Contacts of the helix formed by residues 226 - 240 (chain A) in PDB entry 3VG1
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 LYS 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A TYR* 5.9 1.2 - - - -
225A PRO* 1.3 70.5 - - - +
227A LYS* 1.3 65.7 + - + +
229A PHE* 3.3 1.3 + - - +
230A GLU* 3.0 59.5 + - - +
314A GLN* 3.6 35.7 - - + +
315A SER 3.5 9.5 + - - +
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Residues in contact with LYS 227 (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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203A MET* 3.3 27.7 - - + +
207A GLU* 4.3 22.8 + - - +
225A PRO* 3.0 2.7 + - + +
226A LYS* 1.3 81.5 - - + +
228A VAL* 1.3 61.2 + - + +
230A GLU* 3.8 12.1 + - - +
231A ALA* 3.4 22.3 + - - +
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Residues in contact with VAL 228 (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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194A VAL* 5.2 3.6 - - + -
201A LEU* 4.1 11.8 - - + +
203A MET* 3.8 17.3 - - + -
207A GLU* 3.5 28.5 - - + +
208A TYR* 3.8 35.2 - - + -
224A LEU* 4.3 23.1 - - + -
225A PRO* 2.9 18.2 + - + +
227A LYS* 1.3 75.2 - - + +
229A PHE* 1.3 66.7 + - - +
231A ALA* 3.4 2.3 + - - +
232A ALA* 2.9 22.9 + - - +
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Residues in contact with PHE 229 (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 LEU* 3.9 20.3 - - + +
225A PRO 2.8 15.6 + - - +
226A LYS* 3.5 4.5 - - - +
228A VAL* 1.3 76.6 - - - +
230A GLU* 1.3 69.4 + - + +
232A ALA* 3.1 2.1 + - - +
233A VAL* 2.9 52.4 + - + +
250A TRP 3.5 20.9 - - - -
251A LEU* 5.4 9.2 - - + -
310A PHE* 4.4 0.9 - + - -
312A ILE* 3.5 23.3 - - + -
313A SER* 3.4 37.7 - - - -
314A GLN* 3.9 30.5 - - + -
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Residues in contact with GLU 230 (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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226A LYS* 3.0 53.8 + - + +
227A LYS* 4.0 11.8 - - - +
229A PHE* 1.3 86.2 - - + +
231A ALA* 1.3 62.7 + - - +
233A VAL* 3.5 5.0 + - - +
234A LYS* 3.1 42.7 + - - +
314A GLN* 4.8 4.2 + - - +
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Residues in contact with ALA 231 (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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201A LEU* 4.2 18.7 - - + +
203A MET* 4.8 9.0 - - + -
227A LYS 3.4 15.2 + - - +
228A VAL* 3.4 6.0 + - - +
229A PHE 3.2 0.6 - - - -
230A GLU* 1.3 77.2 - - - +
232A ALA* 1.3 60.5 + - - +
234A LYS* 3.3 10.4 + - - +
235A SER* 3.0 28.9 + - - -
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Residues in contact with ALA 232 (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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194A VAL* 6.0 0.9 - - + -
196A ILE* 4.8 12.6 - - + -
201A LEU* 4.5 15.2 - - + +
224A LEU* 4.2 19.1 - - + -
228A VAL 2.9 17.3 + - - +
229A PHE 3.7 2.9 - - - +
231A ALA* 1.3 75.6 - - - +
233A VAL* 1.3 61.2 + - + +
235A SER* 3.2 6.6 + - - -
236A ILE* 2.8 42.6 + - + +
271A ILE* 6.3 0.4 - - + -
312A ILE* 5.8 3.4 - - + -
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Residues in contact with VAL 233 (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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229A PHE* 2.9 55.8 + - + +
230A GLU* 3.8 6.1 - - - +
232A ALA* 1.3 77.7 - - + +
234A LYS* 1.3 58.5 + - + +
236A ILE* 3.8 7.1 - - - +
237A LYS* 2.8 64.2 + - + +
250A TRP* 4.1 19.3 - - + +
310A PHE* 4.1 13.7 - - + -
312A ILE* 5.7 0.9 - - + -
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Residues in contact with LYS 234 (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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230A GLU* 3.1 34.7 + - - +
231A ALA* 3.6 8.7 - - - +
233A VAL* 1.3 77.4 - - + +
235A SER* 1.3 62.8 + - - +
237A LYS* 3.4 14.3 + - + +
238A ALA* 3.1 23.6 + - - +
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Residues in contact with SER 235 (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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196A ILE* 3.4 34.2 + - - +
199A GLN* 5.5 4.0 + - - +
201A LEU* 4.4 8.6 - - - +
231A ALA 3.0 17.4 + - - -
232A ALA* 3.5 5.2 - - - -
234A LYS* 1.3 78.3 - - - +
236A ILE* 1.3 61.0 + - - +
238A ALA* 3.5 8.8 + - - +
239A ALA* 3.4 19.1 + - - +
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Residues in contact with ILE 236 (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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196A ILE* 4.1 17.7 - - + -
232A ALA* 2.8 29.5 + - + +
233A VAL* 3.8 4.3 - - + +
235A SER* 1.3 74.1 - - - +
237A LYS* 1.3 65.6 + - - +
239A ALA* 3.2 4.5 + - - +
240A SER* 3.1 21.5 + - - +
250A TRP* 3.9 22.4 - - + -
268A PHE* 4.8 3.4 - - + -
269A PRO* 4.1 24.0 - - + -
271A ILE* 4.1 13.2 - - + -
293A TYR* 4.4 11.9 - - + +
310A PHE* 4.1 13.0 - - + -
312A ILE* 4.0 26.7 - - + -
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Residues in contact with LYS 237 (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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233A VAL* 2.8 40.1 + - + +
234A LYS* 3.6 12.1 - - + +
236A ILE* 1.3 76.5 - - - +
238A ALA* 1.3 62.7 + - - +
240A SER* 3.2 10.5 + - - +
241A SER* 3.1 23.2 + - - -
247A ASP* 5.5 4.2 + - - -
250A TRP* 3.3 48.5 - - + +
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Residues in contact with ALA 238 (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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234A LYS 3.1 16.3 + - - +
235A SER* 3.6 9.2 - - - +
237A LYS* 1.3 76.0 - - - +
239A ALA* 1.3 61.2 + - - +
241A SER* 3.1 22.5 + - - -
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Residues in contact with ALA 239 (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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196A ILE* 5.7 0.4 - - + -
197A ASN* 4.9 8.1 - - + +
235A SER 3.4 6.7 + - - +
236A ILE 3.2 9.5 + - - +
237A LYS 3.2 0.2 - - - -
238A ALA* 1.3 82.4 - - - +
240A SER* 1.3 57.1 + - - +
241A SER* 3.2 4.9 + - - -
242A THR* 5.0 4.3 + - - +
267A ILE* 3.3 13.8 - - - +
269A PRO* 3.6 33.9 - - + -
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Residues in contact with SER 240 (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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236A ILE 3.1 15.9 + - - -
237A LYS* 3.2 9.9 + - - -
239A ALA* 1.3 74.5 - - - +
241A SER* 1.3 59.2 + - - +
242A THR* 3.2 4.6 + - - -
243A GLU 2.8 25.3 + - - +
245A PHE* 3.6 16.0 - - - -
250A TRP* 3.9 6.8 - - - -
267A ILE* 3.8 19.5 - - - -
268A PHE* 4.0 27.1 - - - -
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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