Contacts of the helix formed by residues 229 - 239 (chain A) in PDB entry 2FVJ
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 THR 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A TYR* 4.3 11.2 - - + -
223A ILE* 3.8 30.1 - - + +
226A PHE 3.9 15.5 - - - +
227A PRO 3.7 5.4 + - - +
228A LEU* 1.3 77.8 - - - +
230A LYS* 1.3 59.6 + - - +
231A ALA* 3.6 4.4 + - - +
232A LYS* 3.3 21.9 + - - +
233A ALA* 2.9 27.5 + - - +
332A SER* 5.3 0.7 - - - -
381A ASP* 3.5 16.1 + - - -
501A RO0 6.2 0.4 - - - -
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Residues in contact with LYS 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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222A TYR* 4.3 2.0 + - - -
229A THR* 1.3 68.9 - - - +
231A ALA* 1.3 65.5 + - - +
233A ALA* 4.2 2.2 - - - -
234A ARG* 2.8 52.0 + - + +
332A SER* 3.5 38.2 - - - +
374A PHE* 6.0 3.2 - - - -
375A ASN* 4.2 24.6 + - - +
378A GLU* 4.4 6.3 - - - +
379A LEU* 2.7 39.7 + - - +
380A ASP* 4.6 4.0 - - - +
381A ASP* 2.9 22.2 + - - +
384A LEU* 3.9 11.6 - - + +
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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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229A THR* 3.2 5.1 - - - +
230A LYS* 1.3 77.3 - - - +
232A LYS* 1.3 57.2 + - - +
234A ARG* 4.0 4.3 - - - +
235A ALA* 3.1 27.9 + - - +
240A LYS* 5.0 2.6 - - - -
381A ASP* 3.1 18.4 + - - +
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Residues in contact with LYS 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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227A PRO 5.7 2.0 - - - +
228A LEU* 3.9 17.5 - - + -
229A THR* 3.3 18.4 + - - +
230A LYS 3.3 0.2 - - - -
231A ALA* 1.3 73.1 - - - +
233A ALA* 1.3 67.0 + - - +
235A ALA* 3.2 11.7 + - + +
236A ILE* 3.0 41.9 + - + +
241A THR* 3.5 30.5 + - - +
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Residues in contact with ALA 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 LEU* 4.0 5.1 - - + +
229A THR 2.9 17.7 + - - +
230A LYS* 3.7 3.8 - - - +
232A LYS* 1.3 76.1 - - - +
234A ARG* 1.3 59.0 + - - +
236A ILE* 3.2 5.1 + - - +
237A LEU* 2.9 32.3 + - - +
332A SER* 3.3 24.2 - - - +
333A LEU* 3.6 24.5 - - + -
340A LEU* 3.6 12.9 - - + +
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Residues in contact with ARG 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 LYS* 2.8 48.2 + - + +
231A ALA* 4.0 4.0 - - - +
233A ALA* 1.3 73.8 - - - +
235A ALA* 1.3 56.5 + - - +
237A LEU* 3.4 20.1 + - - +
238A THR* 2.8 41.6 + - + +
240A LYS* 3.9 11.0 - - - +
331A ALA 3.7 3.2 + - - -
332A SER* 2.8 37.0 + - - +
334A MET 2.8 29.3 + - - -
335A ASN* 4.1 11.1 - - - +
375A ASN* 3.8 16.2 - - - +
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Residues in contact with ALA 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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231A ALA 3.1 14.6 + - - +
232A LYS* 3.4 15.7 - - + +
234A ARG* 1.3 77.2 - - - +
236A ILE* 1.3 57.3 + - - +
238A THR* 3.4 0.3 + - - -
239A GLY* 3.0 25.5 + - - -
240A LYS* 3.0 39.9 + - + +
241A THR* 3.8 14.1 - - - +
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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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228A LEU* 5.0 3.4 - - + -
232A LYS* 3.0 39.2 + - + +
233A ALA* 3.6 5.6 - - - +
235A ALA* 1.3 74.1 - - - +
237A LEU* 1.3 65.0 + - - +
238A THR 3.0 1.4 + - - -
239A GLY* 3.2 12.2 + - - -
241A THR* 3.8 15.7 + - + +
244A LYS 5.8 1.8 - - - +
246A PRO* 4.0 24.0 - - + +
340A LEU* 3.6 21.8 - - + -
343A GLU 4.9 2.2 - - - +
344A GLY* 3.6 41.3 - - - +
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Residues in contact with LEU 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 ALA 2.9 21.5 + - - +
234A ARG* 3.4 44.0 - - - +
236A ILE* 1.3 73.6 - - - +
238A THR* 1.3 63.9 + - + +
246A PRO* 6.2 0.9 - - + -
332A SER 4.2 2.0 - - - +
333A LEU 3.9 17.9 - - - +
334A MET 4.1 5.6 - - - +
335A ASN* 4.1 17.1 + - - +
340A LEU* 3.6 24.5 - - + -
347A PHE* 3.6 31.9 - - + -
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Residues in contact with THR 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 ARG* 2.8 27.8 + - + +
237A LEU* 1.3 82.5 - - + +
239A GLY* 1.3 60.7 + - - +
240A LYS* 3.0 32.9 + - - +
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Residues in contact with GLY 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 ALA 3.0 5.2 + - - -
236A ILE* 3.2 9.7 + - - -
237A LEU 3.6 0.4 - - - -
238A THR* 1.3 76.4 - - - +
240A LYS* 1.3 56.4 + - - +
241A THR* 3.0 16.0 + - - +
242A THR 4.7 1.7 + - - +
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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