Contacts of the helix formed by residues 230 - 242 (chain A) in PDB entry 1VZP
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 GLY 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A LEU* 3.9 4.9 - - - -
228A GLY 3.2 8.2 + - - -
229A LEU* 1.3 73.3 - - - +
231A ASN* 1.3 65.1 + - - -
232A ILE* 3.2 2.9 - - - -
233A ILE* 3.2 11.9 + - - +
234A LYS* 2.4 30.6 + - - +
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Residues in contact with ASN 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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217A CYS* 5.5 0.9 - - - -
221A LEU* 3.9 15.7 - - + +
230A GLY* 1.3 72.3 - - - -
232A ILE* 1.3 65.7 + - + +
234A LYS* 3.4 11.1 + - - +
235A ASN* 3.1 20.4 + - - -
286A TYR* 4.1 16.4 + - + +
287A GLN* 5.4 0.2 - - - +
310A ARG* 3.7 42.4 - - - +
311A LEU* 2.9 38.8 + - - +
312A THR* 4.4 6.1 - - - +
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Residues in contact with ILE 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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230A GLY 3.2 0.2 - - - -
231A ASN* 1.3 81.8 - - + +
233A ILE* 1.3 70.5 + - + +
234A LYS 3.1 1.0 + - - -
235A ASN* 3.6 4.2 + - - -
236A GLU* 3.2 28.3 + - + +
277A GLN* 5.9 4.7 - - - +
279A ARG* 3.9 38.8 - - - +
283A THR* 4.8 0.2 - - - +
286A TYR* 3.5 47.0 - - + +
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Residues in contact with ILE 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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228A GLY 4.8 6.5 - - - +
229A LEU* 3.8 23.8 - - + -
230A GLY* 3.2 18.5 + - - +
232A ILE* 1.3 82.5 - - + +
234A LYS* 1.3 63.6 + - - +
236A GLU* 3.9 4.7 - - + -
237A ALA* 2.9 47.4 + - + +
264A VAL* 5.2 7.6 - - + +
267A PHE* 4.9 7.9 - - + +
268A SER* 4.9 14.6 - - - +
271A TRP* 4.5 26.0 - - + -
279A ARG* 4.5 18.8 - - - +
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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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217A CYS* 3.3 43.3 - - - +
220A LEU* 3.2 43.3 - - + +
221A LEU* 3.3 26.0 - - + +
229A LEU* 3.3 26.9 - - - +
230A GLY 2.4 26.3 + - - +
231A ASN* 3.5 12.1 - - - +
232A ILE 3.0 0.6 - - - -
233A ILE* 1.3 83.8 - - - +
235A ASN* 1.3 64.8 + - - +
237A ALA* 4.0 1.1 - - - +
238A LEU* 3.0 33.0 + - - +
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Residues in contact with ASN 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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217A CYS* 4.9 1.7 - - - -
231A ASN 3.1 20.4 + - - -
232A ILE 3.9 1.5 + - - +
234A LYS* 1.3 74.0 - - - +
236A GLU* 1.3 69.1 + - + +
238A LEU* 3.0 8.0 + - - +
239A TYR* 3.0 30.9 + - + -
245A PRO* 5.5 2.5 - - - +
285A VAL* 3.6 13.9 - - + -
286A TYR* 3.9 20.1 - - - +
311A LEU 4.4 1.2 + - - -
312A THR* 3.1 21.5 + - - +
313A TRP* 2.7 48.6 + - - +
314A TRP* 5.2 1.8 - - - -
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Residues in contact with GLU 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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232A ILE* 3.2 24.1 + - + +
233A ILE* 4.1 6.7 - - + +
235A ASN* 1.3 80.6 - - - +
237A ALA* 1.3 62.9 + - - +
239A TYR* 3.6 11.6 - - - +
240A ARG 3.9 0.9 + - - -
267A PHE* 2.9 51.1 - - + -
279A ARG* 3.3 16.4 + - - +
283A THR* 2.7 24.0 + - - +
284A GLN* 2.9 19.5 + - - +
285A VAL* 3.1 10.4 + - - -
286A TYR* 2.9 27.3 + - + +
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Residues in contact with ALA 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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220A LEU* 6.0 2.0 - - + -
233A ILE* 2.9 28.7 + - + +
234A LYS 4.0 1.6 - - - +
236A GLU* 1.3 75.7 - - - +
238A LEU* 1.3 64.3 + - + +
239A TYR 3.0 2.0 - - - -
240A ARG* 2.9 11.6 + - - +
260A LEU* 5.2 0.9 - - + -
263A HIS* 2.5 42.8 + - + +
264A VAL* 3.8 18.8 - - + -
267A PHE* 4.0 10.1 - - + -
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Residues in contact with LEU 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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216A VAL* 3.8 20.9 - - + -
217A CYS* 4.2 14.8 - - + -
220A LEU* 3.9 19.7 - - + -
234A LYS 3.0 30.1 + - - +
235A ASN* 3.0 4.5 + - - +
237A ALA* 1.3 77.3 - - - +
239A TYR* 1.3 58.3 + - - +
241A ALA* 3.0 5.9 + - - +
242A GLY 2.8 22.0 + - - -
243A ILE* 3.2 27.7 + - + +
245A PRO* 4.0 26.5 - - + -
260A LEU* 3.9 20.9 - - + -
263A HIS* 4.1 4.0 - - - -
314A TRP* 3.6 14.4 - - + -
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Residues in contact with TYR 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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235A ASN 3.0 25.0 + - - +
236A GLU 3.6 8.1 - - - +
238A LEU* 1.3 77.5 - - - +
240A ARG* 1.3 56.4 - - + +
241A ALA 3.0 0.2 - - - -
242A GLY* 2.7 21.3 + - - -
284A GLN* 5.3 5.6 - - + -
285A VAL* 2.8 42.7 - - + +
289A GLU* 2.8 20.5 + - - -
291A CYS* 5.0 2.2 - - - -
293A ALA* 6.1 4.0 - - + -
313A TRP 3.6 2.5 - - - -
314A TRP* 2.6 45.6 + + - -
315A CYS* 2.4 43.1 + - + +
318A CYS* 4.5 19.0 - - + +
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Residues in contact with ARG 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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237A ALA 2.9 12.3 + - - +
239A TYR* 1.3 79.4 - - + +
241A ALA* 1.3 58.4 + - - +
259A VAL* 4.3 5.9 - - - +
263A HIS* 3.5 27.5 - - + +
266A GLU* 2.7 40.2 + - - +
267A PHE* 3.5 32.5 - - + -
284A GLN* 6.4 0.2 - - + -
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Residues in contact with ALA 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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238A LEU 3.0 7.0 + - - +
239A TYR 3.6 0.2 - - - -
240A ARG* 1.3 79.5 - - - +
242A GLY* 1.3 56.7 + - - +
243A ILE* 3.5 26.5 - - + -
256A ARG* 2.7 26.4 + - - +
259A VAL* 3.9 17.6 - - + +
260A LEU* 4.3 2.0 - - - -
263A HIS* 3.2 26.4 - - + +
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Residues in contact with GLY 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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238A LEU 2.8 2.3 + - - -
239A TYR 2.7 17.1 + - - -
241A ALA* 1.3 79.0 - - - +
243A ILE* 1.3 54.7 - - - +
256A ARG* 2.7 20.4 + - - -
314A TRP* 3.7 5.8 - - - -
318A CYS* 3.5 17.9 - - - +
319A GLN* 2.7 23.6 - - - +
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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