Contacts of the helix formed by residues 227 - 237 (chain A) in PDB entry 2A79
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 VAL 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A GLU* 2.7 40.2 + - - +
226A GLU* 1.3 79.8 - - - +
228A GLN* 1.3 65.1 + - + +
230A PRO* 3.1 14.9 - - - +
231A GLU* 4.3 6.4 + - - +
359A PRO* 3.7 26.5 - - + +
360A TYR 4.2 9.2 - - - +
361A SER* 3.9 35.3 + - - +
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Residues in contact with GLN 228 (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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191A SER* 5.5 2.1 - - - -
192A SER* 3.4 36.0 + - - +
223A GLU* 2.7 32.3 + - - +
224A LYS* 3.2 31.2 + - + +
227A VAL* 1.3 79.0 - - + +
229A LEU* 1.3 67.7 + - + +
231A GLU* 3.3 20.8 + - - +
232A LEU* 3.7 4.0 + - - +
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Residues in contact with LEU 229 (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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192A SER* 4.8 4.3 - - - +
195A ILE* 4.6 2.9 - - + -
213A GLU* 3.9 31.0 - - + -
215A ALA* 4.1 15.5 - - + -
224A LYS* 3.0 28.3 + - + +
225A VAL* 4.1 14.4 - - + +
228A GLN* 1.3 72.3 - - - +
230A PRO* 1.3 73.2 - - + +
232A LEU* 3.0 25.0 + - + +
233A PHE* 2.8 22.3 + - - +
238A VAL* 4.6 4.0 - - + +
239A GLY 5.8 0.7 - - - -
240A ALA* 3.7 30.5 - - + -
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Residues in contact with PRO 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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225A VAL 3.4 21.3 - - - +
226A GLU* 3.6 13.5 - - - +
227A VAL 3.1 19.5 - - - +
229A LEU* 1.3 90.0 - - + +
231A GLU* 1.3 59.4 + - - +
233A PHE* 3.3 8.3 + - + +
234A HIS* 2.9 41.9 + - + +
316A GLY* 5.8 10.8 - - - -
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Residues in contact with GLU 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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192A SER* 6.1 1.0 - - - -
227A VAL 4.3 4.0 + - - +
228A GLN* 3.3 13.1 + - - +
229A LEU 3.0 0.4 - - - -
230A PRO* 1.3 79.9 - - - +
232A LEU* 1.3 63.5 + - + +
234A HIS* 3.2 2.8 + - - -
235A LYS* 2.8 51.8 + - + +
62B PRO* 5.1 13.6 - - + +
66B MET* 3.5 26.0 - - + +
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Residues in contact with LEU 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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192A SER* 3.8 35.9 - - - +
195A ILE* 3.8 37.5 - - + -
196A MET* 4.2 15.7 - - + -
228A GLN 3.7 3.6 + - - +
229A LEU* 3.0 16.9 + - + +
231A GLU* 1.3 82.8 - - + +
233A PHE* 1.3 58.4 + - - +
235A LYS* 4.5 5.4 - - + -
236A ILE* 2.9 50.7 + - + +
237A GLY 3.1 5.5 + - - -
238A VAL* 3.4 12.6 + - + +
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Residues in contact with PHE 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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43A GLY* 3.8 27.8 - - - -
44A LYS* 3.4 28.1 - - + -
229A LEU 2.8 11.5 + - - +
230A PRO* 3.5 11.7 - - + +
231A GLU 3.1 0.2 - - - -
232A LEU* 1.3 79.5 - - - +
234A HIS* 1.3 89.2 + + - +
237A GLY* 2.8 27.1 + - - -
238A VAL 3.2 28.7 + - - +
239A GLY* 4.2 6.3 - - - -
315A GLU 5.6 6.3 - - - -
316A GLY* 5.1 16.4 - - - +
318A SER* 5.6 1.8 - - - -
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Residues in contact with HIS 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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44A LYS* 3.2 19.6 + - - +
230A PRO* 2.9 34.7 + - + +
231A GLU* 3.9 3.1 - - - +
233A PHE* 1.3 101.7 - + - +
235A LYS* 1.3 61.7 + - - +
66B MET* 4.2 19.0 - - + +
71B PRO* 5.5 0.5 - - - +
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Residues in contact with LYS 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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44A LYS* 5.0 0.5 + - - -
196A MET* 3.7 30.1 - - + +
231A GLU* 2.8 38.3 + - - +
232A LEU* 4.4 4.7 - - + +
234A HIS* 1.3 78.5 - - - +
236A ILE* 1.3 63.2 + - + +
33B GLU* 5.4 2.6 + - - -
65B ARG* 5.8 2.2 - - - +
66B MET* 3.8 20.1 - - + -
69B PHE* 3.5 41.7 - - + -
71B PRO* 3.4 24.1 - - - +
76B TYR* 3.2 28.3 + - - -
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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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195A ILE* 4.4 6.7 - - + -
196A MET* 4.1 9.4 - - + -
199A TYR* 3.7 64.5 - - + -
210A PRO 5.4 0.5 - - - +
232A LEU* 2.9 40.3 + - + +
235A LYS* 1.3 84.3 - - + +
237A GLY* 1.3 57.5 + - - +
238A VAL* 3.1 30.1 + - + +
69B PHE* 4.0 9.6 - - + -
71B PRO* 4.9 7.2 - - + -
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Residues in contact with GLY 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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43A GLY* 3.4 1.4 - - - -
44A LYS* 2.9 53.6 + - - +
45A SER 4.8 0.2 + - - -
211A ILE* 4.2 2.5 - - - +
233A PHE* 2.8 22.4 + - - -
235A LYS 3.6 1.6 + - - -
236A ILE* 1.3 75.0 - - - +
238A VAL* 1.3 62.6 + - - +
239A GLY 3.3 0.9 + - - -
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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