Contacts of the helix formed by residues 1283 - 1290 (chain A) in PDB entry 5JH5
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 ASP1283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1282A THR* 1.3 74.9 - - - +
1284A GLN* 1.3 61.2 + - - +
1285A CYS 3.2 0.4 - - - -
1286A LEU* 3.3 29.9 + - + +
1287A SER* 4.1 1.7 + - - -
1305A GLN 3.8 3.1 + - - -
1306A VAL* 3.3 12.2 - - - +
1307A THR* 2.1 56.5 + - - +
1309A GLU* 4.8 0.7 - - - +
1310A GLY* 3.4 17.1 - - - -
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Residues in contact with GLN1284 (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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1253A ASP* 3.6 16.6 - - + +
1282A THR* 3.0 7.5 + - - +
1283A ASP* 1.3 76.1 - - - +
1285A CYS* 1.3 65.4 + - - +
1287A SER* 3.1 32.7 + - - -
1288A PHE* 3.8 24.5 + - + -
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Residues in contact with CYS1285 (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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1253A ASP* 3.4 19.6 - - - +
1256A ILE* 3.8 22.7 - - + +
1275A LEU* 4.4 1.6 - - - -
1281A VAL* 3.5 17.0 - - + -
1282A THR 3.3 19.7 + - - -
1283A ASP 3.2 0.8 - - - -
1284A GLN* 1.3 78.1 - - - +
1286A LEU* 1.3 66.8 + - - +
1288A PHE* 3.0 25.5 + - - +
1289A PHE* 3.1 32.1 + - - -
1300A LEU* 4.0 15.7 - - - -
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Residues in contact with LEU1286 (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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1283A ASP* 3.4 25.8 - - - +
1284A GLN 3.1 0.8 - - - -
1285A CYS* 1.3 78.8 - - - +
1287A SER* 1.3 61.5 + - - +
1289A PHE* 3.1 21.0 + - + -
1290A LYS* 3.2 11.2 + - - +
1298A ILE* 5.3 0.2 - - + -
1300A LEU* 3.4 31.9 - - + -
1306A VAL* 5.6 0.4 - - + -
1310A GLY* 3.1 38.8 - - - +
1311A CYS* 3.7 10.8 - - - +
1314A PHE* 3.3 25.9 - - + -
1332A LEU* 4.0 18.8 - - + -
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Residues in contact with SER1287 (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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1283A ASP 4.1 1.6 + - - -
1284A GLN* 3.1 33.1 + - - -
1286A LEU* 1.3 80.1 - - - +
1288A PHE* 1.3 66.9 + - - +
1290A LYS* 3.4 29.3 + - - +
1291A ARG* 4.1 6.6 + - - +
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Residues in contact with PHE1288 (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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1253A ASP* 3.4 24.9 - - + -
1254A GLN* 5.2 1.1 - - - -
1256A ILE* 3.8 7.2 - - + -
1257A ASN* 3.4 46.7 - - + -
1260A THR* 3.2 24.4 + - - +
1284A GLN* 4.0 25.8 - - + -
1285A CYS* 3.0 17.6 + - - +
1287A SER* 1.3 81.9 - - - +
1289A PHE* 1.3 61.1 + - - +
1291A ARG* 3.0 51.9 + - - +
1292A CYS 4.2 0.2 + - - -
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Residues in contact with PHE1289 (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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1256A ILE* 3.6 24.2 - - + -
1260A THR* 4.2 12.8 - - + -
1270A LEU* 4.9 4.7 - - + -
1273A ILE* 3.7 41.7 - - + -
1275A LEU* 4.0 9.6 - - + -
1285A CYS* 3.1 36.1 + - - -
1286A LEU* 3.1 15.9 + - + +
1288A PHE* 1.3 71.7 - - - +
1290A LYS* 1.3 62.1 + - - +
1291A ARG 3.0 5.4 - - - -
1292A CYS* 3.0 28.1 + - - +
1295A ILE* 4.3 5.7 - - + +
1298A ILE* 3.6 40.6 - - + -
1314A PHE* 3.6 14.4 - - + -
1318A MSE 4.0 6.6 - - - +
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Residues in contact with LYS1290 (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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1286A LEU 3.2 4.7 + - - +
1287A SER* 3.6 23.1 - - - +
1288A PHE 3.2 1.2 - - - -
1289A PHE* 1.3 74.7 - - - +
1291A ARG* 1.3 60.3 + - - +
1292A CYS 3.3 1.0 + - - +
1314A PHE* 3.3 28.3 - - + +
1317A GLU* 2.3 61.8 + - + +
1318A MSE 3.7 29.8 - - - +
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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