Contacts of the helix formed by residues 1281 - 1302 (chain A) in PDB entry 6AH0
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 THR1281 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1231A ARG* 5.8 0.7 - - - +
1232A VAL 5.4 7.2 - - - +
1277A ALA 3.8 4.6 + - - -
1278A VAL 3.1 15.4 + - - +
1279A VAL 3.3 1.5 - - - -
1280A ASN* 1.3 79.4 - - - +
1282A GLN* 1.3 64.7 + - - +
1283A GLU 3.1 3.4 - - - +
1284A LEU* 3.0 14.3 + - - +
1285A LEU 3.3 7.4 + - - -
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Residues in contact with GLN1282 (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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1279A VAL 5.3 0.6 + - - -
1280A ASN 3.8 4.4 + - - -
1281A THR* 1.3 72.4 - - - +
1283A GLU* 1.3 61.4 + - - +
1285A LEU* 2.9 5.4 + - - +
1286A ASP* 2.9 21.1 + - - -
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Residues in contact with GLU1283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1281A THR 3.1 1.4 - - - -
1282A GLN* 1.3 76.3 - - - +
1284A LEU* 1.3 55.3 + - - +
1286A ASP* 3.3 2.4 + - - +
1287A LEU* 2.9 24.8 + - - -
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Residues in contact with LEU1284 (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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1278A VAL 5.6 1.3 - - - -
1281A THR* 3.0 11.0 + - - +
1283A GLU* 1.3 73.0 - - - +
1285A LEU* 1.3 60.6 + - - +
1287A LEU* 4.3 1.3 - - - +
1288A LEU* 2.7 31.1 + - - +
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Residues in contact with LEU1285 (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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1278A VAL 5.3 1.2 + - - -
1281A THR 3.3 7.6 + - - -
1282A GLN* 2.9 9.0 + - - +
1284A LEU* 1.3 76.4 - - - +
1286A ASP* 1.3 61.1 - - - +
1288A LEU* 3.5 1.0 + - - +
1289A VAL* 3.1 19.4 + - - -
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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
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1282A GLN 2.9 12.5 + - - -
1283A GLU* 3.8 3.1 - - - +
1285A LEU* 1.3 77.9 - - - +
1287A LEU* 1.3 56.2 + - - +
1289A VAL* 3.2 2.3 + - - -
1290A LYS* 2.9 25.3 + - - -
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Residues in contact with LEU1287 (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 GLU 2.9 14.9 + - - -
1284A LEU* 3.6 3.8 - - - +
1286A ASP* 1.3 77.6 - - - +
1288A LEU* 1.3 55.8 + - - +
1290A LYS* 3.2 2.7 + - - +
1291A CYS* 2.9 27.2 + - - -
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Residues in contact with LEU1288 (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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1284A LEU 2.7 20.5 + - - -
1285A LEU* 4.0 1.3 - - - +
1287A LEU* 1.3 72.3 - - - +
1289A VAL* 1.3 62.3 + - - +
1291A CYS* 3.4 1.2 + - - +
1292A GLU* 3.0 21.5 + - - -
1331A GLY 6.3 0.9 - - - -
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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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1285A LEU 3.1 15.3 + - - -
1286A ASP 3.7 2.9 - - - -
1287A LEU 3.2 0.2 - - - -
1288A LEU* 1.3 75.4 - - - +
1290A LYS* 1.3 62.6 + - - +
1292A GLU* 3.5 0.9 + - - +
1293A ASN* 3.1 18.9 + - - -
1331A GLY* 5.4 11.9 - - - -
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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 ASP 2.9 14.1 + - - -
1287A LEU* 3.7 3.1 - - - +
1289A VAL* 1.3 77.9 - - - +
1291A CYS* 1.3 54.7 + - - +
1293A ASN* 3.2 2.7 + - - +
1294A LYS* 2.9 24.9 + - - -
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Residues in contact with CYS1291 (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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1287A LEU 2.9 15.5 + - - -
1288A LEU* 3.9 1.6 - - - +
1290A LYS* 1.3 75.6 - - - +
1292A GLU* 1.3 59.1 + - - +
1294A LYS* 3.2 2.9 + - - +
1295A ILE* 2.8 26.0 + - - -
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Residues in contact with GLU1292 (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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1288A LEU 3.0 16.4 + - - -
1289A VAL 4.0 0.7 - - - -
1291A CYS* 1.3 76.5 - - - +
1293A ASN* 1.3 64.1 + - - +
1295A ILE* 3.1 3.1 + - - +
1296A GLN* 3.0 21.3 + - - -
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Residues in contact with ASN1293 (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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1289A VAL 3.1 14.5 + - - -
1290A LYS* 3.5 4.0 - - - +
1292A GLU* 1.3 78.0 - - - +
1294A LYS* 1.3 60.9 + - - +
1296A GLN* 3.6 7.0 + - - +
1297A THR* 3.8 7.1 + - - -
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Residues in contact with LYS1294 (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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1290A LYS 2.9 14.5 + - - -
1291A CYS* 3.2 4.7 + - - +
1293A ASN* 1.3 76.3 - - - +
1295A ILE* 1.3 61.8 + - - +
1297A THR* 3.4 11.1 + - - -
1298A ARG* 3.7 7.3 + - - -
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Residues in contact with ILE1295 (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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1291A CYS 2.8 14.5 + - - -
1292A GLU* 3.1 4.4 + - - +
1294A LYS* 1.3 75.4 - - - +
1296A GLN* 1.3 63.4 + - - +
1298A ARG* 3.3 11.3 + - - +
1299A ILE* 3.8 5.7 + - - -
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Residues in contact with GLN1296 (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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1292A GLU 3.0 13.0 + - - -
1293A ASN* 3.6 2.8 + - - +
1294A LYS 3.4 0.4 - - - -
1295A ILE* 1.3 75.1 - - - +
1297A THR* 1.3 61.7 + - - +
1299A ILE* 3.3 3.6 + - - -
1300A LYS* 3.1 19.4 + - - -
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Residues in contact with THR1297 (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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1293A ASN 3.8 7.1 + - - -
1294A LYS 3.4 7.4 + - - -
1295A ILE 3.2 0.8 - - - -
1296A GLN* 1.3 74.7 - - - +
1298A ARG* 1.3 55.1 + - - +
1300A LYS* 3.6 2.4 - - - +
1301A ILE* 2.7 34.5 + - - -
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Residues in contact with ARG1298 (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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1294A LYS 3.7 7.0 + - - -
1295A ILE 3.3 8.2 + - - -
1296A GLN 3.3 1.0 - - - -
1297A THR* 1.3 75.7 - - - +
1299A ILE* 1.3 58.0 + - - +
1301A ILE* 3.6 1.1 + - - +
1302A GLY* 3.0 22.3 + - - -
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Residues in contact with ILE1299 (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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1295A ILE 3.8 5.8 + - - -
1296A GLN 3.3 5.6 + - - -
1297A THR 3.2 0.4 - - - -
1298A ARG* 1.3 73.2 - - - +
1300A LYS* 1.3 65.1 + - - +
1302A GLY* 3.1 11.2 + - - -
1303A LEU* 3.3 9.4 + - - -
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Residues in contact with LYS1300 (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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1296A GLN 3.1 14.6 + - - -
1297A THR* 3.2 4.2 + - - +
1299A ILE* 1.3 76.3 - - - +
1301A ILE* 1.3 55.6 + - - +
1303A LEU* 3.0 24.3 + - - +
1304A ASN 5.3 0.3 - - - +
1305A SER 4.3 4.7 - - - +
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Residues in contact with ILE1301 (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 THR 2.7 19.9 + - - -
1298A ARG* 3.8 2.0 - - - +
1300A LYS* 1.3 67.5 - - - +
1302A GLY* 1.3 59.4 + - - +
1303A LEU 3.0 14.1 + - - +
1305A SER 4.7 5.5 - - - +
1306A LYS* 6.1 2.2 - - - +
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Residues in contact with GLY1302 (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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1298A ARG 3.0 15.4 + - - -
1299A ILE* 3.1 7.3 + - - -
1301A ILE* 1.3 75.8 - - - +
1303A LEU* 1.3 59.5 + - - +
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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