Contacts of the helix formed by residues 1331 - 1339 (chain J) in PDB entry 4XLN
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 ASP1331 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1265J ALA 5.4 0.2 - - - +
1266J ARG 4.8 0.3 - - - -
1267J ARG* 3.5 34.8 + - - +
1268J PRO* 3.7 7.3 - - + +
1271J LYS* 3.9 27.5 - - + +
1329J ALA 4.3 0.2 + - - -
1330J ILE* 1.3 73.3 - - - +
1332J PRO* 1.3 71.2 - - - +
1333J HIS* 3.2 16.8 + - - +
1334J GLN* 3.0 47.6 + - - +
1335J LEU* 3.2 11.2 - - - +
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Residues in contact with PRO1332 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1261J GLU 5.5 1.8 - - - +
1262J LEU* 5.5 6.3 - - + +
1265J ALA* 4.3 23.8 - - + +
1266J ARG 4.1 15.0 - - - +
1268J PRO* 4.3 2.2 - - + -
1330J ILE 3.2 8.7 - - - +
1331J ASP* 1.3 87.8 - - - +
1333J HIS* 1.3 60.5 + - - +
1335J LEU* 3.4 16.8 + - + +
1336J LEU* 2.9 26.7 + - - +
1344J VAL* 4.0 1.4 - - + +
1347J TYR* 5.3 3.1 - - + -
1348J LEU* 4.1 20.4 - - + -
1421J LEU* 3.5 25.8 - - + +
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Residues in contact with HIS1333 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1265J ALA* 3.5 38.3 + - + -
1331J ASP* 3.2 11.8 + - - +
1332J PRO* 1.3 75.4 - - - +
1334J GLN* 1.3 59.9 + - - +
1336J LEU* 3.1 13.2 + - + +
1337J GLU* 2.9 37.5 + - - +
1420J LEU* 5.0 8.3 - - + -
1421J LEU* 2.4 41.5 + - + -
1422J MET* 4.3 2.3 - - - +
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Residues in contact with GLN1334 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1271J LYS* 3.7 26.4 - - - +
1272J ALA 3.7 18.9 - - - +
1273J VAL* 4.7 3.4 - - - +
1274J ILE* 3.6 25.3 + - + +
1331J ASP* 3.0 32.6 + - - +
1333J HIS* 1.3 76.7 - - - +
1335J LEU* 1.3 57.5 + - - +
1337J GLU* 3.2 9.9 + - - +
1338J ALA* 2.9 26.5 + - - +
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Residues in contact with LEU1335 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1274J ILE* 3.5 10.5 - - + +
1322J GLY* 5.1 7.9 - - - +
1330J ILE* 3.7 22.4 - - + +
1331J ASP 3.2 25.8 + - - +
1332J PRO* 3.5 18.8 - - + +
1334J GLN* 1.3 75.8 - - - +
1336J LEU* 1.3 60.4 + - - +
1337J GLU 3.2 0.2 - - - -
1338J ALA* 3.5 9.9 - - + -
1339J LYS* 3.0 27.7 + - + +
1340J GLY 3.3 10.6 + - - +
1343J ALA* 3.9 13.0 - - + +
1344J VAL* 3.6 35.0 - - + +
1346J ARG* 5.7 0.2 - - - +
1347J TYR* 4.2 18.8 - - + -
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Residues in contact with LEU1336 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1332J PRO 2.9 14.5 + - - +
1333J HIS* 3.1 19.7 + - + +
1335J LEU* 1.3 80.3 - - - +
1337J GLU* 1.3 64.6 + - + +
1338J ALA 3.6 0.3 + - - -
1340J GLY* 4.0 13.1 - - - -
1341J PRO* 4.2 14.4 - - + +
1344J VAL* 3.5 21.5 - - + -
1376J LEU* 5.2 5.8 - - + -
1419J PRO* 3.3 48.3 - - + +
1420J LEU* 4.0 2.5 - - + -
1421J LEU* 3.4 37.2 - - + +
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Residues in contact with GLU1337 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1276J GLU 5.5 0.5 - - - +
1333J HIS* 2.9 21.8 + - - +
1334J GLN* 3.5 6.9 - - - +
1336J LEU* 1.3 84.4 - - + +
1338J ALA* 1.3 60.3 + - - +
1418J LYS* 4.3 24.1 + - - -
1419J PRO 5.7 2.0 - - - +
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Residues in contact with ALA1338 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1274J ILE* 4.2 6.1 - - + -
1275J SER 4.4 5.6 - - - +
1276J GLU* 4.6 14.8 - - + +
1321J ALA* 3.9 13.7 - - - +
1322J GLY* 3.7 26.0 - - - +
1334J GLN 2.9 16.6 + - - +
1335J LEU* 3.4 4.9 + - - -
1336J LEU 3.3 0.6 - - - -
1337J GLU* 1.3 81.1 - - - +
1339J LYS* 1.3 68.1 + - - +
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Residues in contact with LYS1339 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1320J GLU* 4.1 16.1 + - - -
1321J ALA* 3.2 30.3 - - + +
1322J GLY* 3.6 22.8 + - - +
1323J GLN* 4.1 4.6 - - - +
1324J PRO* 5.8 1.6 - - - +
1335J LEU* 3.0 14.3 + - + +
1336J LEU 4.8 0.4 - - - -
1338J ALA* 1.3 80.5 - - - +
1340J GLY* 1.3 59.5 + - - +
1343J ALA* 3.6 26.7 - - + -
1346J ARG* 3.6 21.6 - - - +
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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