Contacts of the helix formed by residues 1266 - 1276 (chain A) in PDB entry 2NZ6
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 ASP1266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0A MET* 3.7 22.3 - - - +
1019A LYS 3.0 30.4 + - - +
1020A LEU* 3.8 13.7 - - + +
1255A LEU* 4.0 1.6 - - - +
1258A GLN* 3.7 15.6 + - - +
1265A VAL* 1.3 76.4 - - - +
1267A VAL* 1.3 60.8 + - - +
1268A TYR 3.9 0.7 + - - -
1269A GLY* 2.7 35.0 + - - -
1270A ILE* 3.0 34.9 + - + +
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Residues in contact with VAL1267 (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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1019A LYS 4.9 0.4 + - - -
1026A PHE* 5.2 0.4 - - + -
1044A GLU* 5.7 0.4 - - - +
1251A ALA* 6.0 0.2 - - + -
1255A LEU* 3.8 29.6 - - + -
1265A VAL* 3.9 12.1 - - + -
1266A ASP* 1.3 68.2 - - - +
1268A TYR* 1.3 66.8 + - - +
1270A ILE* 3.4 3.7 + - - +
1271A VAL* 3.0 30.2 + - + +
1288A TYR* 3.8 23.8 - - + +
1291A LEU* 4.1 26.7 - - + +
1292A ASN* 3.7 33.7 - - - +
1295A VAL* 4.4 4.7 - - + -
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Residues in contact with TYR1268 (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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-6A ASN* 5.6 0.2 + - - -
-2A GLN* 3.7 28.0 + - + +
-1A SER 4.2 0.7 - - - -
0A MET 4.1 21.5 - - - -
1019A LYS* 4.0 23.1 + - + +
1044A GLU* 3.2 41.5 + - + +
1047A ASP* 3.7 28.9 + - + +
1048A LEU* 3.5 20.3 - - + +
1266A ASP* 3.3 0.8 - - - +
1267A VAL* 1.3 79.7 - - - +
1269A GLY* 1.3 58.5 + - - +
1271A VAL* 3.4 0.7 + - - -
1272A TYR* 2.9 44.5 + + - +
1288A TYR* 3.4 24.7 + - - +
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Residues in contact with GLY1269 (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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-1A SER 3.4 23.7 - - - +
0A MET* 4.2 0.7 - - - -
1254A ARG* 5.3 0.2 + - - -
1266A ASP* 2.7 31.1 + - - -
1268A TYR* 1.3 72.8 - - - +
1270A ILE* 1.3 60.9 + - - +
1272A TYR* 3.6 2.5 - - - +
1273A ASP* 3.1 26.5 + - - +
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Residues in contact with ILE1270 (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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1251A ALA* 4.0 24.9 - - + -
1254A ARG* 3.7 52.2 + - + +
1255A LEU* 3.9 27.1 - - + +
1258A GLN* 3.6 21.8 - - - +
1266A ASP* 3.0 22.8 + - + +
1267A VAL* 3.9 4.3 - - - +
1269A GLY* 1.3 73.7 - - - +
1271A VAL* 1.3 61.4 + - - +
1273A ASP* 3.4 7.7 + - - +
1274A LEU* 3.0 29.8 + - + +
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Residues in contact with VAL1271 (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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1045A TYR* 5.4 0.7 - - + -
1048A LEU* 3.8 20.9 - - + -
1251A ALA* 4.8 4.7 - - + -
1267A VAL* 3.0 22.1 + - + +
1268A TYR 4.0 2.2 - - - +
1270A ILE* 1.3 73.8 - - + +
1272A TYR* 1.3 65.5 + - - +
1274A LEU* 3.2 7.9 + - - +
1275A ARG* 2.9 33.4 + - + +
1281A MET 3.6 23.3 - - - +
1282A VAL* 3.9 23.3 - - + -
1288A TYR* 4.1 17.3 - - + -
1291A LEU* 4.3 11.0 - - + -
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Residues in contact with TYR1272 (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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-9A GLY 4.3 2.4 + - - -
-6A ASN* 2.6 30.8 + - - +
-5A LEU* 3.4 29.9 + - + +
-2A GLN 3.6 6.1 - - - -
-1A SER* 3.4 43.3 - - - +
1048A LEU* 3.6 17.3 - - + +
1051A VAL* 3.6 34.7 - - + +
1268A TYR* 2.9 25.0 + + - +
1269A GLY 3.6 6.3 - - - +
1271A VAL* 1.3 76.2 - - - +
1273A ASP* 1.3 64.6 + - - +
1275A ARG* 3.2 4.3 + - - +
1276A MET* 3.1 36.5 + - + +
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Residues in contact with ASP1273 (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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1101A PRO* 3.5 11.3 - - - +
1106A LYS* 4.6 3.1 + - - -
1254A ARG* 3.0 33.5 + - - +
1269A GLY 3.1 15.4 + - - +
1270A ILE 3.5 5.6 - - - +
1272A TYR* 1.3 80.3 - - + +
1274A LEU* 1.3 60.0 + - - +
1276A MET* 3.3 9.7 + - - +
1277A HIS* 2.6 54.0 + - - -
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Residues in contact with LEU1274 (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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1100A MET* 3.2 27.8 - - + +
1101A PRO* 4.2 6.1 - - + +
1247A GLY* 3.5 35.0 - - - +
1250A ILE* 3.9 22.0 - - + -
1251A ALA* 4.3 13.2 - - + +
1254A ARG* 3.8 18.4 - - - +
1270A ILE* 3.0 20.5 + - + +
1271A VAL* 3.2 11.9 + - - +
1273A ASP* 1.3 76.5 - - - +
1275A ARG* 1.3 57.5 + - - +
1277A HIS* 2.9 17.5 + - - -
1278A ARG 3.1 11.3 + - - +
1281A MET* 3.6 16.8 - - + -
1282A VAL* 4.7 2.5 - - + -
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Residues in contact with ARG1275 (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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1045A TYR* 3.4 22.8 + - - -
1048A LEU* 3.0 38.9 + - + +
1049A LYS* 3.9 11.9 + - - +
1051A VAL* 3.5 24.3 + - + +
1052A GLY* 3.8 6.6 - - - -
1053A ILE* 6.2 1.6 - - - -
1077A TYR* 3.4 14.4 + - - -
1271A VAL* 2.9 26.3 + - + +
1272A TYR* 3.5 8.7 - - - +
1274A LEU* 1.3 74.9 - - - +
1276A MET* 1.3 61.1 + - - +
1278A ARG 3.2 13.9 - - - +
1279A PRO* 4.8 0.8 - - - +
1280A LEU* 3.6 18.3 - - - +
1281A MET 2.9 31.5 + - - +
1282A VAL 2.9 26.1 + - - -
1283A GLN* 5.0 0.6 - - - +
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Residues in contact with MET1276 (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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-9A GLY 6.0 2.5 - - - +
-5A LEU* 5.3 8.7 - - + -
1051A VAL* 3.7 20.2 - - - -
1052A GLY* 3.7 11.2 - - - -
1055A GLN* 3.1 52.2 + - + +
1077A TYR* 4.2 0.9 - - - -
1079A ILE* 4.8 3.6 - - - +
1272A TYR* 3.1 37.4 + - + +
1273A ASP* 3.5 13.0 - - - +
1274A LEU 3.2 0.6 - - - -
1275A ARG* 1.3 75.8 - - - +
1277A HIS* 1.3 71.9 + - + +
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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