Contacts of the helix formed by residues 242 - 264 (chain A) in PDB entry 2VDE
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 ASN 242 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ALA 2.7 23.2 + - - +
239A GLU 5.0 0.2 - - - -
240A LYS 4.0 0.2 - - - -
241A ARG* 1.3 71.3 - - - +
243A LEU* 1.3 63.3 + - - +
244A SER* 3.8 13.8 + - - +
245A LEU* 3.3 24.7 + - + +
246A LEU* 3.0 26.2 + - - +
341A ALA 5.5 0.2 - - - +
345A VAL* 3.4 27.9 - - + +
424A SER 4.1 8.3 + - - -
425A ALA* 2.9 30.6 + - - +
426A LEU 3.6 7.7 + - - -
427A GLY* 4.4 0.8 - - - +
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Residues in contact with LEU 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A VAL* 3.2 23.5 - - + +
121A GLN* 3.6 40.6 - - + +
122A THR* 3.4 45.1 + - + +
125A GLN* 4.0 23.3 - - + +
241A ARG* 3.4 10.9 + - - +
242A ASN* 1.3 75.1 - - - +
244A SER* 1.3 63.0 + - - +
245A LEU 3.4 0.2 - - - -
246A LEU* 4.1 19.1 - - + -
247A GLN* 3.2 10.0 + - - +
427A GLY* 4.6 10.8 - - - +
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Residues in contact with SER 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A THR* 4.7 11.6 + - - +
242A ASN* 3.4 14.0 + - - +
243A LEU* 1.3 74.4 - - - +
245A LEU* 1.3 60.2 + - - +
247A GLN* 3.6 6.1 + - - +
248A ALA* 3.0 27.0 + - - +
341A ALA* 4.6 6.1 - - - +
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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
----------------------------------------------------------
238A ALA 4.7 1.6 - - - +
239A GLU* 3.9 22.7 - - - +
242A ASN* 3.3 18.8 + - + +
244A SER* 1.3 76.5 - - - +
246A LEU* 1.3 66.6 + - - +
248A ALA* 3.3 4.9 + - - +
249A ARG* 3.0 57.4 + - - +
338A LEU* 3.7 24.0 - - + -
341A ALA* 4.1 4.4 - - + +
342A HIS* 4.0 28.7 - - + +
345A VAL* 3.6 31.0 - - + -
1453A CL 4.6 0.2 - - + -
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Residues in contact with LEU 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A VAL* 3.6 30.3 - - + -
121A GLN* 5.2 3.8 - - - +
240A LYS 5.6 5.4 - - - +
241A ARG* 5.7 4.3 - - - +
242A ASN 3.0 17.0 + - - +
243A LEU* 3.6 19.1 - - + +
244A SER 3.2 0.2 - - - -
245A LEU* 1.3 77.5 - - - +
247A GLN* 1.3 57.7 + - - +
249A ARG* 3.2 15.7 + - + +
250A LEU* 2.9 35.2 + - + +
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Residues in contact with GLN 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ILE* 3.2 24.9 - - + +
118A VAL* 3.5 9.8 - - + +
119A THR* 2.7 46.7 + - - +
122A THR* 5.0 1.5 + - - -
243A LEU 3.2 12.7 + - - +
244A SER* 3.9 5.8 - - - +
246A LEU* 1.3 76.4 - - - +
248A ALA* 1.3 56.6 + - - +
250A LEU* 3.2 8.3 + - - +
251A SER* 2.8 42.0 + - - +
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Residues in contact with ALA 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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244A SER 3.0 18.4 + - - +
245A LEU 3.4 6.5 - - - +
247A GLN* 1.3 77.2 - - - +
249A ARG* 1.3 60.0 + - - +
251A SER* 3.6 6.0 + - - -
252A GLN* 3.2 21.3 + - - +
334A ALA 4.7 1.9 - - - +
337A GLN* 4.7 3.1 - - + +
338A LEU* 3.7 20.5 - - + +
341A ALA* 3.5 26.9 - - + -
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Residues in contact with ARG 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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239A GLU* 3.2 28.8 + - - +
240A LYS* 5.4 1.4 - - - +
245A LEU* 3.0 41.1 + - - +
246A LEU* 3.5 15.2 - - + +
248A ALA* 1.3 74.1 - - - +
250A LEU* 1.3 65.2 + - + +
252A GLN* 3.2 7.0 + - - +
253A ASP* 3.1 20.1 + - - +
338A LEU* 3.6 24.2 - - + +
1453A CL 2.9 33.0 - - - +
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Residues in contact with LEU 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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111A LYS* 5.2 1.5 - - - +
114A GLY* 3.9 9.4 - - - -
115A ILE* 3.5 44.8 - - + +
118A VAL* 3.9 18.6 - - + -
246A LEU* 2.9 25.9 + - + +
247A GLN* 3.2 8.9 + - - +
249A ARG* 1.3 78.5 - - + +
251A SER* 1.3 56.0 + - - +
253A ASP* 3.1 12.7 + - + +
254A LEU* 2.9 22.7 + - - +
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Residues in contact with SER 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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115A ILE* 3.8 25.2 - - - +
247A GLN* 2.8 26.6 + - - +
248A ALA* 3.9 6.7 - - - -
250A LEU* 1.3 69.8 - - - +
252A GLN* 1.3 65.6 + - - +
254A LEU* 3.2 6.7 + - - +
255A ALA* 3.0 22.0 + - - +
334A ALA* 4.1 6.7 - - - +
337A GLN* 5.6 6.5 - - - -
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Residues in contact with GLN 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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248A ALA 3.2 11.3 + - - +
249A ARG* 3.2 10.8 + - - +
251A SER* 1.3 78.7 - - - +
253A ASP* 1.3 61.2 + - - +
255A ALA* 3.6 0.7 + - - +
256A ARG* 3.3 23.9 + - - +
331A PHE* 3.4 32.7 - - + -
334A ALA* 3.7 15.2 + - + +
335A SER* 3.0 41.5 + - - +
338A LEU* 3.5 24.8 - - + +
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Residues in contact with ASP 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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111A LYS* 3.3 37.2 + - - +
249A ARG 3.1 11.8 + - - +
250A LEU* 3.1 15.6 + - + +
252A GLN* 1.3 76.0 + - - +
254A LEU* 1.3 64.9 + - - +
256A ARG* 3.2 26.3 + - - +
257A GLU* 3.1 23.0 + - - +
260A ARG* 5.4 0.9 + - - -
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Residues in contact with LEU 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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108A LEU* 4.0 24.5 - - + +
111A LYS* 3.8 30.9 - - + +
112A ALA* 4.2 10.5 - - + +
115A ILE* 4.0 15.0 - - + -
250A LEU 2.9 13.5 + - - +
251A SER* 3.2 11.6 + - - +
253A ASP* 1.3 74.8 - - - +
255A ALA* 1.3 63.5 - - - +
257A GLU* 3.3 6.7 + - - +
258A GLN* 2.9 46.5 + - - +
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Residues in contact with ALA 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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251A SER 3.0 6.3 + - - +
252A GLN 3.6 9.6 - - - +
254A LEU* 1.3 76.7 - - - +
256A ARG* 1.3 63.2 + - - +
258A GLN* 3.1 23.4 + - - +
259A ILE* 3.1 15.7 + - - +
327A ALA 4.6 2.3 - - - +
330A ASN* 3.8 11.6 - - - +
331A PHE* 3.7 19.1 - - + -
334A ALA* 3.6 26.7 - - + -
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Residues in contact with ARG 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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252A GLN* 3.3 16.7 + - - +
253A ASP* 3.2 27.7 + - - +
255A ALA* 1.3 79.1 - - - +
257A GLU* 1.3 55.4 + - - +
259A ILE* 2.9 33.2 + - + +
260A ARG* 3.4 38.5 + - - +
331A PHE* 3.6 36.2 - - + -
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Residues in contact with GLU 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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104A ARG* 3.1 36.5 + - - +
107A THR* 4.0 14.7 - - + +
108A LEU* 3.9 14.8 - - + -
111A LYS* 3.5 29.5 - - + -
253A ASP* 3.1 14.2 + - - +
254A LEU 3.3 7.2 + - - +
256A ARG* 1.3 75.5 - - - +
258A GLN* 1.3 58.0 + - - +
260A ARG* 3.0 27.7 + - - +
261A GLN* 3.0 24.3 + - - +
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Residues in contact with GLN 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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108A LEU* 3.8 21.4 - - + +
254A LEU* 2.9 43.6 + - - +
255A ALA* 3.1 14.4 + - - +
257A GLU* 1.3 73.8 - - - +
259A ILE* 1.3 59.4 - - - +
261A GLN* 3.4 18.4 + - - +
262A ALA* 3.1 25.5 + - - +
327A ALA* 4.0 8.0 - - + +
330A ASN* 4.5 10.8 + - - +
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Residues in contact with ILE 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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255A ALA 3.1 11.6 + - - +
256A ARG* 2.9 20.2 + - + +
258A GLN* 1.3 73.6 - - - +
260A ARG* 1.3 64.4 + - + +
262A ALA* 3.2 5.9 + - - +
263A GLN* 3.2 30.9 + - - +
324A VAL* 4.0 21.4 - - + +
327A ALA* 3.5 24.0 - - + +
328A GLN* 4.0 20.4 - - + -
331A PHE* 3.7 32.3 - - + -
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Residues in contact with ARG 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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104A ARG* 3.4 33.9 - - - +
253A ASP* 5.4 1.2 + - - -
256A ARG* 3.4 42.6 + - + +
257A GLU* 3.0 40.1 + - - +
259A ILE* 1.3 77.7 - - + +
261A GLN* 1.3 62.6 + - - +
263A GLN* 3.2 24.7 + - - +
264A ASP* 3.0 27.8 + - - +
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Residues in contact with GLN 261 (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 SER* 5.6 6.1 - - - +
104A ARG* 3.6 23.5 - - + +
105A ALA* 5.5 4.2 - - - +
108A LEU* 3.3 21.4 - - + +
257A GLU 3.0 11.3 + - - +
258A GLN* 3.4 24.0 + - - +
260A ARG* 1.3 74.8 - - - +
262A ALA* 1.3 64.3 + - - +
264A ASP* 3.2 25.2 + - - +
265A GLY 4.2 0.7 + - - -
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Residues in contact with ALA 262 (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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258A GLN 3.1 12.9 + - - +
259A ILE 3.2 9.4 + - - +
261A GLN* 1.3 77.3 + - - +
263A GLN* 1.3 58.5 + - - +
265A GLY* 3.0 18.0 + - - -
320A VAL* 3.5 11.1 - - - +
323A GLN* 3.8 38.9 - - + +
324A VAL* 3.8 15.7 - - + -
327A ALA* 4.1 3.8 - - + -
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Residues in contact with GLN 263 (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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259A ILE* 3.2 16.0 + - - +
260A ARG* 3.3 35.5 - - - +
262A ALA* 1.3 74.9 - - - +
264A ASP* 1.3 60.8 + - - +
265A GLY 3.0 5.7 + - - -
266A HIS* 3.5 31.7 + - + +
267A LEU* 4.6 4.9 + - - +
320A VAL* 4.3 0.4 - - - -
324A VAL* 3.6 30.9 - - + +
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Residues in contact with ASP 264 (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 MET* 3.9 16.8 - - + +
101A SER* 3.9 21.4 + - - +
104A ARG* 2.8 57.2 + - - +
260A ARG 3.0 17.1 + - - +
261A GLN* 3.3 10.6 - - - +
262A ALA 3.1 0.6 - - - -
263A GLN* 1.3 76.8 - - - +
265A GLY* 1.3 62.4 + - - +
266A HIS 3.2 1.3 - - - -
267A LEU* 3.2 29.8 + - - +
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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