Contacts of the helix formed by residues 235 - 256 (chain A) in PDB entry 6XAV
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 PRO 235 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ASP 4.8 0.2 - - - +
234A GLU* 1.3 95.0 - - + +
236A ALA* 1.3 63.2 + - - +
237A SER* 3.1 21.1 + - - +
238A ARG* 3.4 12.7 + - + +
239A HIS* 3.6 10.2 + - - -
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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
----------------------------------------------------------
235A PRO* 1.3 71.7 - - - +
237A SER* 1.3 63.3 + - - +
238A ARG 3.3 0.4 - - - -
239A HIS* 3.5 16.2 - - + +
240A VAL* 3.0 28.3 + - - +
273A ALA* 3.8 28.7 - - + -
276A THR* 5.4 4.7 - - + -
277A VAL* 3.8 21.8 - - + -
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Residues in contact with SER 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A PRO* 3.1 14.6 - - - +
236A ALA* 1.3 78.8 - - - +
238A ARG* 1.3 60.9 - - - +
240A VAL* 3.6 5.5 + - - +
241A GLN* 3.3 20.4 + - - +
277A VAL* 4.7 9.4 - - - +
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Residues in contact with ARG 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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70A SER 3.6 9.3 + - - -
71A SER* 3.3 34.6 + - - -
72A TYR 5.2 2.0 - - - +
73A LEU* 3.6 31.7 - - + +
229A ALA 3.7 4.6 + - - -
230A SER* 2.7 39.8 + - - +
231A THR* 4.3 2.4 + - - +
234A GLU* 2.6 46.1 + - + +
235A PRO* 3.4 10.6 + - + +
236A ALA 3.3 0.2 - - - -
237A SER* 1.3 75.9 - - - +
239A HIS* 1.3 60.9 + - - +
241A GLN* 4.2 6.7 - - + -
242A VAL* 2.8 40.6 + - + +
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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
----------------------------------------------------------
209A ILE* 3.7 28.0 - - + +
210A ASP* 4.2 20.6 + - + +
230A SER* 2.8 36.1 + - - -
231A THR 3.1 26.9 + - - -
232A PHE* 4.3 1.4 - - - -
234A GLU* 3.4 22.2 + - + -
235A PRO 3.6 2.2 + - - -
236A ALA* 3.2 29.3 + - + +
238A ARG* 1.3 76.7 - - - +
240A VAL* 1.3 61.5 + - - +
242A VAL* 4.1 1.3 - - - +
243A ALA* 3.2 24.3 + - - +
270A LEU* 4.2 4.6 - - + +
273A ALA* 4.6 11.2 - - + -
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Residues in contact with VAL 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ALA 3.0 17.2 + - - +
237A SER* 4.0 5.4 - - - +
239A HIS* 1.3 74.4 - - - +
241A GLN* 1.3 59.8 + - - +
243A ALA* 3.3 4.2 + - - +
244A GLU* 3.0 34.9 + - + +
270A LEU* 4.9 1.1 - - + -
273A ALA* 4.7 10.1 - - + -
274A TYR* 3.4 49.8 - - + +
277A VAL* 4.4 16.4 - - + -
296A ARG* 4.6 5.6 - - - +
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Residues in contact with GLN 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLU* 2.8 41.7 + - - +
72A TYR 5.2 7.6 - - - +
93A THR* 5.8 0.2 - - - +
237A SER 3.3 15.1 + - - +
238A ARG* 3.2 9.9 + - + +
240A VAL* 1.3 80.5 - - - +
242A VAL* 1.3 58.8 + - + +
244A GLU* 3.2 10.4 + - - +
245A MET* 3.0 53.8 + - + +
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Residues in contact with VAL 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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71A SER 3.5 20.2 - - - +
72A TYR* 4.0 11.2 - - + +
207A LEU* 3.8 24.7 - - + -
209A ILE* 4.3 9.4 - - + -
228A VAL* 4.0 17.9 - - + -
229A ALA 4.9 1.1 - - - +
230A SER* 4.5 6.1 - - - -
238A ARG* 2.8 45.5 + - + +
239A HIS 4.3 2.2 - - - +
241A GLN* 1.3 72.1 - - + +
243A ALA* 1.3 61.9 + - - +
245A MET* 3.3 7.9 + - - +
246A VAL* 3.1 24.1 + - + +
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Residues in contact with ALA 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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207A LEU* 4.1 17.9 - - + +
209A ILE* 5.0 2.9 - - + +
239A HIS 3.2 20.5 + - - +
240A VAL* 3.6 4.9 - - - +
242A VAL* 1.3 77.4 - - - +
244A GLU* 1.3 60.1 + - - +
246A VAL* 3.5 1.4 + - - +
247A ILE* 3.2 25.1 + - - +
270A LEU* 4.1 29.2 - - + -
274A TYR* 4.7 5.2 - - - +
300A PHE* 3.9 11.6 - - + -
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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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93A THR* 6.3 0.9 - - + -
240A VAL* 3.0 25.0 + - + +
241A GLN* 3.2 13.9 + - - +
243A ALA* 1.3 75.3 - - - +
245A MET* 1.3 60.8 + - - +
247A ILE* 3.2 17.1 - - - +
248A GLU* 3.0 39.9 + - + +
274A TYR* 4.3 8.7 + - - +
296A ARG* 2.4 35.4 + - - +
300A PHE* 5.3 2.8 - - - +
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Residues in contact with MET 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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54A VAL* 3.7 27.5 - - + +
55A LEU 3.4 23.3 - - - +
56A GLU* 3.7 24.2 - - + +
66A ARG* 4.6 2.7 - - + -
72A TYR* 4.3 36.0 - - + -
93A THR* 3.9 15.3 - - + -
94A GLY 4.9 0.2 - - - +
241A GLN* 3.0 46.1 + - + +
242A VAL 3.7 4.9 - - - +
244A GLU* 1.3 77.4 - - - +
246A VAL* 1.3 58.3 + - - +
248A GLU* 4.1 2.7 - - - +
249A LYS* 3.1 28.9 + - - +
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Residues in contact with VAL 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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72A TYR* 4.7 14.1 - - + -
205A MET* 3.8 28.0 - - + +
207A LEU* 3.7 43.3 - - + -
228A VAL* 4.8 2.9 - - + -
242A VAL* 3.1 20.7 + - + +
243A ALA 3.9 1.8 - - - +
245A MET* 1.3 75.5 - - - +
247A ILE* 1.3 60.0 + - - +
249A LYS* 3.3 5.8 + - - +
250A ALA* 2.8 27.7 + - - +
262A ILE* 4.0 21.3 - - + -
300A PHE* 5.7 2.2 - - + -
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Residues in contact with ILE 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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243A ALA 3.2 11.2 + - - +
244A GLU* 3.2 30.5 - - - +
246A VAL* 1.3 80.2 - - - +
248A GLU* 1.3 65.0 + - + +
250A ALA* 3.4 6.0 + - + -
251A LYS* 2.9 48.3 + - + +
262A ILE* 5.0 2.9 - - + -
300A PHE* 3.5 33.6 - - + -
303A ALA* 3.9 25.1 - - + -
313A LEU* 4.2 16.2 - - + -
315A ILE* 4.6 6.7 - - + -
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Residues in contact with GLU 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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93A THR* 3.0 38.8 - - + +
94A GLY* 4.1 3.1 - - - -
244A GLU* 3.0 26.6 + - + +
245A MET 4.1 2.2 - - - +
247A ILE* 1.3 80.0 - - + +
249A LYS* 1.3 63.9 + - - +
251A LYS* 3.3 14.9 + - - +
252A ARG* 2.8 60.7 + - - +
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Residues in contact with LYS 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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54A VAL* 4.4 17.2 - - + +
68A ALA* 6.0 1.2 - - - +
72A TYR* 3.3 25.8 + - + +
94A GLY* 4.0 22.8 - - - +
96A THR* 4.7 9.4 - - - +
121A PHE* 5.6 7.6 - - - -
205A MET* 4.5 15.0 - - + -
226A GLU* 3.2 28.7 + - - -
245A MET 3.1 19.6 + - - +
246A VAL* 3.7 4.5 - - - +
248A GLU* 1.3 75.9 - - - +
250A ALA* 1.3 62.4 + - - +
252A ARG* 3.5 2.5 + - - +
253A LEU* 3.2 42.3 + - + +
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Residues in contact with ALA 250 (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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205A MET* 5.5 2.4 - - - -
246A VAL* 2.8 18.5 + - + +
247A ILE* 3.7 7.9 - - + +
248A GLU 3.2 0.2 - - - -
249A LYS* 1.3 77.7 - - - +
251A LYS* 1.3 63.3 + - - +
253A LEU* 3.3 5.2 + - - +
254A VAL* 3.1 28.4 + - - +
260A VAL* 3.8 31.2 - - + +
262A ILE* 3.8 15.0 - - + -
313A LEU* 4.1 10.3 - - + -
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Residues in contact with LYS 251 (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 PHE* 3.8 47.5 - - + -
134A GLU* 5.3 6.3 + - - +
247A ILE* 2.9 45.0 + - + +
248A GLU* 3.3 14.5 + - - +
250A ALA* 1.3 76.3 - - - +
252A ARG* 1.3 79.8 + - - +
254A VAL* 3.3 5.2 + - - +
255A GLU* 3.0 31.7 + - - +
299A ARG* 5.7 4.4 + - - +
303A ALA* 4.0 13.2 - - - +
313A LEU* 5.1 2.0 - - + -
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Residues in contact with ARG 252 (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 ARG* 3.2 42.1 - - - +
93A THR 3.1 10.3 + - - -
94A GLY 3.9 19.1 - - - +
95A ASP* 3.2 27.8 - - - +
120A ASN* 4.5 10.5 - - - +
130A LYS* 4.2 4.0 - - - +
133A PHE* 4.3 5.3 - - - +
134A GLU* 4.7 4.9 + - - -
248A GLU* 2.8 45.0 + - - +
249A LYS 3.8 4.5 - - - +
250A ALA 3.3 0.2 - - - -
251A LYS* 1.3 97.1 - - - +
253A LEU* 1.3 57.7 + - + +
255A GLU* 2.8 32.5 + - - +
256A HIS* 3.0 34.7 + - - -
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Residues in contact with LEU 253 (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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96A THR* 6.0 2.0 - - - +
120A ASN* 5.6 11.4 - - + +
121A PHE* 5.3 15.5 - - + -
203A VAL* 4.6 22.0 - - + -
205A MET* 5.2 2.9 - - - -
249A LYS* 3.2 36.4 + - + +
250A ALA* 3.7 2.0 - - - +
251A LYS 3.3 0.2 - - - -
252A ARG* 1.3 76.5 - - + +
254A VAL* 1.3 63.0 + - - +
256A HIS* 3.0 15.7 + - + +
257A LYS 3.1 0.5 + - - -
258A LYS* 2.9 41.6 + - + +
260A VAL* 3.6 29.6 - - + -
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Residues in contact with VAL 254 (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 PHE* 3.8 19.1 - - + -
136A LEU* 4.2 3.1 - - + +
250A ALA 3.1 17.3 + - - +
251A LYS 3.6 7.0 - - - +
252A ARG 3.3 0.2 - - - -
253A LEU* 1.3 74.8 - - - +
255A GLU* 1.3 62.1 + - - +
257A LYS* 3.1 10.7 + - - +
258A LYS 3.7 9.2 - - - +
260A VAL* 4.3 5.6 - - + -
307A VAL* 3.7 30.7 - - + -
310A GLY 3.5 16.1 - - - +
312A SER 3.5 31.2 - - - +
313A LEU* 4.0 13.9 - - + +
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Residues in contact with GLU 255 (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 ARG* 2.8 22.1 + - - -
130A LYS* 3.0 35.0 + - - +
131A ILE 3.4 21.6 + - - +
132A LEU* 3.3 0.4 - - - -
133A PHE* 2.5 40.5 + - + +
136A LEU* 4.6 7.0 - - + -
251A LYS 3.0 15.1 + - - +
252A ARG* 2.8 31.7 + - - +
254A VAL* 1.3 76.0 - - - +
256A HIS* 1.3 58.9 + - - +
257A LYS* 3.4 13.3 + - - +
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Residues in contact with HIS 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A VAL 4.7 2.2 - - - -
120A ASN* 3.1 46.6 + - + +
122A ASP* 4.6 14.6 + - + +
126A ASN 5.2 1.8 + - - -
127A ALA* 3.8 30.2 - - + +
130A LYS* 3.2 22.4 + - + -
252A ARG 3.0 24.5 + - - +
253A LEU* 3.0 16.3 + - + +
255A GLU* 1.3 75.0 - - - +
257A LYS* 1.3 73.0 + - - +
258A LYS* 3.8 15.9 - - + +
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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