Contacts of the strand formed by residues 1352 - 1357 (chain D) in PDB entry 6CET
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 ARG1352 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1251D PHE 3.2 19.0 + - - -
1252D ILE* 3.4 25.5 - - - +
1253D TYR* 5.2 1.6 - - - +
1258D TYR* 5.4 10.5 - - + -
1348D VAL* 4.9 15.4 - - - +
1349D PRO* 5.3 11.2 - - + +
1351D GLN* 1.3 77.7 + - - +
1353D THR* 1.3 70.3 + - - +
1354D VAL* 5.3 2.2 - - + -
1372D CYS 3.5 0.5 - - - +
1373D TYR* 3.5 1.4 - - - -
1374D TYR* 3.0 79.6 + - + +
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Residues in contact with THR1353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1258D TYR* 2.5 36.2 + - - -
1283D VAL* 5.7 4.2 - - - +
1351D GLN* 3.9 13.9 - - + +
1352D ARG* 1.3 80.3 - - - +
1354D VAL* 1.3 56.7 + - - +
1355D THR* 4.1 6.9 + - - +
1371D SER* 5.9 0.4 - - - -
1372D CYS 3.2 4.9 - - - -
1373D TYR* 3.6 32.1 - - + -
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Residues in contact with VAL1354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1253D TYR* 3.8 23.1 - - + -
1254D GLY 4.9 8.1 - - - +
1255D PHE* 4.0 18.4 - - + -
1258D TYR* 3.5 6.5 - - + +
1352D ARG* 5.3 2.7 - - + -
1353D THR* 1.3 75.8 - - - +
1355D THR* 1.3 61.6 + - - +
1356D LEU* 3.2 26.2 + - + +
1370D CYS 3.1 3.8 - - - +
1371D SER* 4.4 0.4 - - - -
1372D CYS* 2.9 47.6 + - + +
1374D TYR* 3.8 29.6 - - + -
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Residues in contact with THR1355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796D GLN* 3.4 29.5 + - + +
1255D PHE* 3.1 29.0 - - - -
1258D TYR* 4.2 5.8 + - + +
1283D VAL* 5.9 5.8 - - + -
1353D THR* 4.2 8.0 + - - +
1354D VAL* 1.3 73.7 - - - +
1356D LEU* 1.3 63.9 + - - +
1357D ASP* 3.5 1.4 + - - +
1369D TRP* 4.5 16.1 - - + +
1370D CYS 3.4 8.7 - - - -
1371D SER* 4.6 13.7 - - - -
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Residues in contact with LEU1356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087D ARG* 3.8 16.6 - - - +
1088D LYS* 4.7 22.0 - - + -
1089D ASP* 5.3 18.2 - - + +
1255D PHE* 4.6 8.7 - - + -
1354D VAL* 3.2 23.1 + - + +
1355D THR* 1.3 73.6 - - - +
1357D ASP* 1.3 89.4 + - - +
1358D VAL* 3.4 20.5 + - + +
1369D TRP* 3.0 5.4 - - - -
1370D CYS* 2.9 39.8 + - - +
1372D CYS* 5.0 5.8 - - - -
1401D MET* 5.3 5.4 - - + -
1405D TRP* 5.5 5.4 - - + -
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Residues in contact with ASP1357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087D ARG* 2.8 28.9 + - - -
1255D PHE* 5.1 4.0 - - + -
1355D THR 3.5 3.9 + - - +
1356D LEU* 1.3 74.2 - - - +
1358D VAL* 1.3 52.7 + - - +
1359D ASP* 3.2 14.0 + - - +
1367D LEU* 3.8 25.5 - - - +
1368D GLU* 3.5 19.0 + - - +
1369D TRP* 4.3 4.8 - - + +
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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