Contacts of the helix formed by residues 225 - 240 (chain A) in PDB entry 3GBA
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 PRO 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A GLY 3.3 6.5 - - - +
224A SER* 1.3 86.9 - - - +
226A TYR* 1.3 75.0 + - + +
227A ARG 3.2 0.6 + - - -
228A ASP* 3.9 5.9 + - - +
229A LYS* 3.6 35.6 + - - +
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Residues in contact with TYR 226 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ALA 5.0 7.3 + - - -
4A ARG* 6.1 1.1 - - - -
6A LEU* 3.9 41.2 - - + +
47A LEU* 5.2 7.6 - - + -
49A PHE* 4.5 21.2 - + + +
83A ASP* 5.7 5.4 - - + -
84A LEU* 4.0 22.7 - - + -
220A THR* 4.6 0.7 - - + -
224A SER* 3.1 16.6 + - - +
225A PRO* 1.3 87.9 - - + +
227A ARG* 1.3 64.7 + - - +
229A LYS* 3.3 24.2 + - + +
230A ILE* 2.8 31.5 + - + +
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Residues in contact with ARG 227 (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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100A ASP* 3.7 33.2 + - + +
101A PHE* 3.0 51.1 + - - +
102A SER* 3.8 6.3 - - - +
220A THR* 3.7 22.5 - - + +
224A SER* 3.3 15.1 + - - +
225A PRO 3.2 1.4 - - - -
226A TYR* 1.3 78.6 - - - +
228A ASP* 1.3 78.3 + - - +
230A ILE* 3.3 4.0 + - - +
231A THR* 3.0 32.7 + - - -
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Residues in contact with ASP 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A SER 4.8 1.3 + - - -
225A PRO 3.9 6.9 + - - +
226A TYR 3.4 0.4 - - - -
227A ARG* 1.3 103.9 + - - +
229A LYS* 1.3 61.4 + - + +
231A THR* 3.3 7.8 + - - -
232A ILE* 3.1 32.4 + - + +
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Residues in contact with LYS 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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47A LEU* 3.8 30.5 - - + +
225A PRO* 3.6 28.6 + - - +
226A TYR* 3.3 28.8 + - + +
228A ASP* 1.3 77.3 - - + +
230A ILE* 1.3 57.6 + - - +
232A ILE* 3.4 13.1 + - + +
233A ALA* 3.1 26.3 + - - +
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Residues in contact with ILE 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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43A LEU* 4.1 16.6 - - + -
47A LEU* 3.7 23.1 - - + -
49A PHE* 5.5 1.6 - - + -
84A LEU* 3.6 38.1 - - + -
102A SER* 3.8 17.9 - - - -
218A VAL* 3.9 24.5 - - + -
220A THR* 4.8 2.2 - - + -
226A TYR* 2.8 26.0 + - + +
227A ARG* 3.7 3.6 - - - +
229A LYS* 1.3 75.0 - - - +
231A THR* 1.3 59.5 + - - +
233A ALA* 3.2 2.4 + - - +
234A ILE* 2.8 41.2 + - + +
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Residues in contact with THR 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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102A SER* 3.4 10.5 - - - -
103A LYS* 2.9 51.3 + - + +
227A ARG* 3.0 14.8 + - - -
228A ASP* 3.5 13.0 - - - +
230A ILE* 1.3 77.6 - - - +
232A ILE* 1.3 66.2 + - + +
234A ILE* 3.3 6.4 + - - +
235A LEU* 3.1 23.0 + - + +
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Residues in contact with ILE 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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47A LEU* 6.5 0.2 - - + -
228A ASP* 3.1 21.9 + - + +
229A LYS* 3.6 12.3 - - + +
231A THR* 1.3 79.1 - - + +
233A ALA* 1.3 62.5 + - - +
235A LEU* 3.3 10.3 + - - +
236A GLN* 3.1 22.8 + - + +
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Residues in contact with ALA 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 LEU* 3.7 19.7 - - + -
46A ILE* 4.0 30.0 - - + +
47A LEU* 4.3 6.1 - - + -
229A LYS 3.1 16.5 + - - +
230A ILE* 3.2 5.6 + - - +
232A ILE* 1.3 76.0 - - - +
234A ILE* 1.3 59.5 + - - +
236A GLN* 3.2 8.8 + - - +
237A LEU* 2.9 33.8 + - - +
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Residues in contact with ILE 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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39A LEU* 5.0 7.4 - - + -
43A LEU* 4.5 8.1 - - + -
102A SER* 3.3 28.0 - - - +
103A LYS* 3.5 13.0 - - + +
104A PRO 3.9 18.8 - - - +
105A PHE* 4.2 28.9 - - + -
218A VAL* 4.6 2.7 - - + -
230A ILE* 2.8 31.3 + - + +
231A THR* 3.6 6.3 - - - +
233A ALA* 1.3 74.7 - - - +
235A LEU* 1.3 58.8 + - - +
237A LEU* 3.2 8.5 + - + +
238A GLN* 2.9 28.8 + - + +
243A LEU* 4.0 8.4 - - + +
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Residues in contact with LEU 235 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A THR* 3.1 13.3 + - + +
232A ILE* 3.5 12.1 - - + +
233A ALA 3.3 0.2 - - - -
234A ILE* 1.3 78.5 - - - +
236A GLN* 1.3 62.1 + - - +
238A GLN* 3.3 12.8 + - + -
239A GLU* 3.0 30.3 + - + +
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Residues in contact with GLN 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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46A ILE* 3.7 38.5 - - - +
232A ILE* 3.1 14.7 + - + +
233A ALA* 3.2 8.6 + - - +
235A LEU* 1.3 76.6 - - - +
237A LEU* 1.3 63.0 + - - +
239A GLU* 3.2 11.2 + - - +
240A GLU* 2.9 52.9 + - + +
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Residues in contact with LEU 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 LEU* 3.9 27.8 - - + -
42A GLU* 3.8 28.3 - - + +
43A LEU* 4.2 13.5 - - + -
46A ILE* 3.9 16.6 - - + -
233A ALA 2.9 20.1 + - - +
234A ILE* 3.6 5.8 - - - +
236A GLN* 1.3 75.9 - - - +
238A GLN* 1.3 62.2 + - - +
240A GLU* 3.5 7.3 + - - +
241A GLY 3.3 2.4 + - - -
242A LYS* 2.9 61.0 + - + +
243A LEU* 3.5 18.1 + - + -
246A MET* 5.5 0.9 - - - -
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Residues in contact with GLN 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 ILE* 2.9 17.2 + - + +
235A LEU* 3.6 14.8 - - + +
236A GLN 3.2 0.2 - - - -
237A LEU* 1.3 76.3 - - - +
239A GLU* 1.3 65.4 + - - +
241A GLY* 3.0 15.1 + - - -
243A LEU* 3.5 31.7 - - + +
244A HIS* 5.3 4.2 + - - +
259A SO4 4.9 9.8 + - - -
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Residues in contact with GLU 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 LEU* 3.0 25.6 + - + +
236A GLN* 3.2 9.2 + - - +
238A GLN* 1.3 77.2 - - - +
240A GLU* 1.3 59.6 + - + +
241A GLY 3.4 0.5 + - - -
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Residues in contact with GLU 240 (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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46A ILE* 5.1 0.2 - - - +
236A GLN* 2.9 48.4 + - + +
237A LEU* 3.9 12.4 - - - +
238A GLN 3.2 0.2 - - - -
239A GLU* 1.3 78.0 - - + +
241A GLY* 1.3 58.9 + - - +
242A LYS* 3.7 39.4 + - + +
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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