Contacts of the helix formed by residues 1284 - 1303 (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 THR1284 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045A TYR* 3.5 16.0 - - - -
1206A HIS* 3.4 27.8 + - + +
1282A VAL* 4.2 0.9 - - - +
1283A GLN* 1.3 104.4 - - - +
1285A GLU* 1.3 64.2 + - - +
1286A ASP* 3.5 8.0 + - - +
1287A GLN* 3.2 36.6 + - - +
1288A TYR 3.4 8.0 + - - -
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Residues in contact with GLU1285 (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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1037A SER 4.7 3.3 - - - +
1038A ASN* 4.1 19.1 + - - +
1041A PHE 5.0 0.2 - - - +
1042A ALA* 3.8 37.9 - - - +
1045A TYR* 3.8 30.5 - - + -
1284A THR* 1.3 71.6 - - - +
1286A ASP* 1.3 66.6 + - - +
1288A TYR* 3.3 2.9 + - + +
1289A VAL* 2.8 38.9 + - + +
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Residues in contact with ASP1286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1038A ASN* 5.4 4.5 + - - -
1206A HIS 5.3 3.4 - - - +
1207A GLY* 6.2 1.1 - - - -
1208A VAL* 3.9 11.4 - - + +
1284A THR* 3.3 9.0 + - - +
1285A GLU* 1.3 83.8 - - - +
1287A GLN* 1.3 54.9 + - - +
1289A VAL* 3.7 8.1 - - - +
1290A PHE* 2.7 34.9 + - - +
1293A GLN* 5.0 0.7 - - - +
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Residues in contact with GLN1287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A PO4 5.6 0.2 + - - -
1203A TRP* 4.4 0.8 - - - +
1206A HIS* 3.8 16.9 - - - +
1207A GLY 3.0 30.5 + - - +
1208A VAL* 3.8 10.1 - - + -
1244A GLY* 3.4 21.7 - - - +
1245A ARG* 4.1 9.1 - - - +
1248A THR* 3.6 23.3 + - + +
1282A VAL* 3.9 5.4 - - + -
1283A GLN* 2.8 29.4 + - - -
1284A THR* 3.2 23.9 + - - +
1285A GLU 3.3 0.2 - - - -
1286A ASP* 1.3 75.8 - - - +
1288A TYR* 1.3 57.5 + - - +
1290A PHE* 3.3 3.3 + - - +
1291A LEU* 3.0 31.0 + - - +
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Residues in contact with TYR1288 (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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1041A PHE* 3.8 29.8 - + + -
1044A GLU* 2.6 36.9 + - + +
1045A TYR* 3.5 33.7 - + + -
1048A LEU* 3.7 18.8 - - + -
1267A VAL* 3.8 22.7 - - + +
1268A TYR* 3.4 22.9 + - - +
1271A VAL* 4.1 19.3 - - + -
1282A VAL* 3.7 6.6 - - + +
1284A THR 3.4 1.6 + - - -
1285A GLU 3.3 8.5 + - - +
1287A GLN* 1.3 76.5 - - - +
1289A VAL* 1.3 66.6 + - + +
1291A LEU* 3.2 13.8 + - + +
1292A ASN* 3.1 30.6 + - - -
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Residues in contact with VAL1289 (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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1030A PHE* 5.5 1.6 - - + -
1038A ASN* 4.1 35.9 - - + +
1041A PHE* 3.9 33.0 - - + -
1285A GLU* 2.8 30.7 + - + +
1286A ASP* 3.8 8.5 - - - +
1288A TYR* 1.3 75.4 - - + +
1290A PHE* 1.3 52.5 + - - +
1292A ASN* 3.0 13.1 + - - +
1293A GLN* 2.8 55.7 + - + +
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Residues in contact with PHE1290 (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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1208A VAL* 3.5 28.5 - - + -
1209A PRO* 3.7 33.4 - - + -
1210A ASP 5.4 0.4 - - - -
1211A THR* 3.4 25.8 - - - -
1212A THR* 3.8 21.5 - - + -
1215A LEU* 3.7 28.9 - - + -
1248A THR* 4.7 5.2 - - + -
1286A ASP 2.7 23.2 + - - +
1287A GLN 3.3 6.5 - - - +
1289A VAL* 1.3 72.9 - - - +
1291A LEU* 1.3 56.8 + - - +
1293A GLN* 3.2 21.0 + - - +
1294A CYS* 2.9 42.4 + - - -
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Residues in contact with LEU1291 (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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1215A LEU* 4.7 3.6 - - + -
1248A THR* 3.5 34.5 - - + +
1251A ALA* 3.4 23.6 - - + -
1252A ILE* 3.9 25.6 - - + +
1255A LEU* 4.2 7.0 - - + +
1267A VAL* 4.1 22.9 - - + -
1271A VAL* 4.3 3.4 - - + -
1282A VAL* 4.1 22.7 - - + -
1287A GLN 3.0 18.3 + - - +
1288A TYR* 3.2 9.6 + - - +
1290A PHE* 1.3 74.8 - - - +
1292A ASN* 1.3 58.2 + - - +
1294A CYS* 3.4 5.3 - - - +
1295A VAL* 3.1 31.7 + - - +
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Residues in contact with ASN1292 (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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1026A PHE* 3.6 21.5 - - - -
1029A TYR* 4.2 4.2 + - - -
1030A PHE* 3.7 7.2 - - + -
1041A PHE* 3.4 43.2 - - + -
1044A GLU* 4.9 0.8 + - - -
1267A VAL* 3.7 23.4 - - - +
1288A TYR* 3.1 38.2 + - - -
1289A VAL 3.0 9.3 + - - +
1291A LEU* 1.3 78.4 - - - +
1293A GLN* 1.3 58.6 + - - +
1295A VAL* 3.3 7.8 + - - +
1296A LEU* 2.9 27.0 + - - +
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Residues in contact with GLN1293 (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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1030A PHE* 3.7 21.7 - - + -
1034A GLN* 5.6 1.8 + - - -
1038A ASN* 5.8 0.2 + - - -
1212A THR* 4.3 10.5 - - + -
1286A ASP 5.0 0.5 - - - +
1289A VAL* 2.8 36.1 + - + +
1290A PHE* 3.2 29.5 + - - +
1292A ASN* 1.3 69.4 - - - +
1294A CYS* 1.3 63.3 + - - +
1296A LEU* 3.0 5.8 + - + +
1297A ASP* 3.0 32.7 + - - +
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Residues in contact with CYS1294 (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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1212A THR* 3.8 27.2 - - - +
1215A LEU* 3.8 16.8 - - - -
1216A ILE* 4.0 8.5 - - + +
1252A ILE* 3.9 17.0 - - + -
1290A PHE* 2.9 43.4 + - - -
1291A LEU* 3.4 11.2 - - - +
1293A GLN* 1.3 75.6 - - - +
1295A VAL* 1.3 62.4 + - - +
1297A ASP* 3.3 2.1 + - - +
1298A ILE* 3.0 28.9 + - - +
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Residues in contact with VAL1295 (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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1026A PHE* 3.4 29.4 - - + -
1252A ILE* 4.9 3.1 - - + -
1255A LEU* 3.8 25.1 - - + -
1259A ILE* 4.1 11.4 - - + -
1265A VAL* 3.7 32.3 - - + -
1267A VAL* 4.4 3.4 - - + -
1291A LEU 3.1 17.2 + - - +
1292A ASN 3.3 7.4 + - - +
1294A CYS* 1.3 75.8 - - - +
1296A LEU* 1.3 56.5 - - - +
1298A ILE* 3.3 8.9 + - + +
1299A VAL* 2.9 40.1 + - + +
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Residues in contact with LEU1296 (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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1026A PHE* 3.8 8.5 - - + -
1027A GLU* 3.7 41.3 - - + +
1030A PHE* 3.6 44.4 - - + -
1292A ASN 2.9 14.2 + - - +
1293A GLN* 3.0 10.7 + - + +
1295A VAL* 1.3 75.1 - - - +
1297A ASP* 1.3 63.5 + - - +
1299A VAL* 3.3 2.6 + - + +
1300A ARG* 2.8 70.5 + - - +
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Residues in contact with ASP1297 (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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1212A THR* 2.7 39.5 + - - +
1213A ASP* 5.8 1.3 - - - +
1216A ILE* 5.0 4.9 - - + -
1293A GLN* 3.0 19.4 + - - +
1294A CYS* 3.8 3.8 - - - +
1296A LEU* 1.3 84.7 - - - +
1298A ILE* 1.3 63.1 + - - +
1300A ARG* 4.0 13.0 + - - +
1301A SER* 3.1 25.8 + - - -
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Residues in contact with ILE1298 (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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1216A ILE* 3.8 29.6 - - + -
1220A TYR* 6.0 3.6 - - + +
1252A ILE* 4.5 5.6 - - + -
1256A ILE* 3.9 30.3 - - + -
1259A ILE* 4.3 31.2 - - + -
1294A CYS 3.0 24.7 + - - +
1295A VAL* 3.6 9.9 - - - +
1297A ASP* 1.3 76.4 - - - +
1299A VAL* 1.3 59.6 + - - +
1301A SER* 3.0 19.1 + - - +
1302A GLN* 3.2 16.7 + - + +
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Residues in contact with VAL1299 (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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1023A VAL* 3.8 41.7 - - + +
1026A PHE* 4.4 9.4 - - + -
1027A GLU* 4.1 24.6 - - + +
1259A ILE* 5.0 5.4 - - + -
1295A VAL* 2.9 36.7 + - + +
1296A LEU* 3.7 5.8 - - - +
1298A ILE* 1.3 73.5 - - + +
1300A ARG* 1.3 65.1 + - - +
1302A GLN* 3.0 30.2 + - + +
1303A LYS* 3.4 9.0 + - - +
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Residues in contact with ARG1300 (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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1027A GLU* 3.6 31.1 + - - +
1296A LEU* 2.8 59.5 + - + +
1297A ASP* 4.0 14.0 + - - +
1298A ILE 3.4 0.4 - - - -
1299A VAL* 1.3 73.2 - - - +
1301A SER* 1.3 58.4 + - - +
1303A LYS* 3.8 16.1 + - - +
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Residues in contact with SER1301 (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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1297A ASP 3.1 13.8 + - - -
1298A ILE* 3.0 17.0 + - - -
1300A ARG* 1.3 73.6 - - - +
1302A GLN* 1.3 62.8 + - - +
1303A LYS 3.2 5.2 + - - -
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Residues in contact with GLN1302 (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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1023A VAL* 4.0 23.3 - - - +
1259A ILE* 3.9 26.5 + - - +
1263A ASN* 5.0 6.0 + - - +
1298A ILE* 3.2 17.6 + - + +
1299A VAL* 3.0 29.1 - - - +
1301A SER* 1.3 75.6 + - - +
1303A LYS* 1.3 64.8 + - - +
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Residues in contact with LYS1303 (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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1027A GLU* 5.4 6.5 - - - +
1299A VAL 3.4 10.3 + - - +
1300A ARG* 3.8 16.6 - - - +
1301A SER 3.2 5.4 - - - -
1302A GLN* 1.3 83.7 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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