Contacts of the helix formed by residues 1290 - 1308 (chain A) in PDB entry 3RYT
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 VAL1290 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1286A LEU 3.1 20.2 + - - +
1287A GLU* 3.8 2.9 - - - +
1289A ARG* 1.3 77.7 - - + +
1291A ALA* 1.3 64.9 + - - +
1292A LEU 3.4 1.6 - - - -
1293A GLU* 3.3 16.7 + - + -
1294A CYS* 3.0 25.6 + - - -
1679A THR* 3.5 36.3 - - + +
1682A LEU* 4.6 5.8 - - + +
1683A ALA* 3.4 40.4 - - + +
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Residues in contact with ALA1291 (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 GLU 3.0 18.3 + - - +
1288A SER* 3.3 16.4 - - - +
1289A ARG 3.2 1.2 - - - -
1290A VAL* 1.3 76.2 - - - +
1292A LEU* 1.3 69.2 + - + +
1294A CYS* 3.2 22.4 + - - +
1295A LYS* 3.5 7.1 + - - +
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Residues in contact with LEU1292 (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 SER 4.3 8.7 - - - +
1289A ARG 4.5 5.1 + - - +
1290A VAL 3.4 0.2 - - - -
1291A ALA* 1.3 86.8 - - + +
1293A GLU* 1.3 66.2 + - - +
1294A CYS 3.3 0.3 + - - -
1295A LYS* 3.4 16.0 + - - +
1296A GLU* 3.6 19.4 + - - +
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Residues in contact with GLU1293 (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 ARG 4.8 2.4 + - - +
1290A VAL* 3.3 26.3 + - + +
1292A LEU* 1.3 78.0 - - - +
1294A CYS* 1.3 56.5 + - - +
1296A GLU* 3.5 8.5 + - - +
1297A ALA* 3.0 28.0 + - - +
1683A ALA* 5.9 1.3 - - + -
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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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1290A VAL* 3.0 36.1 + - - -
1291A ALA* 3.3 10.3 - - - +
1292A LEU 3.1 0.4 - - - -
1293A GLU* 1.3 75.3 - - - +
1295A LYS* 1.3 58.5 + - - +
1297A ALA* 2.8 2.4 + - - +
1298A PHE* 2.7 37.5 + - + +
1682A LEU 4.2 2.2 - - - -
1683A ALA* 4.0 8.5 - - - -
1686A GLY* 3.7 39.5 - - - +
1687A THR* 3.9 10.2 + - - -
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Residues in contact with LYS1295 (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 ALA 3.5 6.0 + - - +
1292A LEU* 3.4 12.2 + - - +
1294A CYS* 1.3 78.3 - - - +
1296A GLU* 1.3 60.3 + - + +
1298A PHE* 4.6 5.5 - - - +
1299A ALA* 3.2 26.7 + - - +
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Residues in contact with GLU1296 (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 LEU* 3.6 15.4 + - - +
1293A GLU* 3.5 8.7 + - - +
1294A CYS 3.1 0.8 - - - -
1295A LYS* 1.3 78.4 - - + +
1297A ALA* 1.3 62.9 + - - +
1299A ALA* 4.1 5.5 - - - +
1300A GLU* 3.5 21.1 + - - +
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Residues in contact with ALA1297 (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 GLU 3.0 17.4 + - - +
1294A CYS* 2.8 1.9 + - - +
1296A GLU* 1.3 77.7 - - - +
1298A PHE* 1.3 64.2 + - - +
1299A ALA 3.3 0.2 - - - -
1300A GLU* 3.5 5.9 + - - +
1301A LEU* 3.4 24.8 + - - +
1469A GLN* 5.1 7.1 + - - +
1472A LYS* 4.9 5.1 + - - +
1687A THR* 3.4 27.4 - - + +
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Residues in contact with PHE1298 (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 CYS 2.7 19.0 + - - +
1295A LYS* 4.6 4.5 - - - +
1297A ALA* 1.3 71.7 - - - +
1299A ALA* 1.3 69.7 + - + +
1301A LEU* 3.0 6.3 + - - +
1302A GLN* 3.0 58.3 + - + +
1686A GLY 5.5 0.9 - - - +
1687A THR* 3.4 34.5 - - + +
1690A LYS* 3.5 41.7 - - + -
1691A PHE* 3.6 30.7 - + - -
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Residues in contact with ALA1299 (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 LYS 3.2 20.9 + - - +
1296A GLU* 4.3 5.6 - - - +
1297A ALA 3.3 0.4 - - - -
1298A PHE* 1.3 86.9 - - + +
1300A GLU* 1.3 62.3 + - - +
1301A LEU 3.1 1.0 + - - -
1302A GLN* 3.3 5.6 + - - +
1303A THR* 3.1 28.5 + - - +
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Residues in contact with GLU1300 (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 GLU 3.5 16.8 + - - +
1297A ALA* 3.5 6.6 + - - +
1298A PHE 3.3 0.4 - - - -
1299A ALA* 1.3 77.5 - - - +
1301A LEU* 1.3 59.3 + - - +
1303A THR* 4.7 3.9 - - - -
1304A ASP* 3.3 25.0 + - - +
1472A LYS* 4.2 18.4 + - - +
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Residues in contact with LEU1301 (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 ALA 3.4 9.4 + - - +
1298A PHE 3.0 8.1 + - - +
1300A GLU* 1.3 77.8 - - - +
1302A GLN* 1.3 57.1 + - - +
1303A THR 3.2 0.4 - - - -
1304A ASP* 3.0 7.1 + - + +
1305A ILE* 2.6 41.4 + - + +
1465A ALA* 4.2 15.9 - - - +
1468A GLN* 4.2 24.9 - - + +
1469A GLN* 3.4 32.1 - - + +
1472A LYS* 4.1 13.5 - - + +
1687A THR* 3.9 22.7 - - + -
1688A LEU* 4.4 2.2 - - + -
1691A PHE* 4.4 20.0 - - + -
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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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1298A PHE* 3.0 52.5 + - + +
1299A ALA* 4.0 5.1 - - - +
1301A LEU* 1.3 75.1 - - - +
1303A THR* 1.3 55.1 + - - +
1305A ILE* 3.3 11.3 - - + +
1306A HIS* 2.8 41.5 + - + +
1461A MET* 5.4 8.5 - - + +
1690A LYS* 4.7 8.5 + - - +
1691A PHE* 4.8 6.1 - - + -
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Residues in contact with THR1303 (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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1299A ALA 3.1 16.2 + - - -
1300A GLU* 4.7 4.7 - - - +
1302A GLN* 1.3 78.1 - - - +
1304A ASP* 1.3 61.2 + - - +
1306A HIS* 4.2 3.7 - - - +
1307A GLU* 3.5 22.9 + - - +
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Residues in contact with ASP1304 (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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1300A GLU 3.3 21.2 + - - +
1301A LEU* 3.0 9.0 + - + +
1303A THR* 1.3 79.4 - - + +
1305A ILE* 1.3 61.3 + - - +
1307A GLU* 4.0 2.8 - - - +
1308A LEU* 3.1 28.2 + - - +
1468A GLN* 4.4 18.9 + - - +
1472A LYS* 6.0 0.2 + - - -
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Residues in contact with ILE1305 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1301A LEU* 2.6 31.4 + - + +
1302A GLN* 3.3 14.8 - - - +
1304A ASP* 1.3 71.3 - - - +
1306A HIS* 1.3 72.3 + - + +
1308A LEU* 3.1 14.8 + - + +
1309A THR* 3.1 19.7 + - + +
1460A PHE* 6.1 0.9 - - + -
1461A MET* 3.6 50.7 - - + +
1464A CYS* 3.5 41.5 - - + +
1465A ALA* 4.3 1.3 - - - +
1468A GLN* 5.6 7.2 - - + +
1691A PHE* 4.5 7.6 - - + -
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Residues in contact with HIS1306 (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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1302A GLN* 2.8 30.6 + - + +
1303A THR* 4.2 4.5 - - - +
1305A ILE* 1.3 75.0 - - + +
1307A GLU* 1.3 52.9 + - - +
1309A THR* 2.9 9.7 + - - -
1310A SER* 2.5 44.7 + - - -
1461A MET* 5.7 3.6 - - + -
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Residues in contact with GLU1307 (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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1303A THR 3.5 16.3 + - - +
1304A ASP* 4.2 2.9 - - - +
1305A ILE 3.4 0.4 - - - -
1306A HIS* 1.3 79.4 - - - +
1308A LEU* 1.3 56.2 + - - +
1309A THR 3.1 4.6 + - - -
1310A SER* 4.1 9.7 + - - -
1311A ASP* 4.1 15.7 + - + +
1539A LYS* 4.3 11.6 + - - -
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Residues in contact with LEU1308 (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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1304A ASP* 3.1 23.3 + - - +
1305A ILE* 3.1 11.0 + - + +
1306A HIS 3.0 1.6 - - - -
1307A GLU* 1.3 76.0 - - - +
1309A THR* 1.3 60.6 + - - +
1311A ASP 6.1 0.7 - - - -
1468A GLN* 6.5 2.0 - - + -
1539A LYS* 4.7 31.4 - - + +
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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