Contacts of the helix formed by residues 1327 - 1338 (chain J) in PDB entry 6PSS
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 GLU1327 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339J ARG* 4.7 4.7 - - - +
1314J LEU* 5.5 0.5 - - - +
1326J GLN* 1.3 75.9 - - - +
1328J THR* 1.3 64.8 + - - +
1329J THR* 3.4 5.6 - - + +
1330J ARG* 2.6 51.9 + - + +
1331J VAL* 3.2 23.6 + - - +
71L THR* 4.0 21.1 + - - +
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Residues in contact with THR1328 (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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331J ILE* 4.0 11.4 + - + -
332J LYS* 3.9 24.5 - - - +
338J PHE* 3.7 32.1 - - + -
339J ARG* 3.8 12.7 + - - +
1323J ALA* 3.1 22.9 + - + -
1326J GLN 4.2 0.4 - - - -
1327J GLU* 1.3 73.0 - - - +
1329J THR* 1.3 52.8 + - - +
1331J VAL* 3.6 4.2 - - - +
1332J LEU* 2.6 52.6 + - + +
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Residues in contact with THR1329 (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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115J TRP* 3.4 42.0 - - + +
308J ASP* 4.0 7.9 - - - +
311J ARG* 2.5 33.9 + - - +
328J ALA* 4.3 1.1 - - + -
331J ILE* 6.0 0.4 - - + -
332J LYS* 3.7 32.8 - - + +
1327J GLU* 3.4 4.2 - - + +
1328J THR* 1.3 76.7 - - - +
1330J ARG* 1.3 53.0 + - - +
1332J LEU* 4.4 0.2 - - - +
1333J THR* 2.3 42.1 + - - +
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Residues in contact with ARG1330 (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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119J SER* 4.7 8.3 - - - +
121J PRO* 5.1 9.6 - - + -
123J ARG* 3.8 12.7 + - - +
311J ARG* 4.8 5.6 - - - +
1314J LEU* 3.9 7.5 - - - +
1326J GLN* 2.8 37.0 + - - +
1327J GLU* 2.6 52.2 + - + +
1329J THR* 1.3 83.7 + - - +
1331J VAL* 1.3 65.6 + - - +
1333J THR* 3.5 5.6 + - - -
1334J GLU* 3.3 34.3 + - - +
72L ALA* 3.6 31.7 - - - +
76L ALA* 5.7 8.1 - - - -
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Residues in contact with VAL1331 (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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1319J PHE* 3.8 29.2 - - + +
1322J ALA* 3.9 21.5 - - + +
1323J ALA* 3.8 15.7 - - + +
1326J GLN* 3.7 25.4 - - + +
1327J GLU 3.2 19.5 + - - +
1328J THR* 3.6 4.7 - - - +
1329J THR 3.2 0.2 - - - -
1330J ARG* 1.3 83.3 - - - +
1332J LEU* 1.3 61.2 + - + +
1334J GLU* 3.2 8.6 + - - +
1335J ALA* 2.8 27.5 + - - +
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Residues in contact with LEU1332 (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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1330I ILE* 3.7 35.2 - - + -
1335I ILE* 5.0 0.4 - - + +
22J ILE* 3.7 15.1 - - + +
115J TRP* 3.6 31.7 - - + -
331J ILE* 3.8 6.3 - - + -
338J PHE* 4.6 3.1 - - + -
1319J PHE* 3.7 33.4 - - + +
1323J ALA* 4.8 2.9 - - + -
1328J THR* 2.6 39.4 + - + +
1331J VAL* 1.3 76.3 - - + +
1333J THR* 1.3 60.7 + - - +
1335J ALA* 4.2 1.1 - - - -
1336J ALA* 2.9 29.3 + - - +
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Residues in contact with THR1333 (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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115J TRP* 3.4 52.0 - - + +
116J PHE* 3.7 17.5 - - + -
119J SER* 4.3 3.5 + - - -
123J ARG* 3.6 20.1 + - - -
1329J THR 2.3 34.5 + - - +
1330J ARG* 3.5 7.8 + - - -
1332J LEU* 1.3 75.0 - - - +
1334J GLU* 1.3 63.5 + - - +
1336J ALA* 4.6 0.2 - - - -
1337J VAL* 3.3 31.2 + - - +
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Residues in contact with GLU1334 (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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123J ARG* 4.0 20.5 - - - +
1330J ARG* 3.3 31.9 + - - +
1331J VAL* 3.2 7.7 + - - +
1333J THR* 1.3 79.7 - - - +
1335J ALA* 1.3 60.8 + - - +
1337J VAL* 3.9 6.0 - - + +
1338J ALA* 3.7 20.1 + - - +
1340J LYS* 4.0 12.9 - - - +
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Residues in contact with ALA1335 (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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22J ILE* 3.3 13.4 - - + +
1319J PHE* 3.7 40.8 - - + -
1331J VAL 2.8 17.5 + - - +
1332J LEU* 3.9 1.3 - - - +
1333J THR 3.2 0.2 - - - -
1334J GLU* 1.3 78.7 - - - +
1336J ALA* 1.3 64.0 + - - +
1338J ALA 3.5 2.9 + - - -
1340J LYS* 3.2 39.0 + - - +
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Residues in contact with ALA1336 (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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1335I ILE* 3.7 19.5 - - + -
22J ILE* 3.7 12.5 - - + +
23J ALA* 3.4 25.2 - - - +
24J LEU* 3.5 10.3 - - + +
116J PHE* 4.4 3.4 - - + -
232J ASN* 3.2 10.4 + - - -
1332J LEU 2.9 19.3 + - - +
1333J THR 3.5 3.1 + - - +
1335J ALA* 1.3 76.6 - - - +
1337J VAL* 1.3 57.0 + - - +
1339J GLY* 2.9 18.7 + - - -
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Residues in contact with VAL1337 (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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24J LEU* 3.8 11.7 - - + -
116J PHE* 3.6 28.0 - - + -
123J ARG* 4.1 22.2 - - + +
223J LEU* 4.2 22.7 - - + +
226J ALA* 4.7 2.1 - - - +
227J PHE* 4.2 31.9 - - + -
230J SER* 3.8 6.8 + - - -
232J ASN* 3.6 8.6 + - - +
237J MET* 4.8 2.7 - - + -
1333J THR 3.3 19.3 + - - +
1334J GLU* 3.9 10.8 - - + +
1336J ALA* 1.3 74.2 - - - +
1338J ALA* 1.3 62.3 + - + +
1339J GLY 3.6 0.2 + - - -
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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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223J LEU* 6.2 0.7 - - + -
226J ALA* 4.4 17.9 - - + +
229J GLN* 5.4 3.1 + - - +
230J SER* 3.3 16.7 - - - -
1334J GLU 3.7 15.0 + - - +
1335J ALA 3.5 5.5 + - - +
1336J ALA 3.1 1.0 - - - -
1337J VAL* 1.3 81.0 - - + +
1339J GLY* 1.3 61.5 + - - +
1340J LYS* 3.4 19.4 + - + +
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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