Contacts of the helix formed by residues 238 - 260 (chain A) in PDB entry 5H1C
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 LEU 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A TYR* 4.6 1.0 - - - +
234A GLY* 4.2 6.0 - - - -
235A ARG* 3.5 44.9 - - + +
237A GLU* 1.3 75.1 - - - +
239A SER* 1.3 61.0 + - - +
240A ALA 3.0 0.7 - - - -
241A ARG* 2.7 51.8 + - - +
242A GLN* 2.7 32.4 + - + +
1D T 3.8 38.4 - - + +
2D T 4.7 7.6 - - - +
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Residues in contact with SER 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A GLY 5.3 0.2 - - - -
237A GLU 2.2 27.6 + - - -
238A LEU* 1.3 78.0 - - - +
240A ALA* 1.3 57.6 + - - +
242A GLN* 4.5 4.6 - - - +
243A MET* 3.2 24.0 + - - +
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Residues in contact with ALA 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A TYR* 4.9 15.0 - - + -
237A GLU* 3.4 15.8 + - - +
238A LEU 3.0 0.4 - - - -
239A SER* 1.3 82.0 + - - +
241A ARG* 1.3 58.7 + - - +
243A MET* 3.1 15.9 + - - +
244A HIS* 2.9 28.2 + - - +
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Residues in contact with ARG 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A TYR* 3.3 39.6 - - + +
229A ARG* 5.3 1.5 - - - +
232A TYR* 3.5 37.0 + - + -
238A LEU* 2.7 31.5 + - - +
240A ALA* 1.3 79.1 - - - +
242A GLN* 1.3 86.9 + - - +
244A HIS* 3.1 5.2 + - - +
245A LEU* 2.9 35.3 + - + +
287A ILE* 4.1 12.5 - - - +
288A GLY* 3.8 18.2 - - - +
1D T 3.6 2.6 + - - -
2D T 3.2 35.6 + - - -
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Residues in contact with GLN 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* 2.7 30.4 + - + +
239A SER* 4.5 4.7 - - - +
241A ARG* 1.3 111.5 - - - +
243A MET* 1.3 58.3 + - - +
245A LEU* 3.8 7.7 - - - +
246A ALA* 3.0 33.1 + - - +
288A GLY* 2.9 29.6 + - - +
291A ILE* 3.3 35.1 - - + +
1D T 3.9 18.4 + - - +
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Residues in contact with MET 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A SER 3.2 17.6 + - - +
240A ALA* 3.1 19.7 - - - +
241A ARG 3.1 0.4 - - - -
242A GLN* 1.3 80.3 - - - +
244A HIS* 1.3 58.6 + - - +
246A ALA* 4.0 5.1 + - - +
247A ARG* 3.8 47.1 + - - +
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Residues in contact with HIS 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A THR* 3.8 16.8 - - - -
198A ASP* 3.6 22.0 + - - -
201A THR* 3.8 23.4 - - + +
228A TYR* 2.7 37.5 + + + -
232A TYR* 4.5 13.9 - - - +
240A ALA 2.9 10.8 + - - +
241A ARG* 3.1 8.2 + - - +
243A MET* 1.3 76.5 - - + +
245A LEU* 1.3 65.5 + - - +
246A ALA 3.2 1.6 - - - -
247A ARG* 3.1 13.6 + - + +
248A PHE* 3.0 22.9 + + + -
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Residues in contact with LEU 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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224A ALA* 4.8 3.4 - - + +
225A THR* 5.3 8.7 - - + -
228A TYR* 3.4 40.8 - - + +
241A ARG* 2.9 44.7 + - + +
242A GLN* 3.3 13.4 + - - +
244A HIS* 1.3 77.4 - - - +
246A ALA* 1.3 64.4 + - - +
248A PHE* 3.1 12.7 + - + +
249A LEU* 2.9 38.6 + - + +
287A ILE* 5.8 0.4 - - + -
288A GLY* 4.4 13.7 - - - -
291A ILE* 5.1 5.2 - - + -
292A ILE* 4.6 12.3 - - + -
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Residues in contact with ALA 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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242A GLN 3.0 17.6 + - - +
243A MET* 4.2 6.3 - - - +
244A HIS 3.2 0.2 - - - -
245A LEU* 1.3 77.2 - - - +
247A ARG* 1.3 59.1 + - + +
249A LEU* 3.9 3.5 - - - +
250A ARG* 3.0 28.6 + - - +
291A ILE* 4.0 25.3 - - + +
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Residues in contact with ARG 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 MET* 3.8 41.2 + - - +
244A HIS* 3.1 13.0 + - + +
246A ALA* 1.3 76.0 - - + +
248A PHE* 1.3 67.1 + - - +
250A ARG* 3.2 8.3 + - - +
251A MET* 2.9 31.0 + - + +
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Residues in contact with PHE 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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160A ILE* 6.4 0.7 - - + -
200A GLN* 3.9 38.6 - - + -
201A THR* 5.2 7.9 - - + -
204A LEU* 3.6 29.6 - - + -
221A VAL* 5.0 11.2 - - + -
224A ALA* 3.8 25.6 - - + -
228A TYR* 4.3 11.0 - + - +
244A HIS* 3.0 16.7 + - + +
245A LEU* 3.1 18.6 + - + +
247A ARG* 1.3 77.1 - - - +
249A LEU* 1.3 73.0 + - + +
251A MET* 3.0 10.3 + - - +
252A LEU* 3.0 53.3 + - + +
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Residues in contact with LEU 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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122A ILE* 4.3 5.0 - - + +
224A ALA* 6.1 0.9 - - + -
245A LEU* 2.9 25.4 + - + +
246A ALA* 4.0 3.4 - - - +
248A PHE* 1.3 89.6 - - + +
250A ARG* 1.3 65.3 + - - +
252A LEU* 3.1 17.4 + - + +
253A LEU* 2.9 27.2 + - + +
265A ILE* 4.3 18.6 - - + -
291A ILE* 3.8 30.7 - - + +
292A ILE* 3.8 26.7 - - + -
295A ALA* 4.1 17.5 - - + -
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Residues in contact with ARG 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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54A TYR 4.6 13.7 + - - -
56A PRO* 4.7 17.6 - - - +
246A ALA 3.0 19.3 + - - +
247A ARG* 3.2 8.9 + - - +
249A LEU* 1.3 76.7 - - - +
251A MET* 1.3 62.1 + - + +
253A LEU* 3.1 17.1 + - + +
254A ARG* 2.9 35.4 + - + +
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Residues in contact with MET 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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59A GLU* 5.8 0.7 - - - +
204A LEU* 3.8 26.9 - - + -
205A TYR* 4.5 30.5 - - + +
208A SER* 6.4 2.2 - - - -
247A ARG* 2.9 22.3 + - + +
248A PHE* 3.0 8.5 + - - +
250A ARG* 1.3 78.8 - - - +
252A LEU* 1.3 62.3 + - - +
254A ARG* 2.8 71.3 + - + +
255A LEU* 3.0 23.1 + - + +
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Residues in contact with LEU 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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122A ILE* 4.0 11.4 - - + -
204A LEU* 3.8 27.8 - - + -
219A LEU* 4.7 7.0 - - + -
221A VAL* 5.6 9.0 - - + -
248A PHE* 3.0 45.9 + - + +
249A LEU* 3.1 20.6 + - + +
251A MET* 1.3 76.0 - - - +
253A LEU* 1.3 57.9 + - - +
255A LEU* 3.3 11.8 + - + +
256A ALA* 2.9 30.9 + - - +
263A VAL* 4.3 25.8 - - + +
265A ILE* 4.4 11.7 - - + -
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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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120A GLY 6.0 0.9 - - - +
121A SER* 6.1 1.1 - - - -
122A ILE* 3.9 24.2 - - + -
249A LEU 2.9 17.6 + - - +
250A ARG* 3.1 17.9 + - + +
252A LEU* 1.3 75.8 - - - +
254A ARG* 1.3 58.9 + - - +
256A ALA* 4.4 4.5 - - + +
257A ASP* 2.9 57.0 + - - +
295A ALA* 5.1 17.7 - - + +
297A THR* 5.8 6.5 - - + -
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Residues in contact with ARG 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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46A PHE* 3.2 29.5 - - - -
51A ALA* 5.0 14.6 + - + -
54A TYR* 5.2 14.5 + - + -
55A ALA* 5.1 1.5 - - - +
56A PRO* 4.4 11.7 - - - +
59A GLU* 2.9 31.1 + - - -
205A TYR* 5.0 5.3 - - - -
250A ARG* 2.9 22.3 + - + +
251A MET* 2.8 52.0 + - - +
253A LEU* 1.3 77.5 - - - +
255A LEU* 1.3 62.7 + - + +
257A ASP* 4.1 2.1 + - - +
258A GLU* 3.0 47.2 - - - +
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Residues in contact with LEU 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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204A LEU* 4.4 22.4 - - + +
207A ALA* 4.7 9.4 - - + -
208A SER* 3.9 31.9 - - - +
211A MET* 4.7 12.3 - - + -
219A LEU* 3.5 32.3 - - + -
251A MET* 3.0 21.1 + - + +
252A LEU* 3.8 8.7 - - + +
254A ARG* 1.3 85.0 - - + +
256A ALA* 1.3 60.9 + - - +
258A GLU* 3.1 12.8 + - - +
259A PHE* 3.0 34.8 + - + +
260A GLY 4.4 1.0 + - - +
263A VAL* 6.1 0.4 - - + -
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Residues in contact with ALA 256 (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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120A GLY* 3.3 37.5 - - - +
121A SER* 4.2 2.7 - - - +
122A ILE* 5.2 2.0 - - + -
252A LEU 2.9 18.2 + - - +
253A LEU* 4.2 5.8 - - + +
255A LEU* 1.3 78.1 - - - +
257A ASP* 1.3 64.7 + - - +
258A GLU 3.1 1.1 + - - -
260A GLY 3.6 17.8 + - - +
263A VAL* 3.4 26.2 - - + -
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Residues in contact with ASP 257 (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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50A GLU* 5.2 0.3 - - - +
54A TYR* 4.6 17.3 + - + -
120A GLY 4.1 9.5 - - - +
253A LEU* 2.9 46.9 + - - +
254A ARG* 4.6 3.8 - - - +
256A ALA* 1.3 78.8 - - - +
258A GLU* 1.3 62.2 + - + +
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Residues in contact with GLU 258 (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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22A PRO* 4.7 5.7 - - - +
48A THR* 3.9 4.4 + - - -
50A GLU* 4.2 17.5 - - + +
51A ALA* 3.1 38.9 + - - +
54A TYR* 4.0 20.7 - - + -
254A ARG* 3.0 29.2 - - - +
255A LEU* 3.1 8.1 + - - +
257A ASP* 1.3 83.9 - - - +
259A PHE* 1.3 100.4 + - + +
260A GLY 3.5 2.3 + - - -
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Residues in contact with PHE 259 (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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22A PRO* 3.6 31.0 - - + -
48A THR* 3.4 30.7 - - + -
50A GLU* 4.7 2.0 - - - -
208A SER* 5.1 3.4 - - - -
211A MET* 3.4 60.6 - - + -
212A VAL* 6.0 0.2 - - - -
215A ARG* 5.7 8.2 + - - +
255A LEU* 3.0 16.7 + - + +
258A GLU* 1.3 112.4 - - + +
260A GLY* 1.3 67.9 + - - +
261A VAL* 2.9 13.6 + - + +
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Residues in contact with GLY 260 (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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119A THR* 4.2 5.2 - - - -
120A GLY* 3.5 26.6 + - - -
255A LEU 4.7 0.5 - - - +
256A ALA* 3.6 16.6 + - - -
258A GLU 3.5 4.0 + - - -
259A PHE* 1.3 76.4 - - - +
261A VAL* 1.3 68.8 + - - +
262A ALA* 3.1 7.1 + - - -
263A VAL* 5.6 0.3 - - - +
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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