Contacts of the helix formed by residues 1348 - 1366 (chain A) in PDB entry 5XJY
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 PHE1348 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1340A ALA 4.8 11.9 - - - -
1341A ARG* 6.3 0.4 - - - -
1343A SER* 4.3 13.5 - - - -
1344A ARG* 4.2 23.3 - - + +
1346A GLY 2.6 13.5 + - - +
1347A PHE* 1.3 75.6 - - - +
1349A ALA* 1.3 58.8 + - - +
1350A GLN 3.1 2.0 - - - -
1351A ILE* 3.0 21.9 + - + +
1352A VAL* 2.9 36.0 + - + +
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Residues in contact with ALA1349 (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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1347A PHE* 3.2 11.9 - - + +
1348A PHE* 1.3 78.1 - - - +
1350A GLN* 1.3 65.8 + - + +
1351A ILE 3.2 0.9 - - - -
1352A VAL* 4.3 7.4 - - - +
1353A LEU* 2.9 37.7 + - + +
1767A TYR* 5.7 1.8 - - - +
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Residues in contact with GLN1350 (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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1347A PHE* 3.9 29.5 + - + +
1348A PHE 3.1 1.0 - - - -
1349A ALA* 1.3 83.8 - - - +
1351A ILE* 1.3 69.4 + - + +
1353A LEU* 5.0 0.4 - - - +
1354A PRO* 3.6 18.4 - - - +
1667A PHE* 3.5 29.8 + - - +
1668A VAL* 5.1 9.2 - - - +
1670A ALA* 5.0 0.2 - - - +
1671A SER* 3.7 39.6 - - - +
1674A VAL* 6.5 0.2 - - - -
1713A PRO* 4.8 2.9 - - - +
1767A TYR* 3.3 44.6 + - - -
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Residues in contact with ILE1351 (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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1347A PHE 5.0 1.8 - - - +
1348A PHE* 3.0 28.6 + - + +
1350A GLN* 1.3 92.3 - - + +
1352A VAL* 1.3 67.0 + - + +
1353A LEU 3.4 1.1 - - - -
1354A PRO* 3.4 9.6 - - - +
1355A ALA* 3.7 15.1 + - - +
1668A VAL* 6.1 1.1 - - + -
1709A ASN* 4.9 11.7 - - - +
1712A VAL* 4.9 7.6 - - + -
1713A PRO* 3.7 34.8 - - + +
1716A LEU* 3.9 27.4 - - + -
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Residues in contact with VAL1352 (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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1348A PHE* 2.9 26.9 + - + +
1349A ALA* 4.4 6.1 - - - -
1351A ILE* 1.3 80.9 - - + +
1353A LEU* 1.3 63.0 + - - +
1355A ALA* 4.1 1.5 - - - +
1356A VAL* 3.1 38.8 + - + +
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Residues in contact with LEU1353 (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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1349A ALA* 2.9 24.1 + - + +
1350A GLN* 5.2 0.2 - - - +
1352A VAL* 1.3 79.3 - - - +
1354A PRO* 1.4 66.8 - - + +
1356A VAL* 3.9 2.7 - - - +
1357A PHE* 3.0 64.0 + - + +
1663A PHE* 4.4 6.7 - - + -
1664A ALA* 6.1 0.7 - - - -
1667A PHE* 3.6 39.3 - - + -
1767A TYR* 5.7 0.4 - - - +
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Residues in contact with PRO1354 (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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1350A GLN* 3.6 22.9 - - - +
1351A ILE* 3.4 14.4 - - - +
1353A LEU* 1.4 92.6 - - + +
1355A ALA* 1.3 55.1 + - - +
1357A PHE* 3.3 1.0 + - + -
1358A VAL* 2.9 35.5 + - - +
1664A ALA* 3.6 27.8 - - + +
1665A MET* 3.7 28.0 - - + -
1667A PHE* 4.5 10.8 - - + -
1668A VAL* 4.9 7.0 - - + +
1713A PRO* 5.3 5.2 - - + -
1717A VAL* 4.8 1.1 - - + -
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Residues in contact with ALA1355 (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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1351A ILE 3.7 15.0 + - - +
1352A VAL* 4.1 2.9 - - - +
1353A LEU 3.4 0.4 - - - -
1354A PRO* 1.3 80.5 - - - +
1356A VAL* 1.3 59.5 + - + +
1358A VAL* 3.4 1.4 + - - -
1359A CYS* 3.0 32.4 + - - -
1713A PRO* 5.5 1.7 - - + +
1716A LEU* 5.0 13.7 - - + -
1717A VAL* 4.4 8.9 - - + +
1720A ILE* 3.3 25.4 - - + +
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Residues in contact with VAL1356 (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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1352A VAL* 3.1 35.0 + - + +
1353A LEU* 4.1 3.1 - - - +
1355A ALA* 1.3 78.4 - - + +
1357A PHE* 1.3 71.9 + - + +
1359A CYS* 3.0 12.0 + - + +
1360A ILE* 2.9 26.5 + - + +
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Residues in contact with PHE1357 (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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1353A LEU* 3.0 50.9 + - + +
1354A PRO* 4.2 4.0 - - + +
1356A VAL* 1.3 88.4 - - + +
1358A VAL* 1.3 60.0 + - - +
1360A ILE* 3.3 19.8 - - + +
1361A ALA 3.0 22.0 + - - -
1660A CYS* 3.3 20.1 - - - -
1663A PHE* 3.5 34.3 - + + -
1664A ALA* 5.1 2.9 - - + -
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Residues in contact with VAL1358 (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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1354A PRO 2.9 20.3 + - - +
1355A ALA 3.5 4.9 - - - +
1357A PHE* 1.3 76.8 - - - +
1359A CYS* 1.3 56.5 + - - +
1361A ALA* 3.3 5.1 + - - +
1362A LEU* 2.9 44.5 + - + +
1660A CYS* 5.2 0.4 - - - +
1661A VAL* 3.9 20.6 - - + -
1664A ALA* 4.1 13.7 - - + -
1665A MET* 5.8 0.2 - - + -
1717A VAL* 3.8 33.2 - - + -
1720A ILE* 3.8 24.5 - - + -
1721A PHE* 4.0 4.9 - - + -
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Residues in contact with CYS1359 (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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1355A ALA 3.0 19.8 + - - -
1356A VAL* 3.0 18.2 + - + +
1358A VAL* 1.3 77.8 - - - +
1360A ILE* 1.3 55.3 + - - +
1362A LEU* 4.5 3.4 - - - +
1363A VAL* 2.9 39.4 + - + +
1720A ILE* 3.7 28.5 - - - -
1724A PHE* 5.0 6.5 - - + -
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Residues in contact with ILE1360 (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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1356A VAL* 2.9 11.4 + - + +
1357A PHE* 3.3 36.8 - - + +
1359A CYS* 1.3 73.9 - - - +
1361A ALA* 1.3 60.8 + - - +
1363A VAL* 4.7 9.6 - - + -
1364A PHE* 3.0 30.7 + - + +
1660A CYS* 4.8 5.4 - - - -
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Residues in contact with ALA1361 (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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1357A PHE 3.0 14.3 + - - +
1358A VAL* 3.5 10.5 - - - +
1360A ILE* 1.3 79.3 - - - +
1362A LEU* 1.3 64.4 + - + +
1364A PHE* 3.2 8.8 + - - +
1365A SER* 2.9 29.9 + - - -
1656A LEU* 5.5 4.9 - - + +
1657A VAL* 5.0 11.9 - - + -
1660A CYS* 3.6 27.8 - - + -
1661A VAL* 5.2 2.0 - - + -
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Residues in contact with LEU1362 (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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1358A VAL* 2.9 40.6 + - + +
1359A CYS* 4.7 0.2 - - - -
1361A ALA* 1.3 79.2 - - + +
1363A VAL* 1.3 59.8 + - - +
1365A SER* 2.8 22.2 + - - -
1366A LEU* 3.0 20.5 + - - +
1657A VAL* 4.2 24.9 - - + -
1661A VAL* 5.0 1.3 - - + -
1720A ILE* 5.2 0.4 - - + -
1721A PHE* 4.0 30.5 - - + -
1724A PHE* 3.5 28.5 - - + -
1726A GLN* 4.0 32.3 - - + +
1727A LYS* 5.5 3.4 - - + -
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Residues in contact with VAL1363 (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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1359A CYS* 2.9 23.1 + - + +
1360A ILE* 4.6 10.3 - - + +
1362A LEU* 1.3 71.8 - - - +
1364A PHE* 1.3 63.5 + - - +
1366A LEU* 3.6 12.3 + - + +
1367A ILE* 3.5 21.4 - - + +
1724A PHE* 3.6 28.7 - - + -
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Residues in contact with PHE1364 (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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1360A ILE* 3.0 24.8 + - + +
1361A ALA* 3.2 7.6 + - - +
1363A VAL* 1.3 78.6 - - - +
1365A SER* 1.3 60.0 + - - +
1366A LEU 3.6 0.2 + - - -
1367A ILE* 3.6 15.5 + - + +
1368A VAL* 3.7 25.0 - - + +
1656A LEU* 3.5 33.4 - - + -
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Residues in contact with SER1365 (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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1361A ALA 2.9 13.2 + - - -
1362A LEU* 2.8 15.4 + - - -
1364A PHE* 1.3 77.0 - - - +
1366A LEU* 1.3 62.5 + - - +
1367A ILE 3.2 3.6 + - - -
1368A VAL* 3.3 23.0 - - - +
1653A VAL* 5.1 3.5 + - - +
1654A ASP* 5.8 0.7 - - - -
1656A LEU* 5.1 3.3 - - - +
1657A VAL* 3.3 26.8 - - - +
1726A GLN* 3.3 23.7 + - - -
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Residues in contact with LEU1366 (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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1362A LEU 3.0 27.1 + - - +
1363A VAL* 3.6 12.1 + - + +
1364A PHE 3.4 1.0 - - - -
1365A SER* 1.3 77.0 - - - +
1367A ILE* 1.3 67.8 + - + +
1368A VAL 3.7 1.9 - - - +
1724A PHE* 4.7 20.2 - - + -
1725A GLN 6.0 0.9 - - - +
1726A GLN* 3.4 32.3 + - + +
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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