Contacts of the helix formed by residues 240 - 255 (chain A) in PDB entry 1VPE
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 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A LYS* 5.6 5.8 + - - +
238A VAL* 3.3 8.5 + - - +
239A GLU* 1.3 73.1 + - - +
241A ASP* 1.3 60.7 + - - +
242A LYS 3.1 5.2 + - - -
243A ILE* 3.2 36.0 + - + +
244A ASP* 5.0 1.7 + - - +
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Residues in contact with ASP 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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199A SER* 6.0 0.4 - - - +
239A GLU* 3.0 9.3 + - + +
240A GLU* 1.3 81.0 - - - +
242A LYS* 1.3 72.0 + - + +
243A ILE 3.7 0.2 - - - -
244A ASP* 3.6 12.2 - - - +
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Residues in contact with LYS 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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198A VAL* 5.0 1.3 - - + -
199A SER* 4.0 42.2 + - - +
202A ILE* 3.8 31.7 - - + +
224A THR* 4.0 5.8 - - + -
239A GLU* 2.8 17.2 + - + +
241A ASP* 1.3 90.5 + - + +
243A ILE* 1.3 64.8 + - - +
244A ASP* 3.4 6.3 - - - -
245A LEU* 3.3 17.3 + - + +
246A ALA* 3.0 22.3 + - - +
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Residues in contact with ILE 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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224A THR* 4.1 14.1 - - + +
227A LYS* 3.9 34.3 - - + +
228A ALA* 3.8 30.4 - - + +
238A VAL* 4.2 4.9 - - + -
239A GLU 3.6 9.9 - - - +
240A GLU* 3.2 38.2 + - + +
242A LYS* 1.3 78.2 - - - +
244A ASP* 1.3 59.0 + - - +
246A ALA* 3.1 5.1 + - - +
247A LYS* 2.9 27.3 + - + +
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Residues in contact with ASP 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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240A GLU 5.6 1.3 - - - -
241A ASP 3.6 21.4 - - - +
242A LYS* 3.6 2.1 - - - -
243A ILE* 1.3 76.6 + - - +
245A LEU* 1.3 68.2 + - - +
247A LYS* 3.4 11.7 + - - +
248A GLU* 3.2 27.6 + - - +
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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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202A ILE* 4.0 32.5 - - + +
203A GLY* 4.9 5.6 - - - -
206A THR* 6.3 0.7 - - - -
242A LYS* 3.3 22.4 + - + +
243A ILE 3.2 0.4 - - - -
244A ASP* 1.3 82.1 + - - +
246A ALA* 1.3 68.8 + - - +
248A GLU* 3.0 14.5 + - + +
249A LEU* 2.9 47.4 + - + +
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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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202A ILE* 4.1 15.4 - - + +
224A THR* 3.9 22.7 - - + +
225A PHE* 3.9 20.7 - - + -
228A ALA* 4.1 5.2 - - + -
242A LYS 3.0 13.6 + - - +
243A ILE* 3.3 10.1 - - - +
245A LEU* 1.3 77.9 - - - +
247A LYS* 1.3 61.6 + - - +
249A LEU* 3.2 4.2 + - - +
250A VAL* 3.0 28.5 + - - +
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Residues in contact with LYS 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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228A ALA* 4.1 24.4 - - + +
229A LEU* 6.5 0.7 - - + -
243A ILE* 2.9 13.0 + - + +
244A ASP* 3.4 14.8 - - - +
245A LEU 3.1 0.2 - - - -
246A ALA* 1.3 77.8 - - - +
248A GLU* 1.3 65.7 + - - +
250A VAL* 2.8 27.5 - - + +
251A GLU* 3.2 14.3 + - - +
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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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244A ASP 3.5 15.5 - - - +
245A LEU* 3.0 17.7 + - + +
247A LYS* 1.3 85.4 - - - +
249A LEU* 1.3 61.1 + - + +
251A GLU* 3.5 21.7 + - - +
252A LYS* 2.9 30.9 + - - +
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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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202A ILE* 3.6 41.5 - - + +
205A ILE* 3.9 14.4 - - + -
206A THR* 4.0 31.9 - - - +
209A MET* 3.4 21.2 - - + +
225A PHE* 4.3 11.4 - - + -
245A LEU* 2.9 36.6 + - + +
246A ALA 3.6 4.7 - - - +
248A GLU* 1.3 76.8 - - + +
250A VAL* 1.3 60.7 + - - +
252A LYS* 3.4 7.7 + - + -
253A ALA* 2.9 26.5 + - - +
260A ILE* 4.7 1.8 - - + -
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Residues in contact with VAL 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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225A PHE* 3.6 32.3 - - + +
228A ALA* 5.7 2.2 - - + +
229A LEU* 4.7 24.2 - - + -
246A ALA 3.0 10.9 + - - +
247A LYS* 2.8 33.4 - - + +
249A LEU* 1.3 75.0 - - - +
251A GLU* 1.3 64.0 + - + +
253A ALA* 3.4 12.7 + - - +
254A LYS* 3.4 22.1 + - - +
260A ILE* 4.6 11.2 - - + -
262A LEU* 4.9 12.3 - - + -
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Residues in contact with GLU 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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247A LYS* 3.2 16.1 + - - +
248A GLU* 3.6 24.5 - - - +
250A VAL* 1.3 83.1 - - + +
252A LYS* 1.3 61.7 + - - +
254A LYS* 3.3 19.6 + - - +
255A GLU* 3.4 31.5 + - - +
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Residues in contact with LYS 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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206A THR* 3.1 31.2 + - - +
209A MET* 4.0 15.9 - - + -
210A GLU* 4.5 8.2 + - - -
248A GLU 2.9 20.1 + - - +
249A LEU* 3.8 8.3 - - + +
251A GLU* 1.3 73.6 - - - +
253A ALA* 1.3 65.9 - - - +
255A GLU* 3.3 11.1 + - + +
256A LYS* 3.0 57.5 + - + +
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Residues in contact with ALA 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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209A MET* 3.6 15.0 - - + -
249A LEU 2.9 18.6 + - - +
250A VAL* 3.5 6.5 - - - +
251A GLU 3.3 0.2 - - - -
252A LYS* 1.3 74.7 - - - +
254A LYS* 1.3 62.3 + - + +
256A LYS* 3.2 2.6 + - - -
257A GLY 3.1 3.8 + - - -
258A VAL* 3.0 45.6 + - + +
260A ILE* 3.6 27.4 - - + -
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Residues in contact with LYS 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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250A VAL* 3.4 14.9 + - - +
251A GLU* 3.3 12.9 + - - +
252A LYS 3.2 0.2 - - - -
253A ALA* 1.3 76.1 - - + +
255A GLU* 1.3 66.8 + - + +
257A GLY* 3.0 15.3 + - - +
258A VAL 4.7 2.7 - - - +
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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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251A GLU* 3.4 31.4 + - + +
252A LYS* 3.3 13.9 + - + +
254A LYS* 1.3 79.2 - - + +
256A LYS* 1.3 63.0 + - + +
257A GLY 3.7 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