Contacts of the helix formed by residues 324 - 345 (chain A) in PDB entry 2XR9
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 MET 324 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A TYR* 3.9 15.7 - - + +
180A LYS* 5.1 6.7 - - - -
310A PRO* 4.4 9.0 - - - +
313A SER* 2.9 50.3 - - - +
314A GLY* 3.6 15.5 - - - -
317A TYR* 4.0 9.6 - - + -
318A GLY 3.4 22.7 - - - +
319A PRO 3.5 16.4 - - - +
321A GLY* 3.1 16.2 + - - +
323A GLU* 1.3 74.8 - - - +
325A THR* 1.3 63.8 + - - +
326A ASN 3.3 0.4 - - - -
327A PRO* 3.4 5.6 - - - +
328A LEU* 3.2 34.5 + - + +
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Residues in contact with THR 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LYS* 4.3 17.0 - - - +
184A VAL* 3.9 26.7 - - + +
322A PRO* 3.6 15.3 + - - +
323A GLU 3.2 1.8 - - - -
324A MET* 1.3 78.4 - - - +
326A ASN* 1.3 59.1 + - - +
328A LEU* 3.2 9.5 + - - +
329A ARG* 2.9 49.6 + - - +
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Residues in contact with ASN 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A PRO 5.0 0.6 + - - -
323A GLU* 3.7 7.1 + - - +
325A THR* 1.3 75.1 - - - +
327A PRO* 1.4 74.1 - - + +
329A ARG* 3.1 22.3 + - - +
330A GLU* 2.9 28.9 + - + +
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Residues in contact with PRO 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A GLN* 4.1 19.4 - - + +
310A PRO* 4.9 10.1 - - + -
313A SER* 3.4 33.7 - - - +
323A GLU 3.0 27.4 - - - +
324A MET* 3.4 12.3 - - + +
326A ASN* 1.4 85.2 - - + +
328A LEU* 1.3 56.0 + - - +
330A GLU* 3.3 8.5 + - + +
331A ILE* 3.0 33.4 + - - +
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Residues in contact with LEU 328 (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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173A PHE* 3.6 32.8 - - + -
177A TYR* 3.9 31.4 - - + -
180A LYS* 3.5 34.5 - - + -
184A VAL* 4.2 5.4 - - + -
185A MET* 4.0 21.0 - - - +
310A PRO* 4.2 16.4 - - + -
324A MET* 3.2 20.3 + - + +
325A THR* 3.2 5.7 + - - +
326A ASN 3.2 0.8 - - - -
327A PRO* 1.3 76.2 - - - +
329A ARG* 1.3 58.0 + - - +
331A ILE* 3.3 6.3 + - + +
332A ASP* 3.0 27.5 + - - +
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Residues in contact with ARG 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LYS* 3.2 28.3 + - - +
184A VAL* 3.7 34.7 + - + +
186A PRO* 5.6 0.6 - - - +
325A THR* 2.9 30.9 + - - +
326A ASN* 3.4 22.9 + - - +
328A LEU* 1.3 76.4 - - - +
330A GLU* 1.3 61.3 + - + +
332A ASP* 3.4 2.8 + - - +
333A LYS* 3.0 33.6 + - - +
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Residues in contact with GLU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLU* 5.7 0.7 - - - +
326A ASN* 2.9 21.7 + - + +
327A PRO* 3.7 7.9 - - + +
328A LEU 3.2 0.2 - - - -
329A ARG* 1.3 76.5 - - + +
331A ILE* 1.3 65.5 + - + +
333A LYS* 2.7 46.3 + - - +
334A THR* 3.1 24.4 + - - -
1879A IOD 4.6 1.6 - - - -
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Residues in contact with ILE 331 (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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168A PHE* 4.5 4.9 - - + -
170A VAL* 3.9 20.2 - - + -
173A PHE* 4.8 4.0 - - + -
188A ILE* 4.0 17.9 - - + -
307A SER* 3.2 17.7 - - - +
309A GLN* 3.6 23.6 - - + +
310A PRO* 4.5 10.1 - - + -
327A PRO 3.0 22.0 + - - +
328A LEU* 3.6 10.8 - - + +
330A GLU* 1.3 74.3 - - + +
332A ASP* 1.3 65.0 + - - +
334A THR* 3.0 5.4 + - - -
335A VAL* 3.0 20.4 + - - +
355A PHE* 4.5 4.5 - - + -
1879A IOD 3.2 28.0 - - + -
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Residues in contact with ASP 332 (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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184A VAL 4.1 3.1 - - - +
185A MET* 3.1 32.4 - - + +
186A PRO* 3.2 10.3 - - - +
187A ASN* 2.8 34.6 + - - -
188A ILE* 2.9 36.4 + - + +
328A LEU 3.0 14.2 + - - +
329A ARG 3.6 7.6 - - - +
330A GLU 3.2 0.2 - - - -
331A ILE* 1.3 77.4 - - - +
333A LYS* 1.3 63.9 + - - +
335A VAL* 3.1 3.3 + - - +
336A GLY 2.9 18.7 + - - -
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Residues in contact with LYS 333 (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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101A GLU* 5.1 10.1 - - - +
187A ASN* 5.0 2.9 - - - +
329A ARG* 3.0 19.7 + - - +
330A GLU* 2.7 47.0 + - - +
332A ASP* 1.3 77.1 + - - +
334A THR* 1.3 63.3 + - - +
336A GLY* 3.1 3.3 + - - -
337A GLN* 2.9 33.7 + - + +
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Residues in contact with THR 334 (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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168A PHE* 3.9 5.4 - - + -
281A HIS* 4.3 9.2 - - + +
282A GLU* 5.8 2.3 - - - +
285A ILE* 3.6 28.1 - - + +
305A PHE* 3.7 23.3 - - + -
330A GLU 3.1 8.0 + - - -
331A ILE 3.0 10.3 + - - -
333A LYS* 1.3 73.9 - - - +
335A VAL* 1.3 62.9 + - - +
337A GLN* 3.2 17.1 + - - +
338A LEU* 3.0 20.1 + - - +
1879A IOD 3.2 23.7 - - + +
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Residues in contact with VAL 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PHE* 3.6 34.1 - - + -
187A ASN* 4.0 17.7 - - + -
188A ILE* 3.8 19.7 - - + -
191A LEU* 3.6 28.3 - - + -
331A ILE 3.0 14.4 + - - +
332A ASP 3.1 6.0 + - - +
334A THR* 1.3 74.2 - - - +
336A GLY* 1.3 58.6 + - - +
338A LEU* 3.1 6.5 + - + +
339A MET* 2.9 36.6 + - + +
355A PHE* 3.9 8.5 - - + -
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Residues in contact with GLY 336 (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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187A ASN* 3.3 30.7 - - - -
332A ASP 2.9 10.3 + - - -
333A LYS* 3.1 4.7 + - - -
335A VAL* 1.3 73.8 - - - +
337A GLN* 1.3 57.7 + - - +
339A MET* 3.9 2.6 - - - +
340A ASP* 2.8 41.3 + - - +
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Residues in contact with GLN 337 (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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100A TRP* 4.3 15.8 + - - +
101A GLU* 5.4 7.7 + - - +
131A THR* 3.4 38.6 + - + +
282A GLU* 3.8 37.4 - - - +
285A ILE* 4.2 9.2 - - + +
333A LYS* 2.9 24.9 + - + +
334A THR* 3.4 21.0 + - - +
336A GLY* 1.3 76.0 - - - +
338A LEU* 1.3 56.1 - - - +
340A ASP* 4.6 1.6 - - - -
341A GLY* 2.9 24.3 + - - -
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Residues in contact with LEU 338 (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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166A ILE* 4.3 31.6 - - + -
168A PHE* 3.9 24.9 - - + -
285A ILE* 3.9 26.4 - - + +
288A ILE* 4.9 8.5 - - + -
289A LEU* 4.3 13.5 - - + -
305A PHE* 6.0 0.4 - - + -
334A THR 3.0 13.0 + - - +
335A VAL* 3.4 11.2 - - + +
337A GLN* 1.3 76.8 - - - +
339A MET* 1.3 64.9 + - - +
341A GLY* 3.3 1.4 + - - -
342A LEU* 2.9 55.8 + - + +
353A VAL* 5.0 8.5 - - + -
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Residues in contact with MET 339 (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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143A TRP* 3.5 66.9 - - + +
191A LEU* 4.2 12.3 - - + -
335A VAL* 2.9 30.4 + - + +
336A GLY 4.1 3.1 - - - +
337A GLN 3.3 0.2 - - - -
338A LEU* 1.3 75.0 - - - +
340A ASP* 1.3 67.0 + - - +
342A LEU* 3.2 26.0 + - + +
343A LYS* 2.9 24.6 + - - +
348A HIS* 4.6 13.9 - - + +
353A VAL* 4.5 12.8 - - + -
490A TYR* 4.4 16.2 - - + -
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Residues in contact with ASP 340 (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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131A THR* 3.3 23.6 + - - +
132A ASN* 4.8 2.9 - - - +
135A VAL* 4.8 5.1 - - + +
141A SER 5.6 0.2 - - - -
142A HIS* 2.7 35.6 + - - +
143A TRP* 3.1 28.1 + - - +
144A VAL 4.7 0.7 + - - -
187A ASN* 5.4 0.7 - - - +
336A GLY* 2.8 28.6 + - - +
337A GLN* 3.9 3.4 - - - +
339A MET* 1.3 70.7 - - - +
341A GLY* 1.3 62.8 + - - +
343A LYS* 3.2 9.6 + - - +
344A GLN* 3.0 26.7 + - - +
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Residues in contact with GLY 341 (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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131A THR* 4.2 6.2 + - - -
289A LEU* 3.6 26.9 - - - +
337A GLN 2.9 18.1 + - - -
338A LEU 3.7 0.4 - - - -
339A MET 3.2 0.2 - - - -
340A ASP* 1.3 78.1 - - - +
342A LEU* 1.3 60.7 + - - +
344A GLN* 3.4 14.3 + - - +
345A LEU* 3.2 24.4 + - - +
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Residues in contact with LEU 342 (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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166A ILE* 4.1 17.9 - - + -
289A LEU* 4.0 7.4 - - + -
292A LEU* 3.8 28.9 - - + -
338A LEU* 2.9 36.6 + - + +
339A MET* 3.2 25.5 + - + +
341A GLY* 1.3 74.8 - - - +
343A LYS* 1.3 57.4 + - - +
345A LEU* 3.0 13.4 + - - -
347A LEU* 2.8 42.8 + - + +
348A HIS* 3.9 15.0 - - + +
351A VAL* 4.3 10.1 - - + -
353A VAL* 4.5 8.5 - - + -
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Residues in contact with LYS 343 (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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134A GLN* 4.5 1.8 - - - +
140A GLU* 3.9 20.8 + - - +
141A SER* 3.0 39.6 + - - +
143A TRP* 4.2 14.4 - - + +
146A ASP* 2.6 30.3 + - - +
339A MET 2.9 16.5 + - - +
340A ASP* 3.5 7.4 - - - +
342A LEU* 1.3 75.1 - - - +
344A GLN* 1.3 65.1 + - + +
346A ARG* 3.0 26.0 + - - +
348A HIS* 3.7 38.1 + - + +
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Residues in contact with GLN 344 (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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124A LEU* 4.5 5.5 - - + +
129A CYS* 3.9 16.4 + - - +
130A CYS 3.3 16.7 + - - -
131A THR* 3.7 17.9 - - - +
133A TYR* 3.4 8.7 + - - +
134A GLN* 3.0 58.0 + - + +
289A LEU* 6.0 0.8 - - - +
340A ASP 3.0 21.6 + - - +
341A GLY* 3.4 10.1 + - - +
343A LYS* 1.3 75.7 - - + +
345A LEU* 1.3 64.6 + - + +
346A ARG* 3.3 5.4 + - - +
1878A IOD 3.7 21.4 - - + +
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Residues in contact with LEU 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU* 3.9 27.8 - - + +
127A GLY* 5.0 5.4 - - - -
157A PRO* 4.2 8.5 - - - +
289A LEU* 3.9 38.8 - - + +
292A LEU* 4.4 5.2 - - + -
293A SER* 3.9 16.4 - - - +
341A GLY 3.2 12.9 + - - +
342A LEU 3.0 8.6 + - - +
344A GLN* 1.3 76.7 - - + +
346A ARG* 1.3 69.0 + - - +
347A LEU* 3.2 28.7 + - + +
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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