Contacts of the helix formed by residues 1323 - 1342 (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 LYS1323 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1322A TRP* 1.3 70.6 - - - +
1324A LEU* 1.3 59.7 + - - +
1325A THR 3.2 0.9 - - - -
1326A GLN* 3.3 8.3 + - - +
1327A GLN* 3.0 25.6 + - - +
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Residues in contact with LEU1324 (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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1322A TRP* 3.2 11.0 - - + +
1323A LYS* 1.3 75.7 - - - +
1325A THR* 1.3 59.9 + - + +
1327A GLN* 3.4 11.3 - - + +
1328A GLN* 2.9 28.8 + - - +
2016A VAL* 3.8 30.3 - - + -
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Residues in contact with THR1325 (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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1322A TRP* 2.3 51.2 + - + +
1324A LEU* 1.3 76.1 - - + +
1326A GLN* 1.3 63.0 + - - +
1328A GLN* 3.1 9.2 + - - +
1329A PHE* 2.9 24.5 + - - +
1697A ILE* 4.7 12.5 - - - +
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Residues in contact with GLN1326 (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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1322A TRP 4.9 0.9 - - - +
1323A LYS* 3.3 10.6 + - - +
1325A THR* 1.3 80.6 + - - +
1327A GLN* 1.3 60.2 + - - +
1329A PHE* 3.3 13.9 - - + +
1330A VAL* 3.0 34.6 + - + +
1697A ILE* 5.9 1.1 - - - -
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Residues in contact with GLN1327 (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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1323A LYS 3.0 15.6 + - - +
1324A LEU* 3.4 14.6 - - + +
1326A GLN* 1.3 78.5 - - - +
1328A GLN* 1.3 56.0 + - - +
1330A VAL* 3.3 12.3 - - - +
1331A ALA* 2.9 27.1 + - - +
2012A LEU 5.6 2.5 - - - +
2016A VAL* 6.5 0.2 - - - -
2018A GLU* 5.8 8.5 - - + -
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Residues in contact with GLN1328 (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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1324A LEU 2.9 13.3 + - - +
1325A THR* 3.4 9.9 - - - +
1327A GLN* 1.3 73.7 - - - +
1329A PHE* 1.3 60.6 + - - +
1331A ALA* 3.1 8.0 + - - +
1332A LEU* 2.9 39.6 + - + +
1693A VAL* 5.9 7.0 - - + -
1697A ILE* 6.0 4.0 - - + -
2012A LEU 5.1 1.8 + - - +
2013A LEU* 4.1 23.8 - - + +
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Residues in contact with PHE1329 (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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1325A THR 2.9 12.2 + - - +
1326A GLN* 3.2 17.0 + - + +
1328A GLN* 1.3 76.0 - - - +
1330A VAL* 1.3 70.8 + - + +
1332A LEU* 3.2 6.1 + - - +
1333A LEU* 3.0 50.6 + - + +
1697A ILE* 3.6 25.3 - - + +
1700A LEU* 3.6 30.5 - - + -
1701A SER* 3.1 40.6 - - - -
1704A VAL* 4.4 13.7 - - + -
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Residues in contact with VAL1330 (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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1326A GLN* 3.0 14.0 + - + +
1327A GLN* 3.3 20.4 - - - +
1329A PHE* 1.3 87.8 - - + +
1331A ALA* 1.3 59.8 + - - +
1333A LEU* 3.8 12.9 - - + +
1334A TRP* 2.9 27.0 + - - +
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Residues in contact with ALA1331 (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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1327A GLN 2.9 20.1 + - - +
1328A GLN* 3.3 11.4 - - - +
1329A PHE 3.1 0.2 - - - -
1330A VAL* 1.3 75.2 - - - +
1332A LEU* 1.3 62.5 + - + +
1334A TRP* 3.2 10.5 + - - +
1335A LYS* 3.0 26.5 + - - +
2009A PHE* 5.6 4.2 - - - +
2012A LEU* 4.7 23.8 - - + +
2013A LEU* 4.8 7.2 - - + -
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Residues in contact with LEU1332 (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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1328A GLN* 2.9 27.2 + - + +
1329A PHE* 3.6 7.0 - - - +
1331A ALA* 1.3 73.4 - - - +
1333A LEU* 1.3 63.2 + - - +
1335A LYS* 3.1 11.2 + - + +
1336A ARG* 3.0 26.3 + - - +
1688A GLN* 3.8 26.7 - - + +
1693A VAL* 5.2 11.9 - - + -
1697A ILE* 5.3 1.6 - - + -
1698A TYR* 3.6 37.5 - - + -
1701A SER* 3.7 26.5 - - - +
2013A LEU* 4.6 9.6 - - + -
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Residues in contact with LEU1333 (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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1329A PHE* 3.0 48.1 + - + +
1330A VAL* 4.0 12.1 - - + +
1332A LEU* 1.3 76.2 - - - +
1334A TRP* 1.3 57.8 + - - +
1336A ARG* 3.4 5.0 + - + +
1337A LEU* 2.9 35.8 + - + +
1701A SER* 3.3 32.5 - - - +
1704A VAL* 4.8 7.9 - - + -
1705A TRP* 4.0 29.3 - - + +
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Residues in contact with TRP1334 (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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1330A VAL 2.9 20.7 + - - +
1331A ALA* 3.2 10.1 - - - +
1332A LEU 3.2 0.2 - - - -
1333A LEU* 1.3 75.4 - - - +
1335A LYS* 1.3 60.2 + - - +
1337A LEU* 3.1 23.4 + - + +
1338A LEU* 2.9 67.6 + - + +
1341A ARG* 5.6 3.8 - - - -
2005A GLU* 5.5 2.0 - - - +
2009A PHE* 5.6 7.2 - - + -
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Residues in contact with LYS1335 (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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1331A ALA 3.0 12.2 + - - +
1332A LEU* 3.1 12.5 + - + +
1334A TRP* 1.3 76.5 - - - +
1336A ARG* 1.3 61.9 + - - +
1338A LEU* 3.1 15.9 + - + +
1339A ILE* 3.0 35.5 + - - +
1675A PHE* 4.4 10.0 - - + -
1679A GLU* 3.4 28.2 + - - +
1683A LYS* 3.8 12.9 - - - +
1998A THR* 4.5 5.4 - - - +
2001A LEU* 3.4 31.5 - - + +
2009A PHE* 5.2 15.5 - - + -
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Residues in contact with ARG1336 (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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1332A LEU 3.0 12.9 + - - +
1333A LEU* 3.7 10.8 - - + +
1334A TRP 3.2 0.4 - - - -
1335A LYS* 1.3 77.3 - - + +
1337A LEU* 1.3 59.5 + - - +
1339A ILE* 3.3 15.0 - - - +
1340A ALA* 2.9 30.5 + - - +
1672A PHE* 5.2 4.4 + - - +
1675A PHE* 3.2 40.6 - - - +
1679A GLU* 5.4 1.0 - - - +
1702A ASN* 2.6 41.9 + - - +
1705A TRP* 3.2 59.4 - - + +
1706A ASP* 3.4 8.3 + - - -
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Residues in contact with LEU1337 (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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1333A LEU* 2.9 22.7 + - + +
1334A TRP* 3.1 30.9 + - + +
1336A ARG* 1.3 74.8 - - - +
1338A LEU* 1.3 59.1 + - + +
1340A ALA* 3.8 4.4 - - + +
1341A ARG* 2.9 36.4 + - - +
1705A TRP* 3.6 30.0 - - + -
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Residues in contact with LEU1338 (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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1334A TRP* 2.9 53.6 + - + +
1335A LYS* 3.3 16.6 - - + +
1337A LEU* 1.3 78.5 - - + +
1339A ILE* 1.3 59.4 + - - +
1341A ARG* 3.7 26.7 - - - +
1342A ARG* 2.9 51.3 + - - +
2001A LEU* 5.5 10.5 - - + +
2002A THR* 5.9 0.9 - - - -
2005A GLU* 3.7 31.4 - - + +
2009A PHE* 5.5 2.2 - - + -
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Residues in contact with ILE1339 (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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1335A LYS* 3.0 23.9 + - - +
1336A ARG* 3.3 32.5 - - - +
1338A LEU* 1.3 76.7 - - - +
1340A ALA* 1.3 58.9 + - - +
1342A ARG* 4.9 2.5 - - + -
1343A SER* 3.1 30.1 + - - -
1675A PHE* 3.8 31.9 - - + -
2000A LEU* 3.3 46.4 - - + +
2001A LEU* 4.0 6.7 - - + +
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Residues in contact with ALA1340 (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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1336A ARG* 2.9 19.9 + - + +
1337A LEU* 3.8 4.9 - - + +
1339A ILE* 1.3 76.7 - - + +
1341A ARG* 1.3 63.7 + - + +
1343A SER* 2.8 24.2 + - - +
1348A PHE* 4.8 11.2 - - - -
1705A TRP* 4.2 22.7 - - + +
1709A ASN* 5.5 4.7 - - - +
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Residues in contact with ARG1341 (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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1334A TRP* 5.6 3.8 - - - -
1337A LEU* 2.9 20.9 + - - +
1338A LEU* 3.7 27.2 - - - +
1340A ALA* 1.3 76.4 - - - +
1342A ARG* 1.3 74.2 + - - +
1343A SER 3.4 1.0 + - - -
1344A ARG* 4.3 14.2 - - - +
1348A PHE* 6.3 0.4 - - - -
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Residues in contact with ARG1342 (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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1338A LEU* 2.9 35.0 + - - +
1339A ILE* 4.3 3.8 - - - +
1341A ARG* 1.3 94.4 - - + +
1343A SER* 1.3 59.1 + - - +
1344A ARG* 3.4 9.1 + - - +
2000A LEU 5.0 6.4 + - - +
2001A LEU 3.3 24.8 + - - +
2002A THR* 4.9 5.1 - - - -
2040A LYS 5.5 0.4 + - - -
2042A ALA* 3.5 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