Contacts of the strand formed by residues 1061 - 1067 (chain B) in PDB entry 3PT6
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 GLY1061 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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935B VAL* 5.9 3.1 - - - -
937B TYR* 3.5 16.6 - - - -
943B VAL* 3.7 2.9 - - - -
944B TYR* 2.9 35.3 + - - +
1059B VAL* 3.5 4.0 - - - +
1060B GLN* 1.3 81.0 - - - +
1062B ARG* 1.3 63.4 + - - -
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Residues in contact with ARG1062 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935B VAL* 3.8 29.5 - - + +
936B VAL* 3.4 30.6 + - - +
937B TYR* 3.7 18.1 + - + -
941B ASP* 4.1 23.7 + - + -
942B SER 3.5 13.5 - - - +
944B TYR* 3.7 10.0 - - - -
1061B GLY* 1.3 75.4 - - - -
1063B CYS* 1.3 83.5 + - - +
1064B THR* 5.0 5.8 - - - -
1084B ASP* 4.3 8.7 - - - +
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Residues in contact with CYS1063 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941B ASP* 5.3 0.9 - - - +
942B SER* 3.1 48.0 + - - +
943B VAL 4.5 1.1 - - - -
944B TYR* 3.6 35.4 - - + +
997B ILE* 3.9 15.3 - - - -
1062B ARG* 1.3 86.9 - - - +
1064B THR* 1.3 64.1 + - - +
1065B VAL* 3.9 14.4 - - - -
1084B ASP* 4.1 10.5 - - + +
1086B PHE* 4.2 6.3 - - + -
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Residues in contact with THR1064 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1062B ARG* 5.0 6.1 - - - -
1063B CYS* 1.3 76.7 + - - +
1065B VAL* 1.3 66.5 + - - +
1066B GLU* 3.9 21.3 - - + +
1078B TYR* 3.5 21.1 - - + +
1084B ASP 3.1 13.3 + - - -
1085B ARG* 3.5 7.7 - - + +
1086B PHE* 2.8 27.7 + - - +
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Residues in contact with VAL1065 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942B SER* 3.5 15.7 - - - +
997B ILE* 4.2 3.8 - - + -
999B ARG* 4.3 17.0 + - - -
1024B PHE* 3.4 34.3 - - + -
1045B LEU* 3.9 14.6 - - + -
1063B CYS* 3.9 19.1 + - - -
1064B THR* 1.3 79.0 - - - +
1066B GLU* 1.3 70.5 + - - +
1086B PHE* 3.1 24.7 - - + +
1087B TYR 4.8 0.2 - - - +
1088B PHE* 4.5 8.8 - - + -
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Residues in contact with GLU1066 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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999B ARG* 5.7 2.4 + - - -
1064B THR* 3.9 14.7 - - + +
1065B VAL* 1.3 82.1 - - - +
1067B TYR* 1.3 68.6 + - - +
1070B ASP* 5.3 2.8 - - - +
1071B LEU* 3.9 23.9 - - + +
1078B TYR* 3.6 26.5 - - + +
1086B PHE 3.0 6.3 + - - -
1087B TYR* 3.1 7.7 - - - +
1088B PHE* 3.0 28.7 + - - -
1108B SER* 4.5 18.0 - - - -
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Residues in contact with TYR1067 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066B GLU* 1.3 75.9 + - - +
1068B GLY* 1.3 68.0 + - - +
1069B GLU* 3.4 34.3 - - + +
1070B ASP* 3.1 40.9 + - + +
1071B LEU* 3.5 7.9 + - - +
1088B PHE* 3.4 41.0 - + + -
1089B LEU* 3.3 24.1 + - - -
1101B ASP* 5.1 2.6 - - - +
1102B PRO* 3.6 16.9 - - + +
1106B ALA 4.8 3.6 - - - +
1107B ARG* 3.4 56.9 + - + -
1108B SER 5.4 1.6 - - - +
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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