Contacts of the helix formed by residues 1349 - 1362 (chain B) 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 VAL1349 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1346B GLN* 3.9 21.3 - - + -
1347B ALA 3.4 1.0 - - - +
1348B ASN* 1.3 80.0 - - - +
1350B GLU* 1.3 65.1 + - - +
1351B LYS 3.4 1.8 - - - -
1352B SER* 3.2 16.8 + - - -
1353B LEU* 3.2 11.6 + - - +
1851B HIS* 4.7 21.8 - - + +
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Residues in contact with GLU1350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1346B GLN* 4.7 13.7 - - - +
1347B ALA* 4.4 13.3 + - - +
1349B VAL* 1.3 78.5 - - - +
1351B LYS* 1.3 61.9 + - - +
1353B LEU* 2.9 34.2 + - + +
1354B THR* 4.0 5.2 + - - +
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Residues in contact with LYS1351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1347B ALA 4.8 6.3 + - - +
1348B ASN* 5.5 4.0 - - - +
1349B VAL 3.4 1.2 - - - +
1350B GLU* 1.3 83.3 - - + +
1352B SER* 1.3 57.0 + - - +
1354B THR* 3.1 23.8 + - - -
1355B LEU* 3.8 5.4 + - - +
1889B THR* 5.6 9.0 - - - +
1890B MET* 5.8 3.6 - - - -
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Residues in contact with SER1352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1348B ASN 4.4 2.1 + - - -
1349B VAL* 3.2 18.3 + - - -
1350B GLU 3.0 0.6 - - - -
1351B LYS* 1.3 77.7 - - - +
1353B LEU* 1.3 63.4 - - - +
1354B THR 3.4 0.2 - - - -
1355B LEU* 3.3 10.5 - - - +
1356B PHE* 3.1 27.5 + - - +
1854B TYR* 5.8 3.8 - - - +
1886B VAL 5.8 0.2 - - - -
1890B MET* 3.9 28.4 - - - +
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Residues in contact with LEU1353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1349B VAL 3.2 8.7 + - - +
1350B GLU* 2.9 19.0 + - + +
1352B SER* 1.3 76.6 - - - +
1354B THR* 1.3 60.9 + - + +
1356B PHE* 4.8 0.4 - - - +
1357B GLY* 2.9 30.6 + - - -
1846B SER* 4.6 11.9 - - - +
1847B MET* 4.4 27.8 - - + -
1850B LEU* 5.0 11.0 - - + -
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Residues in contact with THR1354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1350B GLU 4.0 5.1 + - - +
1351B LYS* 3.1 15.0 + - - +
1353B LEU* 1.3 80.1 - - + +
1355B LEU* 1.3 70.5 + - - +
1357B GLY* 4.8 1.1 - - - -
1358B GLN* 2.9 45.8 + - - +
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Residues in contact with LEU1355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1351B LYS 4.1 3.4 - - - +
1352B SER* 3.2 22.2 + - - +
1353B LEU 3.2 0.2 - - - -
1354B THR* 1.3 87.0 + - - +
1356B PHE* 1.3 59.0 + - - +
1358B GLN* 4.1 1.7 - - - +
1359B LEU* 2.9 28.2 + - - +
1886B VAL* 3.2 47.1 - - + +
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Residues in contact with PHE1356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1352B SER* 3.1 14.0 + - - +
1353B LEU 4.8 0.2 - - - +
1355B LEU* 1.3 79.0 - - - +
1357B GLY* 1.3 61.4 + - - +
1359B LEU* 4.1 10.3 - - + -
1360B LEU* 3.0 32.8 + - + +
1850B LEU* 5.7 12.8 - - + +
1854B TYR* 5.9 6.7 - - + -
1886B VAL* 4.9 0.6 - - - +
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Residues in contact with GLY1357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1353B LEU* 2.9 21.8 + - - -
1354B THR* 3.8 1.1 - - - -
1355B LEU 3.1 0.2 - - - -
1356B PHE* 1.3 78.8 - - - +
1358B GLN* 1.3 52.1 + - - +
1360B LEU* 4.6 2.0 - - - +
1361B THR* 2.6 29.8 + - - -
1850B LEU* 6.3 0.4 - - - +
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Residues in contact with GLN1358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1577A ASN* 3.6 33.4 + - - +
1354B THR* 2.9 38.2 + - - +
1355B LEU* 4.1 1.1 - - - +
1357B GLY* 1.3 74.5 - - - +
1359B LEU* 1.3 68.5 + - - +
1360B LEU 3.2 1.6 - - - -
1361B THR* 2.9 22.5 + - - -
1362B LYS* 3.4 5.9 + - - +
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Residues in contact with LEU1359 (chain B).
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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1355B LEU 2.9 17.4 + - - +
1356B PHE* 4.0 8.5 - - - +
1358B GLN* 1.3 79.1 - - - +
1360B LEU* 1.3 56.0 + - - +
1362B LYS* 3.5 12.7 + - + +
1365B PHE* 2.7 53.4 - - + +
1857B ILE* 6.1 3.8 - - + -
1879B LEU* 4.9 7.9 - - + +
1882B LYS* 4.9 9.6 - - + -
1883B LEU* 3.5 41.1 - - + +
1886B VAL* 4.8 11.7 - - + -
1887B VAL* 5.7 3.4 - - + -
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Residues in contact with LEU1360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1356B PHE* 3.0 22.5 + - + +
1357B GLY* 4.6 2.0 - - - +
1359B LEU* 1.3 75.0 - - - +
1361B THR* 1.3 67.1 + - - +
1362B LYS 3.1 5.7 + - - +
1365B PHE* 3.5 17.2 - - + -
1366B LEU* 3.6 17.8 - - + +
1369B PHE* 6.0 6.7 - - + -
1391B ILE* 4.8 24.7 - - + -
1394B ALA* 6.3 2.9 - - + -
1395B LEU* 5.8 4.7 - - + -
1401B TYR* 3.0 19.6 + - + +
1853B ILE* 4.9 24.9 - - + -
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Residues in contact with THR1361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1578A ASP* 3.9 30.5 - - + +
1357B GLY 2.6 22.6 + - - -
1358B GLN* 2.9 15.3 + - - -
1360B LEU* 1.3 79.2 - - - +
1362B LYS* 1.3 60.7 + - - +
1363B LYS 3.1 0.7 + - - -
1398B GLU* 6.2 3.4 - - + -
1401B TYR* 2.9 39.8 - - + -
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Residues in contact with LYS1362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1358B GLN 3.4 6.1 + - - +
1359B LEU* 3.6 14.4 - - + +
1360B LEU 3.1 5.3 - - - +
1361B THR* 1.3 75.1 - - - +
1363B LYS* 1.3 69.5 + - - +
1364B HIS* 3.5 0.9 - - + +
1365B PHE* 3.2 18.9 + - + +
1366B LEU 3.2 9.4 + - - -
1401B TYR* 3.4 0.2 + - - -
1877B GLN* 5.1 11.0 - - - +
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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