Contacts of the strand formed by residues 1212 - 1217 (chain N) in PDB entry 2JA7
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 ILE1212 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19M PHE* 5.0 9.4 - - + -
20M GLY 3.9 4.0 - - - +
21M LEU* 3.9 18.6 - - + -
92M HIS* 5.0 0.2 - - + -
95M PHE* 4.6 4.3 - - + -
1409M LEU* 3.7 10.3 - - + +
1410M PHE* 3.3 57.0 - - + +
1413M GLY* 4.3 3.4 - - - +
1207N LEU* 3.0 34.7 + - + +
1208N MET* 3.2 21.9 + - - -
1210N MET* 3.2 6.9 - - + +
1211N ASN* 1.3 78.5 - - - +
1213N THR* 1.3 69.1 + - - +
1214N PRO* 3.2 6.5 - - - +
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Residues in contact with THR1213 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18M GLN 3.1 4.7 - - - +
19M PHE* 3.1 5.2 - - - -
20M GLY* 2.6 65.3 + - - -
21M LEU 3.2 2.0 + - - -
22M PHE* 3.4 58.8 - - + +
1168N LEU* 4.7 3.4 - - + -
1212N ILE* 1.3 72.3 - - - +
1214N PRO* 1.3 62.4 - - - +
1215N ARG* 3.8 27.9 + - - +
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Residues in contact with PRO1214 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M VAL* 4.6 3.4 - - + -
18M GLN 3.7 1.3 - - - +
19M PHE* 3.9 22.9 - - + -
1167N GLY 3.1 12.4 - - - +
1168N LEU* 4.3 7.0 - - + +
1204N PHE* 4.0 46.2 - - + +
1207N LEU* 4.9 5.6 - - + -
1208N MET* 3.9 15.7 - - + -
1212N ILE* 3.2 12.1 - - + +
1213N THR* 1.3 82.8 - - - +
1215N ARG* 1.3 64.3 + - - +
1216N LEU* 3.5 7.8 + - + +
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Residues in contact with ARG1215 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M GLU 3.2 1.4 - - - +
17M VAL* 3.0 14.6 - - - -
18M GLN* 2.6 69.7 + - + +
19M PHE 5.4 0.2 - - - -
20M GLY* 5.3 1.0 - - - +
21M LEU 5.3 3.4 + - - -
26M GLU* 3.2 30.3 + - - -
227M VAL 5.7 0.2 + - - -
228M PHE* 4.8 16.7 - - + +
1166N CYS* 3.4 29.9 - - - +
1167N GLY* 3.2 19.7 - - - +
1168N LEU* 3.6 12.2 - - - +
1213N THR* 3.9 27.7 + - - +
1214N PRO* 1.3 72.4 - - - +
1216N LEU* 1.3 63.0 + - - +
1217N TYR* 3.7 20.1 + - + +
15P LEU* 3.7 21.4 - - - +
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Residues in contact with LEU1216 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14M VAL* 3.3 30.5 - - + -
16M GLU 4.1 2.0 - - - -
17M VAL* 4.9 10.8 - - + -
1430M LEU* 4.7 2.7 - - + -
1162N ILE* 3.8 27.4 - - + +
1163N CYS 4.6 1.7 - - - +
1164N GLY* 6.0 0.2 - - - -
1167N GLY* 2.9 23.9 + - - +
1168N LEU* 5.9 1.3 - - - -
1169N MET* 6.1 7.2 - - + -
1194N ILE* 3.5 18.8 - - + -
1196N ILE* 5.1 2.2 - - + -
1204N PHE* 4.2 37.2 - - + -
1214N PRO* 3.7 13.2 - - + +
1215N ARG* 1.3 79.6 - - - +
1217N TYR* 1.3 67.7 + - - +
1218N THR* 4.1 1.0 + - - +
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Residues in contact with TYR1217 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14M VAL* 3.8 2.3 - - - -
15M LYS 2.9 24.8 + - - -
16M GLU* 3.2 41.4 + - + +
18M GLN* 5.3 11.9 - - + -
228M PHE* 5.0 9.1 - + - -
1163N CYS 5.3 0.7 - - - -
1164N GLY 4.9 8.3 - - - -
1165N ILE 2.4 26.9 + - - -
1166N CYS* 4.0 1.6 - - - -
1167N GLY* 3.2 26.9 + - - -
1215N ARG* 3.7 23.2 - - + +
1216N LEU* 1.3 81.5 - - - +
1218N THR* 1.3 60.4 + - - +
1219N ASP* 3.3 16.3 + - - +
1221N SER* 5.8 1.3 - - - -
13P ARG* 4.7 16.2 - - - -
14P ARG* 5.9 1.8 - - - -
15P LEU* 4.5 10.7 + - - +
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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