Contacts of the helix formed by residues 243 - 258 (chain B) in PDB entry 2VE7
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 PHE 243 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232B CYS* 3.4 54.3 - - + -
235B SER* 4.4 7.4 - - - -
236B PHE* 4.0 21.5 - + + -
240B ALA* 4.6 5.2 - - + -
241B ASP 3.8 17.9 - - - -
242B SER* 1.3 81.2 - - - +
244B ASP* 1.3 59.8 + - - +
245B GLU 3.5 2.0 - - - -
246B MET* 4.0 10.8 - - - -
247B ASN* 2.8 43.0 + - - +
130D PHE* 4.0 22.4 - + - -
2198D IPH 3.5 39.3 - + + -
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Residues in contact with ASP 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B SER* 3.3 25.8 + - - -
243B PHE* 1.3 69.9 + - - +
245B GLU* 1.3 59.1 + - - +
247B ASN* 3.8 7.7 + - - +
248B ALA* 2.7 38.7 + - - +
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Residues in contact with GLU 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B PHE 3.5 0.2 - - - -
244B ASP* 1.3 78.2 - - + +
246B MET* 1.3 79.0 + - + +
248B ALA* 3.7 5.4 - - - +
249B GLU* 3.0 28.6 + - - +
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Residues in contact with MET 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B TYR* 3.8 10.6 - - + +
231B LYS* 4.1 19.1 - - + +
232B CYS* 3.7 39.3 - - - +
235B SER* 3.1 34.1 - - - +
242B SER 5.1 0.7 - - - +
243B PHE* 3.5 22.9 + - - +
244B ASP 3.2 0.2 - - - -
245B GLU* 1.3 98.1 - - + +
247B ASN* 1.3 59.9 + - - +
249B GLU* 3.4 8.5 + - - +
250B LEU* 2.9 28.4 + - - +
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Residues in contact with ASN 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B TYR* 2.7 30.7 + - - -
243B PHE* 2.8 36.1 + - - +
244B ASP* 3.8 8.1 + - - +
246B MET* 1.3 74.3 - - - +
248B ALA* 1.3 66.4 + - - +
250B LEU* 3.1 7.7 + - - +
251B GLN* 3.0 31.4 + - - +
137D THR* 3.8 6.1 - - - +
141D PHE* 3.7 27.7 - - + -
2198D IPH 5.0 4.2 - - - -
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Residues in contact with ALA 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B ASP 2.7 23.5 + - - +
245B GLU* 3.7 5.2 - - - +
247B ASN* 1.3 72.9 - - - +
249B GLU* 1.3 62.4 + - - +
251B GLN* 3.2 13.0 + - - +
252B SER* 3.1 23.5 + - - -
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Residues in contact with GLU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ASP* 4.5 0.3 - - - +
231B LYS* 2.9 40.5 + - - +
245B GLU 3.0 17.5 + - - +
246B MET* 3.8 8.0 - - - +
247B ASN 3.3 0.2 - - - -
248B ALA* 1.3 75.8 - - - +
250B LEU* 1.3 62.4 + - - +
252B SER* 3.4 8.9 + - - -
253B LYS* 3.3 51.8 + - + +
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Residues in contact with LEU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B LEU* 4.0 22.7 - - + -
228B TYR* 3.9 33.0 - - + -
246B MET 2.9 17.2 + - - +
247B ASN 3.1 6.2 + - - +
249B GLU* 1.3 77.7 - - - +
251B GLN* 1.3 56.5 + - - +
253B LYS* 3.4 6.1 + - - +
254B LEU* 3.1 35.1 + - + +
138D TYR* 3.7 40.8 - - + -
141D PHE* 3.6 31.9 - - + -
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Residues in contact with GLN 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B ASN* 3.0 24.1 + - - +
248B ALA* 3.2 10.8 + - - +
250B LEU* 1.3 75.2 - - - +
252B SER* 1.3 64.9 + - - +
254B LEU* 3.8 4.9 - - - +
255B LYS* 3.0 40.1 + - - +
141D PHE* 3.5 38.9 - - + -
144D GLN* 5.7 2.4 - - - +
145D TYR* 3.4 31.6 + - + +
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Residues in contact with SER 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B ALA 3.1 12.5 + - - -
249B GLU* 3.5 16.0 - - - -
250B LEU 3.4 0.4 - - - -
251B GLN* 1.3 76.3 - - - +
253B LYS* 1.3 64.9 + - - +
255B LYS* 3.4 16.6 + - - +
256B ASP* 3.4 19.9 + - - +
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Residues in contact with LYS 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B LEU* 3.5 33.1 - - + +
227B ASP* 2.9 29.9 + - - -
231B LYS* 4.0 1.4 - - - +
249B GLU* 3.3 47.2 + - + +
250B LEU* 3.8 6.5 - - - +
252B SER* 1.3 79.0 - - - +
254B LEU* 1.3 59.8 + - - +
255B LYS 3.3 0.2 - - - -
256B ASP* 3.5 10.0 + - - +
257B LEU* 3.1 27.4 + - - +
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Residues in contact with LEU 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B LEU* 4.0 19.1 - - + -
250B LEU* 3.1 34.1 + - + +
251B GLN* 3.3 4.7 + - - +
253B LYS* 1.3 73.8 - - - +
255B LYS* 1.3 64.9 + - - +
257B LEU* 3.7 6.7 - - + -
258B PHE* 3.4 38.7 + - + +
138D TYR* 5.0 3.4 - - + +
141D PHE* 3.7 35.0 - - + +
142D LEU* 3.9 27.1 - - + +
145D TYR* 3.7 30.6 - - + -
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Residues in contact with LYS 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B GLN* 3.0 25.5 + - - +
252B SER* 3.6 11.6 - - - +
253B LYS 3.3 0.4 - - - -
254B LEU* 1.3 78.9 - - - +
256B ASP* 1.3 63.0 + - - +
258B PHE 3.0 21.3 - - - +
259B ASN* 3.5 8.5 + - - +
260B VAL 3.0 25.4 + - - +
261B ASP* 4.5 17.9 - - + +
145D TYR* 3.3 29.1 + - + -
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Residues in contact with ASP 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B SER* 3.4 15.4 + - - +
253B LYS* 3.5 10.6 + - - +
254B LEU 3.3 0.4 - - - -
255B LYS* 1.3 79.2 - - - +
257B LEU* 1.3 62.6 + - - +
258B PHE* 4.5 0.4 - - - -
259B ASN* 4.2 12.0 - - - +
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Residues in contact with LEU 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B HIS* 3.9 44.6 - - + +
224B LEU* 4.7 15.9 - - + -
253B LYS 3.1 15.6 + - - +
254B LEU* 3.5 10.1 + - + +
255B LYS 3.3 0.6 - - - -
256B ASP* 1.3 78.7 - - - +
258B PHE* 1.3 83.2 + - + +
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Residues in contact with PHE 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B HIS* 4.3 17.0 - + - -
254B LEU* 3.4 31.5 + - + +
255B LYS 3.0 8.2 - - - +
257B LEU* 1.3 107.6 - - + +
259B ASN* 1.3 52.2 + - - +
260B VAL* 2.5 31.0 + - + +
142D LEU* 4.4 8.3 - - + -
145D TYR* 3.6 31.9 - - + +
146D LYS* 4.2 20.0 - - + -
149D ALA* 3.8 26.5 - - + -
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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