.9 + - - -
229A ALA* 3.8 6.9 - - - -
231A VAL* 1.3 68.9 - - - +
233A LYS* 1.3 57.2 + - - +
235A VAL* 3.0 9.1 + - - +
236A THR* 2.8 40.0 + - - -
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Residues in contact with LYS 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ALA 3.1 14.4 + - - +
230A GLU* 3.7 11.4 - - - +
231A VAL 3.4 0.2 - - - -
232A SER* 1.3 77.8 - - - +
234A LEU* 1.3 66.3 + - + +
236A THR* 3.2 8.0 + - - -
237A ASP* 2.8 53.1 + - - +
263A TYR* 3.9 47.9 - - + +
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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 LEU* 4.3 13.0 - - + -
223A PHE* 4.1 31.4 - - + -
230A GLU* 3.1 24.1 + - + +
231A VAL* 3.6 11.7 - - + +
233A LYS* 1.3 77.6 - - + +
235A VAL* 1.3 52.0 + - - +
237A ASP* 3.3 5.3 + - - +
238A LEU* 2.8 37.3 + - - +
260A LEU* 3.9 16.3 - - + +
263A TYR* 4.0 21.1 - - + -
264A ILE* 3.8 28.5 - - + -
271A ILE* 4.3 18.8 - - + -
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Residues in contact with VAL 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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211A PHE* 5.1 0.2 - - - -
212A LYS* 3.9 35.7 - - + +
215A ALA* 3.9 10.8 - - + -
216A VAL* 3.6 39.5 - - + +
219A LEU* 4.0 9.0 - - + -
231A VAL* 2.9 22.8 + - + +
232A SER* 3.0 7.6 + - - +
234A LEU* 1.3 74.9 - - - +
236A THR* 1.3 55.2 + - - +
238A LEU* 3.4 6.9 + - - +
239A THR* 2.6 46.9 + - - +
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Residues in contact with THR 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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212A LYS* 4.2 20.2 + - - +
232A SER* 2.8 19.5 + - - -
233A LYS* 3.5 11.3 - - + -
235A VAL* 1.3 73.3 - - - +
237A ASP* 1.3 70.1 + - - +
239A THR* 3.1 7.9 + - - -
240A LYS* 3.1 22.7 + - + +
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Residues in contact with ASP 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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233A LYS* 2.8 50.5 + - - +
234A LEU 3.8 5.4 - - - +
236A THR* 1.3 82.2 - - - +
238A LEU* 1.3 63.6 + - - +
239A THR 3.2 0.2 + - - -
240A LYS* 3.3 7.2 + - - +
241A VAL* 3.0 29.7 + - + +
260A LEU* 3.9 27.1 - - + +
263A TYR* 5.4 1.0 - - - +
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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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150A TYR* 5.0 5.2 - - - +
211A PHE* 4.2 4.0 - - + -
214A TRP* 4.5 15.3 - - + -
215A ALA* 4.3 14.1 - - + -
219A LEU* 4.0 27.6 - - + -
234A LEU 2.8 20.3 + - - +
235A VAL* 3.8 5.4 - - - +
237A ASP* 1.3 73.5 - - - +
239A THR* 1.3 56.8 + - - +
241A VAL* 3.4 5.0 + - + +
242A HIS* 3.0 60.8 + - + +
257A ARG* 6.4 1.6 - - + -
260A LEU* 3.9 21.0 - - + +
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Residues in contact with THR 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LEU* 4.5 1.6 - - + +
208A GLU* 3.7 34.3 - - + +
211A PHE* 3.5 29.1 - - + -
212A LYS* 3.6 17.8 - - + +
235A VAL* 2.6 25.3 + - - +
236A THR* 3.5 7.4 - - - -
237A ASP 3.1 0.2 - - - -
238A LEU* 1.3 74.2 - - - +
240A LYS* 1.3 58.0 + - - +
242A HIS* 3.5 1.2 + - - +
243A THR* 2.8 44.6 + - - +
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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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236A THR* 3.1 13.2 + - + +
237A ASP* 3.7 10.3 - - - +
239A THR* 1.3 74.4 - - - +
241A VAL* 1.3 65.1 + - - +
243A THR* 3.3 5.4 + - - -
244A GLU* 3.1 50.0 + - + +
256A ASP* 4.1 15.0 - - + +
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Residues in contact with VAL 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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150A TYR* 3.6 24.2 - - - +
237A ASP* 3.0 19.1 + - + +
238A LEU* 3.6 12.1 - - + +
239A THR 3.3 0.2 - - - -
240A LYS* 1.3 78.8 - - + +
242A HIS* 1.3 66.2 + - + +
244A GLU* 3.3 7.5 + - - +
245A CYS 3.0 18.4 + - - -
253A CYS* 3.4 28.1 - - - +
256A ASP* 3.9 26.7 - - + +
257A ARG* 3.9 15.9 - - + +
260A LEU* 4.9 6.3 - - + -
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Residues in contact with HIS 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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150A TYR* 3.4 35.3 + + - -
196A GLN* 3.0 39.6 + - - +
199A LYS* 3.7 19.4 - - + +
203A LEU* 3.8 7.9 - - + -
211A PHE* 3.6 32.2 - + + -
238A LEU* 3.0 41.5 + - + +
239A THR 4.3 0.7 - - - +
241A VAL* 1.3 81.5 - - + +
243A THR* 1.3 57.7 + - - +
245A CYS* 4.4 3.1 - - - +
246A CYS* 2.8 37.2 + - - -
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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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203A LEU* 3.7 27.0 - - + +
208A GLU* 5.4 1.2 - - - +
239A THR* 2.8 29.3 + - - +
240A LYS* 3.9 6.5 - - - -
241A VAL 3.2 0.2 - - - -
242A HIS* 1.3 76.2 - - - +
244A GLU* 1.3 61.9 + - + +
246A CYS* 4.1 2.1 - - - +
247A HIS* 3.3 25.4 + - + +
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Residues in contact with GLU 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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10A ARG* 5.7 0.3 + - - -
240A LYS* 3.1 38.3 + - + +
241A VAL* 3.6 3.5 - - - +
243A THR* 1.3 77.0 - - + +
245A CYS* 1.3 62.9 + - - +
247A HIS* 3.3 7.5 + - - -
249A ASP* 2.9 48.5 + - + +
252A GLU* 3.6 25.5 - - + +
253A CYS* 3.7 5.4 - - + -
256A ASP* 2.5 32.4 - - - +
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Residues in contact with CYS 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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106A LYS* 5.2 3.1 + - - -
150A TYR* 3.8 20.0 - - + -
151A ALA* 4.3 5.8 - - - +
152A PRO* 3.7 21.3 - - - -
196A GLN* 4.8 4.0 - - - +
200A CYS* 5.2 0.4 - - - -
241A VAL 3.0 10.5 + - - +
242A HIS* 4.0 3.6 - - - +
244A GLU* 1.3 74.9 - - - +
246A CYS* 1.3 58.2 + - - +
248A GLY* 3.0 19.8 + - - -
250A LEU* 3.8 20.7 - - + +
253A CYS* 2.0 45.7 - - - +
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Residues in contact with CYS 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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103A LEU* 5.1 3.8 - - - +
106A LYS* 5.3 1.7 + - - -
148A TYR* 4.3 12.8 - - - -
196A GLN* 3.6 13.5 - - - -
199A LYS 4.6 0.2 - - - -
200A CYS* 2.0 62.1 - - + +
203A LEU* 4.2 9.6 - - + -
204A GLN* 3.0 28.6 + - + +
242A HIS* 2.8 31.8 + - - +
243A THR 4.3 2.5 - - - +
245A CYS* 1.3 70.8 - - - +
247A HIS* 1.3 57.6 + - - +
248A GLY 3.4 1.5 + - - -
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Residues in contact with HIS 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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30A TYR* 4.7 0.5 + - - -
67A HIS* 4.2 9.9 - + - -
99A ASN* 4.2 13.1 + - - -
100A GLU* 3.0 29.1 + - - -
103A LEU* 3.4 36.2 - - + +
204A GLN* 4.8 5.4 - - - +
243A THR* 3.3 19.7 + - + +
244A GLU* 3.3 1.9 + - - +
245A CYS 3.1 1.2 - - - -
246A CYS* 1.3 77.0 - - - +
248A GLY* 1.3 59.0 + - - +
249A ASP* 2.5 32.2 + - - +
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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
------------------------------------------------------------
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