Contacts of the strand formed by residues 220 - 226 (chain A) in PDB entry 3VEY
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 CYS 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A MET* 3.8 17.8 - - - +
213A CYS* 3.7 21.5 - - - +
214A TYR* 3.9 27.3 - - - +
217A ASP 2.9 17.8 + - - +
218A HIS 3.2 0.4 - - - -
219A GLN* 1.4 73.7 - - - +
221A GLU* 1.3 62.6 + - - +
222A VAL 3.5 22.9 - - - -
405A THR* 3.3 19.6 - - + +
406A VAL 4.2 1.6 - - - -
407A GLY* 3.5 16.4 - - - -
504A 0H5 4.8 2.4 - - - +
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Residues in contact with GLU 221 (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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210A MET* 3.6 12.1 - - - -
218A HIS 4.7 6.1 - - - +
219A GLN* 3.2 16.5 + - - +
220A CYS* 1.3 77.7 - - - +
222A VAL* 1.3 62.0 + - - +
234A TYR* 3.1 4.7 - - - +
235A MET* 3.0 53.0 + - + +
250A ARG* 3.0 27.5 + - - -
393A MET* 4.0 14.9 - - + +
397A ARG* 3.0 28.3 + - - -
404A ILE* 4.2 5.4 - - + +
405A THR 3.4 2.6 + - - -
504A 0H5 5.1 5.4 - - - +
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Residues in contact with VAL 222 (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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210A MET* 3.7 5.5 - - - +
220A CYS* 3.5 7.7 - - - -
221A GLU* 1.3 84.8 - - - +
223A GLY* 1.3 61.5 + - - +
224A MET* 5.1 0.4 - - + -
232A ALA* 5.0 4.0 - - + -
233A CYS 3.3 12.8 - - - +
234A TYR* 4.2 2.5 - - + -
386A LEU* 3.8 25.6 - - + -
389A VAL* 4.4 9.6 - - + -
390A ILE* 4.8 4.7 - - + -
393A MET* 3.7 24.9 - - - -
404A ILE* 3.8 15.0 - - + -
405A THR 3.7 0.8 + - - -
406A VAL* 3.6 21.7 - - + -
407A GLY* 2.8 30.1 + - - -
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Residues in contact with GLY 223 (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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206A THR* 3.6 26.5 - - - -
210A MET* 3.8 7.0 - - - -
222A VAL* 1.3 73.9 - - - +
224A MET* 1.3 59.3 + - - -
232A ALA* 3.1 5.5 - - - +
233A CYS* 2.8 39.7 + - - +
407A GLY 3.4 6.1 - - - -
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Residues in contact with MET 224 (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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206A THR 4.7 0.8 + - - -
209A THR* 4.4 0.9 - - - +
222A VAL* 5.1 1.6 - - + -
223A GLY* 1.3 76.1 - - - +
225A ILE* 1.3 70.5 + - - +
226A VAL* 3.6 24.5 - - + -
231A ASN 3.4 11.9 - - - +
232A ALA* 4.4 2.9 - - + -
257A TRP* 3.9 29.8 - - + -
382A CYS* 4.0 7.4 - - - -
386A LEU* 4.0 8.3 - - + -
406A VAL* 4.4 10.3 - - + -
407A GLY 2.8 10.5 + - - +
408A VAL* 3.4 28.3 - - + +
409A ASP 3.1 22.9 + - - -
413A TYR* 4.4 2.7 - - + -
423A PHE* 3.5 40.6 - - + -
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Residues in contact with ILE 225 (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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205A ASP* 3.6 36.3 - - + +
206A THR* 3.7 19.1 - - + +
209A THR* 3.5 26.5 - - - +
224A MET* 1.3 77.2 - - - +
226A VAL* 1.3 67.1 + - - +
227A GLY 3.8 3.4 - - - +
230A CYS* 3.2 7.6 - - - -
231A ASN 2.9 30.4 + - - +
409A ASP* 3.3 26.7 - - + +
410A GLY* 4.7 0.7 - - - -
501A GLC 3.6 18.2 - - - -
503A AGS 3.7 22.7 - - - +
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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
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224A MET* 3.6 29.2 - - + -
225A ILE* 1.3 76.8 - - - +
227A GLY* 1.3 58.3 + - - +
229A GLY 3.8 2.9 - - - +
230A CYS* 4.3 1.8 - - + -
293A ILE* 3.7 28.7 - - + +
382A CYS* 4.0 15.0 - - - -
408A VAL* 4.9 0.2 - - + -
409A ASP 2.9 8.6 + - - +
410A GLY* 3.2 20.9 - - - -
412A VAL* 3.2 24.1 + - + +
413A TYR* 3.2 17.9 + - + -
419A PHE* 3.7 19.7 - - + -
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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