Contacts of the helix formed by residues 228 - 239 (chain A) in PDB entry 1V72
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 LEU 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A ALA* 3.8 34.1 - - + +
79A MET* 4.2 20.4 - - + -
204A ASP* 5.9 1.1 - - + +
205A ALA* 5.9 1.6 - - + -
223A LEU* 4.0 18.2 - - + -
225A ASN* 3.7 35.2 - - + +
226A THR 2.9 1.4 - - - -
227A SER* 1.3 87.4 - - - +
229A ALA* 1.3 63.9 + - - +
230A THR 3.4 1.8 - - - -
231A GLU* 3.3 19.7 + - - +
232A MET* 2.9 22.4 + - + +
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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
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61A GLU* 3.7 29.6 - - + +
63A PHE* 3.6 16.3 - - + -
223A LEU* 3.9 4.3 - - - +
226A THR 3.0 17.1 + - - +
227A SER 3.3 0.8 - - - -
228A LEU* 1.3 76.6 - - - +
230A THR* 1.3 67.0 + - - +
232A MET* 3.0 4.9 + - - +
233A SER* 3.0 24.0 + - - -
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Residues in contact with THR 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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227A SER 4.8 4.3 + - - -
228A LEU 3.4 0.4 - - - -
229A ALA* 1.3 77.9 - - - +
231A GLU* 1.3 64.9 + - - +
233A SER* 3.1 19.0 + - - -
234A TYR* 3.4 34.1 + - + +
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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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77A SER 3.9 0.2 - - - +
78A ALA* 3.3 27.9 - - + +
227A SER 5.5 0.4 + - - +
228A LEU* 3.3 21.4 + - - +
229A ALA 3.3 0.4 - - - -
230A THR* 1.3 80.6 - - - +
232A MET* 1.3 58.5 + - - +
234A TYR* 3.3 8.9 + - - +
235A ARG* 2.6 70.8 + - + +
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Residues in contact with MET 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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63A PHE* 3.7 37.0 - - + -
74A LEU* 3.5 49.8 - - - +
75A CYS* 4.0 8.3 - - - +
78A ALA* 3.8 18.6 - - + -
221A ILE* 4.2 8.3 - - + -
223A LEU* 4.1 21.3 - - + -
228A LEU* 2.9 13.6 + - + +
229A ALA 3.0 9.2 + - - +
231A GLU* 1.3 75.1 - - - +
233A SER* 1.3 59.6 + - - +
235A ARG* 4.3 4.9 - - - -
236A ARG* 2.8 30.8 + - + +
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Residues in contact with SER 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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63A PHE* 3.6 18.0 - - - -
229A ALA 3.0 13.2 + - - -
230A THR* 3.1 12.0 + - - -
232A MET* 1.3 76.3 - - - +
234A TYR* 1.3 69.9 + - - +
236A ARG* 3.3 10.6 + - - +
237A LYS* 3.0 23.4 + - - +
242A LEU* 5.8 0.7 - - - +
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Residues in contact with TYR 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 THR* 3.4 37.5 + - + +
231A GLU* 3.3 8.8 + - - +
233A SER* 1.3 83.9 - - - +
235A ARG* 1.3 58.7 + - + +
237A LYS* 3.2 6.9 + - + +
238A ARG* 2.7 35.9 + - + +
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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
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74A LEU* 3.6 14.6 - - + +
77A SER* 3.2 34.1 + - - -
78A ALA* 4.2 8.5 - - - +
80A THR 5.2 1.6 + - - -
105A PHE 3.5 23.0 + - - -
106A SER* 5.1 0.8 - - - +
107A ASN* 4.2 11.1 + - - -
231A GLU* 2.6 55.2 + - + +
232A MET* 3.8 7.2 - - - +
233A SER 3.3 0.2 - - - -
234A TYR* 1.3 77.2 - - + +
236A ARG* 1.3 62.9 + - - +
238A ARG* 3.9 9.3 - - - +
239A ALA* 3.0 26.5 + - - +
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Residues in contact with ARG 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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39A TYR 5.1 3.2 + - - -
49A LYS* 6.0 2.0 - - - +
62A VAL 5.4 0.6 + - - -
63A PHE* 3.6 29.7 - - + +
64A LEU 3.1 33.3 + - - +
65A VAL* 3.7 16.6 - - + -
74A LEU* 3.8 16.1 - - + +
232A MET* 2.8 21.3 + - + +
233A SER* 3.7 9.3 + - - +
235A ARG* 1.3 78.7 - - - +
237A LYS* 1.3 60.1 + - - +
239A ALA 3.3 2.8 + - - -
241A HIS* 2.9 59.5 + - + +
242A LEU* 3.4 28.0 - - - +
246A MET* 3.6 14.3 - - - +
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Residues in contact with LYS 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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39A TYR* 4.2 26.1 + - - -
233A SER 3.0 16.8 + - - +
234A TYR* 3.7 7.4 - - + +
236A ARG* 1.3 77.6 - - - +
238A ARG* 1.3 59.1 + - - +
240A GLY* 2.9 21.9 + - - -
242A LEU* 3.8 35.1 + - + +
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Residues in contact with ARG 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 TYR* 2.7 23.2 + - + +
235A ARG* 3.9 8.7 - - - +
237A LYS* 1.3 75.6 - - - +
239A ALA* 1.3 57.0 + - - +
240A GLY 3.2 2.5 + - - -
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Residues in contact with ALA 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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74A LEU* 4.4 1.1 - - + -
104A PHE* 6.2 2.7 - - + -
105A PHE* 3.4 35.5 - - + -
235A ARG 3.0 18.9 + - - +
236A ARG 3.9 2.0 - - - +
237A LYS 3.1 0.4 - - - -
238A ARG* 1.3 76.4 - - - +
240A GLY* 1.3 62.3 + - - +
241A HIS* 3.2 19.5 + - + -
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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