Contacts of the helix formed by residues 1404 - 1414 (chain M) 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 GLU1404 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155 T 5.2 3.2 - - - +
165 T 4.5 0.9 - - - -
326M ARG* 4.8 0.5 + - - -
1386M ARG* 3.7 40.5 - - + +
1390M ASN* 4.9 4.7 + - - +
1402M PHE 3.1 6.4 + - - +
1403M GLU* 1.3 87.5 - - + +
1405M THR* 1.3 71.9 + - - +
1406M VAL 3.1 0.5 + - - -
1407M GLU* 2.8 52.9 + - + +
1408M ILE* 3.8 28.7 - - + +
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Residues in contact with THR1405 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165 T 5.5 0.5 + - - -
329M LEU* 3.9 15.9 - - + +
330M LYS* 4.4 2.6 - - - +
331M GLY* 3.6 22.0 + - - +
336M ILE* 3.7 23.8 - - + -
1400M CYS* 3.1 44.6 + - - +
1402M PHE 5.1 0.9 + - - -
1403M GLU 4.6 4.2 + - - -
1404M GLU* 1.3 76.0 + - - +
1406M VAL* 1.3 58.2 + - - +
1408M ILE* 2.9 9.8 + - - +
1409M LEU* 2.7 37.5 + - + +
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Residues in contact with VAL1406 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326M ARG* 3.8 39.3 - - + +
329M LEU* 3.5 37.7 - - + -
330M LYS* 4.4 6.3 - - + +
1404M GLU 3.1 0.8 + - - -
1405M THR* 1.3 79.2 - - - +
1407M GLU* 1.3 68.4 + - - +
1409M LEU* 2.8 9.9 + - + +
1410M PHE* 2.7 63.7 + - + +
1207N LEU* 6.0 0.2 - - + -
1210N MET* 4.4 4.7 - - + -
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Residues in contact with GLU1407 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155 T 3.4 39.7 + - - +
326M ARG* 3.0 28.9 + - - +
1404M GLU* 2.8 44.7 + - + +
1406M VAL* 1.3 75.5 - - - +
1408M ILE* 1.3 60.3 + - + +
1410M PHE* 3.8 8.8 - - - +
1411M GLU* 3.6 26.1 + - - +
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Residues in contact with ILE1408 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1390M ASN* 3.5 30.3 - - - +
1396M ALA* 4.5 11.4 - - + +
1399M ARG* 3.7 46.4 - - + +
1400M CYS* 4.2 16.8 - - + +
1404M GLU* 3.3 26.0 + - + +
1405M THR 2.9 12.1 + - - +
1406M VAL 2.8 0.2 + - - -
1407M GLU* 1.3 78.8 - - - +
1409M LEU* 1.3 72.4 + - - +
1411M GLU* 3.3 7.7 + - - +
1412M ALA* 3.2 14.7 + - - +
1417M GLU* 4.4 1.6 - - - +
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Residues in contact with LEU1409 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M PHE* 3.9 34.0 - - + -
329M LEU* 4.7 11.0 - - + -
336M ILE* 5.0 2.2 - - + -
1396M ALA* 4.8 4.0 - - + -
1397M LEU* 4.7 5.8 - - + -
1400M CYS* 4.0 30.3 - - + -
1405M THR* 2.7 18.7 + - + +
1406M VAL* 2.8 10.7 + - - +
1408M ILE* 1.3 72.0 - - - +
1410M PHE* 1.3 56.3 + - + +
1412M ALA* 2.6 33.4 + - + +
1413M GLY 3.2 3.5 + - - -
1203N LEU* 4.7 7.0 - - + -
1207N LEU* 3.3 43.7 - - + -
1212N ILE* 3.7 5.8 - - + +
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Residues in contact with PHE1410 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92M HIS* 4.0 23.8 - + - -
94M GLY* 4.0 30.3 - - - +
95M PHE* 3.7 15.6 - + + -
304M MET* 5.2 4.7 - - + -
305M ASP* 5.1 11.7 - - + -
326M ARG* 5.1 4.9 - - + -
1406M VAL* 2.7 40.1 + - + +
1407M GLU* 3.8 8.7 - - - +
1409M LEU* 1.3 74.5 - - + +
1411M GLU* 1.3 61.1 + - + +
1412M ALA 2.9 6.2 + - - -
1413M GLY 3.2 8.7 + - - -
1414M ALA* 3.2 12.1 + - - +
1207N LEU* 5.4 1.3 - - + -
1210N MET* 3.3 42.6 - - + -
1212N ILE* 3.3 23.3 - - + +
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Residues in contact with GLU1411 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95M PHE* 5.6 4.0 - - + -
98M LYS* 4.2 25.7 - - + +
132M LYS* 5.8 5.9 - - - -
1407M GLU 3.6 13.5 + - - +
1408M ILE* 3.3 10.0 + - - +
1409M LEU 3.2 0.8 - - - -
1410M PHE* 1.3 78.1 - - + +
1412M ALA* 1.3 57.9 + - - +
1414M ALA* 4.0 11.2 - - + -
1415M SER* 3.2 25.6 + - - +
1417M GLU* 3.8 4.8 - - - +
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Residues in contact with ALA1412 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M PHE* 3.5 29.8 - - + +
1396M ALA* 4.2 3.6 - - + -
1408M ILE 3.2 7.1 + - - +
1409M LEU* 2.6 28.0 + - - +
1411M GLU* 1.3 71.2 - - - +
1413M GLY* 1.3 59.2 + - - +
1414M ALA 3.1 1.1 - - - -
1415M SER 3.3 1.6 + - - -
1416M ALA 3.0 7.8 + - - -
1417M GLU* 2.9 49.4 + - - +
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Residues in contact with GLY1413 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M PHE* 3.6 16.9 - - - +
20M GLY* 3.1 30.2 - - - -
21M LEU* 2.9 19.4 - - - +
229M SER* 3.3 7.6 - - - -
1409M LEU 3.2 3.0 + - - -
1410M PHE 3.2 5.5 + - - -
1412M ALA* 1.3 80.5 - - - +
1414M ALA* 1.3 60.9 + - - +
1415M SER 3.3 0.2 - - - -
1416M ALA 3.5 1.5 + - - -
1212N ILE* 4.3 5.6 - - - +
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Residues in contact with ALA1414 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M LEU* 3.3 12.3 - - + +
95M PHE* 3.7 23.1 - - + -
98M LYS* 4.7 15.4 + - + +
223M GLY 4.1 1.4 - - - +
224M PHE* 3.9 17.9 - - + -
229M SER* 2.8 16.3 + - - -
234M MET* 5.2 4.0 - - - -
1410M PHE 3.2 14.9 + - - +
1411M GLU* 4.1 9.2 - - + -
1412M ALA 3.1 0.6 - - - -
1413M GLY* 1.3 80.3 - - - +
1415M SER* 1.3 59.9 + - - +
1416M ALA 3.3 1.1 - - - -
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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