Contacts of the helix formed by residues 234 - 247 (chain A) in PDB entry 1VJZ
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 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A TRP* 3.5 18.6 - - - -
224A PRO* 4.0 17.7 - - + -
225A ASN* 4.0 12.7 + - - +
232A TYR 5.8 0.4 - - - -
233A TRP* 1.3 75.2 - - - +
235A ARG* 1.3 64.4 + - - +
236A GLU* 3.2 13.1 + - - +
237A LYS* 2.9 32.6 + - - +
238A LEU* 3.1 18.5 + - - +
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Residues in contact with ARG 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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223A TRP* 3.6 10.6 - - - -
224A PRO* 5.0 2.0 - - + +
234A ASN* 1.3 74.9 - - - +
236A GLU* 1.3 59.0 + - - +
238A LEU* 3.3 6.7 + - - +
239A LEU* 2.9 55.2 + - - +
277A ASP* 3.8 36.5 + - + +
280A GLU* 2.8 33.0 + - - -
281A ILE* 3.6 29.1 - - + +
284A THR* 4.8 6.9 + - - +
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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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234A ASN* 3.2 14.8 + - - +
235A ARG* 1.3 82.4 - - - +
237A LYS* 1.3 57.4 + - - +
239A LEU* 3.2 12.5 + - + +
240A GLU* 3.0 44.9 + - + +
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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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231A GLU* 4.1 22.5 + - - +
232A TYR 3.5 24.7 - - - +
233A TRP* 3.4 50.7 - - + +
234A ASN* 2.9 21.7 + - - +
236A GLU* 1.3 73.3 - - - +
238A LEU* 1.3 65.8 + - - +
240A GLU* 3.4 17.4 + - - +
241A HIS* 3.0 17.3 + - - +
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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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201A ILE* 3.9 25.1 - - + +
223A TRP* 3.7 29.8 - - + -
233A TRP* 3.6 23.5 - - + -
234A ASN 3.1 13.5 + - - +
235A ARG* 3.5 7.4 - - - +
237A LYS* 1.3 76.6 - - - +
239A LEU* 1.3 63.3 + - - +
241A HIS* 3.0 10.6 + - - +
242A TYR* 3.1 38.0 + - + +
274A TRP* 4.4 10.1 - - + +
277A ASP* 5.0 0.7 - - + -
278A LEU* 4.4 21.8 - - + +
281A ILE* 3.6 17.5 - - + -
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Residues in contact with LEU 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 ARG* 2.9 40.9 + - - +
236A GLU* 3.2 15.2 + - + +
238A LEU* 1.3 73.3 - - - +
240A GLU* 1.3 63.3 + - + +
242A TYR* 3.3 1.0 + - - +
243A LEU* 2.9 53.1 + - + +
281A ILE* 3.6 32.9 - - + +
284A THR* 5.7 3.6 - - + -
285A LEU* 4.2 12.8 - - + -
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Residues in contact with GLU 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 GLU* 3.0 34.8 + - + +
237A LYS* 3.8 19.4 - - - +
239A LEU* 1.3 76.6 - - + +
241A HIS* 1.3 64.0 + - - +
243A LEU* 3.4 13.3 + - + +
244A THR* 3.1 25.9 + - - -
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Residues in contact with HIS 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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182A ASN* 3.5 30.7 + - + -
184A PRO* 6.0 0.4 - - + -
197A CYS* 5.5 0.4 - - - +
198A ARG 4.9 0.2 + - - -
201A ILE* 3.9 22.7 - - + +
233A TRP* 3.8 22.0 - + + -
237A LYS 3.0 13.8 + - - +
238A LEU 3.2 8.7 - - - +
240A GLU* 1.3 76.0 - - - +
242A TYR* 1.3 98.5 + + - +
244A THR* 3.1 18.3 + - - -
245A TRP* 3.3 29.3 + + - -
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Residues in contact with TYR 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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197A CYS* 3.8 21.3 - - - -
198A ARG 2.6 31.4 + - - -
199A GLY* 3.6 9.0 - - - -
200A TYR 4.8 0.3 + - - -
201A ILE* 4.6 8.5 + - - +
238A LEU* 3.1 40.3 + - + +
239A LEU 4.3 0.9 - - - +
241A HIS* 1.3 98.9 - + - +
243A LEU* 1.3 59.8 + - - +
245A TRP* 3.1 9.8 + + - +
246A ILE* 3.0 31.5 + - - +
278A LEU* 3.4 22.8 - - + +
281A ILE* 4.3 7.6 - - + -
282A PHE* 3.7 26.5 - + - -
285A LEU* 3.8 11.7 - - + -
287A ILE* 3.8 16.8 - - + -
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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
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239A LEU* 2.9 50.2 + - + +
240A GLU* 3.6 13.2 - - + +
242A TYR* 1.3 76.4 - - - +
244A THR* 1.3 61.7 + - - +
246A ILE* 3.4 28.8 + - + +
247A LYS* 3.5 13.2 + - - +
285A LEU* 3.8 24.2 - - + +
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Residues in contact with THR 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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184A PRO* 4.5 18.3 - - + +
240A GLU 3.1 14.3 + - - -
241A HIS* 3.1 12.7 + - - -
243A LEU* 1.3 77.3 - - - +
245A TRP* 1.3 62.2 + - + +
247A LYS* 3.4 38.1 + - - +
248A LEU* 4.5 0.7 + - - +
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Residues in contact with TRP 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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177A GLY* 3.8 13.9 - - - -
181A GLY 3.9 1.1 - - - -
182A ASN* 3.0 39.1 + - - +
183A ILE 3.6 1.1 - - - -
184A PRO* 3.5 26.9 - - + +
195A GLN* 3.8 26.5 - - + -
196A SER 3.6 17.5 - - - -
197A CYS* 3.3 33.2 - - + +
241A HIS* 3.3 38.5 + + - -
242A TYR* 3.1 16.9 + + + +
244A THR* 1.3 81.1 - - - +
246A ILE* 1.3 57.0 + - - +
248A LEU* 3.1 45.2 + - + +
255A VAL* 3.4 27.7 - - + +
287A ILE* 5.4 0.2 - - + -
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Residues in contact with ILE 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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242A TYR 3.0 17.7 + - - +
243A LEU* 3.4 34.1 - - + +
244A THR 3.4 0.2 - - - -
245A TRP* 1.3 71.1 - - - +
247A LYS* 1.3 55.4 + - - +
248A LEU 3.0 5.8 - - - -
249A ARG* 3.0 64.3 + - - +
250A GLN* 4.3 0.7 + - - +
255A VAL* 4.3 10.8 - - + -
285A LEU* 4.2 16.6 - - + +
287A ILE* 3.8 25.1 - - + -
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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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243A LEU 3.5 15.1 + - - +
244A THR* 3.5 34.2 + - - +
245A TRP 3.2 1.2 - - - -
246A ILE* 1.3 72.9 - - + +
248A LEU* 1.3 63.8 + - - +
249A ARG 3.1 0.4 - - - -
250A GLN* 3.1 22.7 + - + +
251A LYS* 3.0 29.9 + - - +
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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