Contacts of the strand formed by residues 229 - 234 (chain A) in PDB entry 2VZE
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 LYS 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A MET* 5.5 3.1 - - - -
219A TYR 3.6 0.7 - - - +
220A PHE* 3.2 5.2 - - - -
221A THR* 2.8 37.1 + - - +
222A SER 6.2 0.2 - - - -
223A GLY* 3.8 25.7 - - - -
224A THR* 4.8 4.0 - - - +
225A SER 5.0 5.6 + - - -
227A LEU 4.2 6.9 + - - +
228A PRO* 1.3 74.6 - - - +
230A MET* 1.3 63.7 + - - +
231A ALA 3.6 0.7 + - - -
426A TYR* 3.8 48.4 + - + -
429A ASN* 5.7 2.9 - - - +
432A LYS* 3.5 42.4 - - + +
436A ASN* 6.1 0.8 - - - +
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Residues in contact with MET 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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108A ARG* 4.9 0.4 - - - -
151A MET* 3.5 46.4 - - + +
152A SER* 3.9 17.9 - - - -
218A ILE* 3.5 22.0 - - + -
219A TYR 4.0 1.3 - - - -
220A PHE* 3.4 31.6 - - + +
229A LYS* 1.3 72.0 - - - +
231A ALA* 1.3 61.6 + - - +
232A GLU 3.6 0.6 + - - -
426A TYR* 3.2 8.5 - - - +
427A VAL* 2.9 66.8 + - + +
428A ASP* 3.9 11.2 - - + +
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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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217A ALA 4.4 0.2 - - - -
218A ILE* 3.3 3.2 - - - +
219A TYR* 2.8 45.5 + - - +
221A THR* 4.1 13.2 - - + -
229A LYS 3.6 1.0 + - - -
230A MET* 1.3 69.1 - - - +
232A GLU* 1.3 62.7 + - - +
233A HIS* 3.9 4.9 + - + -
364A THR* 4.0 21.8 - - + +
365A GLU* 4.5 3.4 - - + -
423A PHE* 3.8 24.2 - - + -
426A TYR* 4.2 1.8 - - + -
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Residues in contact with GLU 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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108A ARG* 5.3 3.5 + - - -
213A GLN 4.8 2.3 - - - +
215A ALA* 3.5 35.2 + - + +
217A ALA 3.4 11.0 - - - +
218A ILE* 4.4 5.9 - - + +
230A MET 3.6 1.2 + - - -
231A ALA* 1.3 71.3 - - - +
233A HIS* 1.3 60.7 + - - +
423A PHE* 3.1 6.6 - - - +
424A SER* 2.7 51.3 + - - -
425A GLY 3.2 19.6 + - - +
427A VAL* 3.6 24.5 - - + +
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Residues in contact with HIS 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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215A ALA* 3.7 2.4 - - - -
216A SER 2.8 29.1 + - - -
217A ALA* 2.9 18.8 + - + +
219A TYR* 4.8 6.3 - + - -
231A ALA* 3.9 7.8 + - + -
232A GLU* 1.3 76.0 - - - +
234A SER* 1.3 53.4 + - - +
237A SER* 2.7 21.7 + - - +
238A LEU* 3.7 32.5 - - + +
266A ILE* 3.5 19.0 - - + +
364A THR* 2.6 31.5 + - + -
365A GLU 3.9 2.7 - - - -
366A THR 4.7 0.4 - - - -
367A GLY* 4.7 3.6 - - - -
421A GLY 3.8 20.2 - - - -
423A PHE* 3.6 22.9 - - + +
424A SER* 4.5 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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38A GLN* 5.5 0.2 + - - -
212A SER 2.9 19.0 + - - -
213A GLN* 3.7 17.0 + - - -
214A GLU 3.2 13.7 - - - -
216A SER* 3.8 6.1 - - - -
233A HIS* 1.3 73.8 - - - +
235A TYR* 1.3 65.4 + - - +
236A SER* 3.2 3.6 + - - -
237A SER* 2.8 32.3 + - - -
238A LEU* 3.3 21.5 + - - +
424A SER* 4.1 10.8 + - - -
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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