Contacts of the helix formed by residues 1359 - 1373 (chain J) in PDB entry 6ASX
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 ALA1359 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1279I GLU* 4.7 6.7 - - - +
1281I TYR 4.8 0.4 - - - +
1282I GLY* 4.6 15.7 - - - -
1283I ALA 5.9 0.9 - - - +
1284I ALA* 4.4 4.0 - - + +
808J VAL* 4.5 1.3 - - + -
912J GLY 3.5 10.5 - - - +
913J GLU* 5.5 0.2 - - - -
914J ALA* 4.4 21.8 - - + +
1347J LEU* 5.3 1.1 - - + -
1357J ILE* 3.1 21.9 + - + +
1358J PRO* 1.3 77.6 - - - +
1360J GLY* 1.3 55.5 + - - +
1361J THR 2.9 8.9 + - - -
1362J GLY 3.0 6.1 + - - -
1363J TYR* 2.8 19.4 + - - -
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Residues in contact with GLY1360 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1282I GLY* 4.4 2.8 - - - -
911J LYS 5.4 1.4 - - - +
912J GLY* 3.0 22.0 + - - -
1359J ALA* 1.3 71.6 - - - +
1361J THR* 1.3 56.6 + - - +
1363J TYR* 3.5 6.2 - - - +
1364J ALA* 3.0 27.9 + - - +
17K PHE* 3.6 34.9 - - - +
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Residues in contact with THR1361 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1282I GLY 3.1 20.1 + - - -
1284I ALA* 4.1 3.8 - - - -
1285I TYR* 3.5 34.6 + - + -
479J GLU* 3.8 14.5 + - - +
483J LEU* 5.2 1.9 - - - +
1359J ALA 2.9 4.8 + - - -
1360J GLY* 1.3 71.7 - - - +
1362J GLY* 1.3 62.8 + - - -
1364J ALA* 3.1 15.2 + - - +
1365J TYR* 3.2 10.4 + - - +
17K PHE* 4.1 13.8 + - - +
20K VAL* 4.9 10.7 - - + +
21K LEU* 3.8 26.9 - - + +
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Residues in contact with GLY1362 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1284I ALA* 3.8 8.3 - - - +
1356J LEU* 4.2 17.0 - - - +
1357J ILE 3.2 20.4 - - - -
1359J ALA 3.0 3.6 + - - -
1361J THR* 1.3 77.5 - - - +
1363J TYR* 1.3 57.2 + - - +
1365J TYR* 3.3 10.6 + - - +
1366J HIS* 2.7 35.2 + - - -
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Residues in contact with TYR1363 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808J VAL* 4.7 6.1 - - + -
809J VAL 4.6 1.1 - - - -
810J THR* 2.4 42.5 + - - -
911J LYS* 4.0 19.0 - - + +
912J GLY* 3.8 17.7 - - - -
1358J PRO* 3.4 35.4 - - + +
1359J ALA* 2.8 13.2 + - - -
1360J GLY* 3.5 10.8 - - - +
1361J THR 3.1 0.4 - - - -
1362J GLY* 1.3 75.6 - - - +
1364J ALA* 1.3 60.0 + - - +
1366J HIS* 3.3 5.5 + - + +
1367J GLN* 2.9 63.9 + - + +
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Residues in contact with ALA1364 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1360J GLY 3.0 12.4 + - - +
1361J THR 3.1 8.7 + - - +
1363J TYR* 1.3 78.3 - - - +
1365J TYR* 1.3 61.1 + - - +
1367J GLN* 3.3 15.5 + - - +
1368J ASP* 3.1 21.5 + - - +
18K ASP* 5.0 8.7 - - - +
21K LEU* 3.9 21.3 - - + -
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Residues in contact with TYR1365 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1285I TYR* 5.5 5.8 - - - +
1356J LEU* 3.8 27.8 - - + -
1361J THR 3.2 5.6 + - - +
1362J GLY* 3.4 14.8 - - - +
1363J TYR 3.2 0.2 - - - -
1364J ALA* 1.3 80.3 - - - +
1366J HIS* 1.3 76.5 + + - +
1368J ASP* 3.2 16.4 + - + +
1369J ARG* 2.9 40.1 + - + +
21K LEU* 5.6 0.6 - - - +
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Residues in contact with HIS1366 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1345J ARG* 5.9 7.0 - - + -
1350J ASN* 4.5 10.0 + - - -
1355J ARG* 4.8 8.4 - - - -
1356J LEU* 3.1 39.4 + - + -
1357J ILE 4.2 3.8 - - - -
1358J PRO* 4.1 16.0 - - + +
1362J GLY 2.7 32.8 + - - +
1363J TYR* 3.3 10.5 + - + +
1364J ALA 3.3 0.2 - - - -
1365J TYR* 1.3 80.5 - + - +
1367J GLN* 1.3 62.0 + - - +
1369J ARG* 3.7 32.0 + - - +
1370J MET* 2.9 35.5 + - + +
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Residues in contact with GLN1367 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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911J LYS* 3.7 21.6 + - - +
1363J TYR* 2.9 53.7 + - + +
1364J ALA* 3.3 14.8 + - - +
1366J HIS* 1.3 75.8 - - - +
1368J ASP* 1.3 62.0 + - - +
1370J MET* 3.3 5.0 + - - +
1371J ARG* 3.0 26.3 + - - +
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Residues in contact with ASP1368 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1364J ALA 3.1 12.0 + - - +
1365J TYR* 3.3 19.5 - - + +
1366J HIS 3.2 0.2 - - - -
1367J GLN* 1.3 77.7 - - - +
1369J ARG* 1.3 56.5 + - - +
1371J ARG* 2.6 50.1 + - - +
1372J ARG* 2.9 42.6 + - - +
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Residues in contact with ARG1369 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J GLU 6.0 0.8 - - - +
17J PHE 4.1 11.7 + - - -
18J ASP* 4.2 17.8 - - - +
1344J LEU* 5.6 1.6 - - - +
1355J ARG* 3.5 28.7 - - - +
1365J TYR* 2.9 33.5 + - + +
1366J HIS* 3.3 30.0 + - + +
1367J GLN 3.3 0.2 - - - -
1368J ASP* 1.3 77.4 - - - +
1370J MET* 1.3 67.7 + - - +
1372J ARG* 3.2 10.9 + - + +
1373J ARG* 3.0 43.3 + - + +
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Residues in contact with MET1370 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1345J ARG* 5.0 21.1 - - + +
1366J HIS* 2.9 22.3 + - + +
1367J GLN* 3.9 5.6 - - - +
1369J ARG* 1.3 84.5 - - - +
1371J ARG* 1.3 61.2 + - - +
1373J ARG* 3.3 47.9 - - - -
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Residues in contact with ARG1371 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1367J GLN 3.0 21.5 + - - +
1368J ASP* 2.6 39.4 + - - +
1370J MET* 1.3 73.7 - - - +
1372J ARG* 1.3 71.9 + - - +
1373J ARG 4.6 1.5 - - - -
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Residues in contact with ARG1372 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1368J ASP* 2.9 33.1 + - - +
1369J ARG* 3.2 15.7 + - + +
1371J ARG* 1.3 87.5 - - - +
1373J ARG* 1.3 61.4 + - + +
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Residues in contact with ARG1373 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J ASP* 4.8 13.7 + - - +
1369J ARG* 3.0 37.0 + - + +
1370J MET* 3.3 41.7 - - - +
1371J ARG 4.6 1.3 - - - -
1372J ARG* 1.3 81.3 - - + +
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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