Contacts of the helix formed by residues 224 - 239 (chain A) in PDB entry 2VGL
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 224 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A THR* 6.0 0.5 - - - +
190A SER* 5.8 1.4 - - - -
193A VAL* 3.4 27.1 - - - +
221A GLU 4.9 4.5 + - - +
222A PHE* 2.9 4.7 + - - -
223A LYS* 1.3 80.4 - - + +
225A SER* 1.3 63.0 + - - +
226A VAL 3.2 0.6 + - - -
227A SER* 3.8 7.7 + - - -
228A LEU* 3.8 18.8 + - - +
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Residues in contact with SER 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A VAL* 4.0 16.8 - - - -
196A LEU* 4.0 18.7 - - - +
211A ILE* 4.2 22.2 - - - +
222A PHE 2.7 20.1 + - - -
224A THR* 1.3 78.7 + - - +
226A VAL* 1.3 56.0 + - - +
228A LEU* 3.8 1.7 - - - +
229A ALA* 2.7 39.5 + - - +
264A LEU* 4.2 7.2 - - - +
268A TYR* 3.9 12.8 - - - -
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Residues in contact with VAL 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A LYS 3.5 14.1 + - - +
224A THR 3.2 1.6 - - - -
225A SER* 1.3 78.6 + - - +
227A SER* 1.3 62.6 + - - +
229A ALA* 3.3 2.6 - - - +
230A VAL* 2.8 31.4 + - + +
264A LEU* 6.2 0.4 - - - -
265A LEU* 3.9 18.6 - - + +
268A TYR* 3.6 42.6 - - + -
269A PRO 5.4 1.6 - - - +
271A PRO* 3.7 38.4 - - + -
276A VAL* 4.2 2.9 - - + -
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Residues in contact with SER 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A LYS 4.9 0.2 + - - -
224A THR 3.8 7.8 + - - -
225A SER 3.4 0.4 - - - -
226A VAL* 1.3 83.6 - - - +
228A LEU* 1.3 60.2 + - - +
230A VAL* 3.3 0.9 + - - +
231A SER* 2.6 37.3 + - - -
276A VAL* 3.7 30.8 - - - +
279A ARG* 5.2 4.0 + - - -
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Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A VAL* 3.5 40.8 - - + +
194A HIS* 4.6 3.8 - - - +
196A LEU* 4.0 16.4 - - + -
197A ASN* 3.9 32.7 - - - +
224A THR* 3.8 11.6 + - - +
225A SER 3.2 7.4 + - - +
227A SER* 1.3 81.4 - - - +
229A ALA* 1.3 64.3 + - - +
231A SER* 3.4 7.6 + - - +
232A ARG* 3.0 30.7 + - - +
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Residues in contact with ALA 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LEU* 4.2 4.6 - - + +
225A SER 2.7 22.8 + - - +
226A VAL 3.3 4.0 - - - +
228A LEU* 1.3 74.9 - - - +
230A VAL* 1.3 56.5 + - - +
232A ARG* 3.4 2.5 + - - +
233A LEU* 2.9 30.0 + - - +
261A LEU* 4.2 21.4 - - + +
264A LEU* 4.2 21.1 - - + -
265A LEU* 4.1 21.1 - - + -
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Residues in contact with VAL 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A VAL* 2.8 21.2 + - + +
227A SER 3.7 4.5 - - - +
229A ALA* 1.3 72.8 - - - +
231A SER* 1.3 69.2 + - - +
232A ARG 3.0 1.9 + - - -
233A LEU* 3.2 5.4 + - - +
234A SER* 3.0 22.7 + - - -
265A LEU* 4.1 24.7 - - + -
271A PRO* 4.5 2.2 - - + -
276A VAL* 3.9 22.7 - - + +
279A ARG* 3.7 19.7 - - + +
280A LEU* 3.7 39.9 - - + +
283A CYS* 4.9 1.2 - - + -
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Residues in contact with SER 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ASN* 5.7 0.2 + - - -
227A SER* 2.6 28.5 + - - -
228A LEU* 3.4 13.0 + - - +
230A VAL* 1.3 76.6 - - - +
232A ARG* 1.3 56.7 + - - +
234A SER* 3.3 6.6 + - - -
235A ARG* 3.1 46.9 + - - +
279A ARG* 4.2 17.2 - - - +
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Residues in contact with ARG 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LEU* 3.0 23.2 + - + +
197A ASN* 3.2 14.1 + - - +
198A ASP 2.0 36.6 + - - -
199A GLN* 4.2 3.6 + - - +
201A LEU* 3.5 24.7 - - - +
204A VAL* 3.5 16.3 - - + +
228A LEU 3.0 19.3 + - - +
229A ALA* 3.8 4.7 - - - +
231A SER* 1.3 73.9 - - - +
233A LEU* 1.3 66.5 + - - +
235A ARG* 3.2 40.4 + - - +
236A ILE* 3.0 35.6 + - - +
244A LEU* 5.7 3.8 - - - +
261A LEU* 4.3 13.2 - - + -
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Residues in contact with LEU 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 ALA 2.9 20.7 + - - +
230A VAL* 3.8 4.0 - - - +
232A ARG* 1.3 71.5 - - - +
234A SER* 1.3 57.9 + - - +
236A ILE* 2.8 21.4 + - + +
237A VAL* 2.9 26.3 + - + +
258A SER* 3.8 41.7 - - - +
261A LEU* 3.8 12.0 - - + +
262A LEU* 3.1 41.3 - - + +
265A LEU* 4.6 7.0 - - + -
280A LEU* 4.5 12.6 - - + -
283A CYS* 3.7 18.6 - - + -
287A ILE* 4.8 2.5 - - + -
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Residues in contact with SER 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 VAL 3.0 10.2 + - - -
231A SER* 3.3 9.0 + - - -
233A LEU* 1.3 79.5 - - - +
235A ARG* 1.3 68.5 + - - +
237A VAL* 3.7 2.2 - - - +
238A THR* 3.1 33.6 + - - +
279A ARG* 3.9 25.6 - - - +
282A GLU* 6.3 0.4 - - - -
283A CYS* 3.1 28.3 - - - -
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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
----------------------------------------------------------
197A ASN* 4.0 12.7 + - - -
231A SER* 3.1 26.6 + - - +
232A ARG* 3.2 61.7 - - - +
233A LEU 3.2 0.2 - - - -
234A SER* 1.3 85.9 + - - +
236A ILE* 1.3 61.4 + - + +
238A THR* 3.5 4.6 + - - -
239A SER* 3.2 26.0 + - - -
244A LEU* 5.8 0.2 - - - -
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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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201A LEU* 5.0 7.0 - - + -
232A ARG* 3.0 26.8 + - + +
233A LEU 2.8 14.2 + - - +
235A ARG* 1.3 72.6 - - + +
237A VAL* 1.3 64.2 + - + +
239A SER* 2.9 23.1 + - - -
244A LEU* 4.2 16.2 - - + -
253A PRO* 3.6 28.9 - - + +
254A ALA* 4.2 6.7 - - + +
257A LEU* 3.7 32.3 - - + -
258A SER* 3.5 23.6 - - - +
261A LEU* 3.9 16.8 - - + -
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Residues in contact with VAL 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 LEU* 2.9 34.2 + - + +
234A SER* 3.7 7.4 - - - +
236A ILE* 1.3 77.1 - - + +
238A THR* 1.3 63.1 + - + +
239A SER 4.7 1.7 - - - +
253A PRO* 4.8 9.5 - - + +
258A SER* 4.9 3.6 - - - +
283A CYS* 3.6 27.6 - - - +
286A THR* 3.9 23.5 - - + +
287A ILE* 4.0 22.4 - - + -
290A LYS* 3.9 23.6 + - + +
309A VAL* 5.1 5.6 - - + -
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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 SER* 3.1 23.9 + - - +
235A ARG* 3.5 6.6 + - - -
237A VAL* 1.3 86.8 - - + +
239A SER* 1.3 72.3 + - - +
240A ALA* 3.5 2.1 + - - -
283A CYS* 6.5 0.4 - - - -
286A THR* 4.7 14.4 - - + +
290A LYS* 5.8 2.7 + - - +
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Residues in contact with SER 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 3.2 13.0 + - - -
236A ILE 2.9 19.6 + - - +
237A VAL 4.7 1.9 - - - +
238A THR* 1.3 85.2 + - - +
240A ALA* 1.3 69.0 + - - +
243A ASP* 3.6 27.1 + - - +
244A LEU* 3.7 16.9 - - - +
253A PRO* 4.2 10.0 - - - +
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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