Contacts of the strand formed by residues 942 - 945 (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 SER 942 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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937B TYR* 4.7 2.2 - - - -
941B ASP* 1.3 75.8 - - - +
943B VAL* 1.3 61.5 + - - +
997B ILE* 4.6 1.3 - - - -
998B GLY 3.2 15.7 + - - -
999B ARG* 3.4 14.4 - - - -
1000B ILE* 5.1 1.1 - - - -
1024B PHE* 3.6 2.4 - - - -
1062B ARG* 3.5 9.5 - - - +
1063B CYS* 3.1 51.0 + - - +
1065B VAL* 3.5 29.1 - - - +
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Residues in contact with VAL 943 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937B TYR* 4.7 6.7 - - + -
942B SER* 1.3 76.0 - - - +
944B TYR* 1.3 65.1 + - - +
945B LEU* 3.9 8.4 + - + +
996B ARG 3.8 0.2 - - - +
997B ILE* 3.6 9.0 - - - +
998B GLY 3.0 29.2 + - - +
1000B ILE* 4.5 15.7 - - + +
1019B LEU* 5.1 2.5 - - + -
1021B LEU* 5.1 4.0 - - + -
1059B VAL* 4.0 27.1 - - + -
1061B GLY 3.7 4.7 - - - +
1062B ARG* 4.8 0.2 - - - +
1063B CYS* 4.7 2.9 - - - -
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Residues in contact with TYR 944 (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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943B VAL* 1.3 72.4 - - - +
945B LEU* 1.3 66.8 + - - +
995B TYR* 3.2 36.3 - + + -
996B ARG 3.8 0.9 - - - -
997B ILE* 4.1 12.8 - - + -
1059B VAL* 3.6 2.8 - - - +
1060B GLN* 3.0 25.5 + - + -
1061B GLY* 2.9 27.9 + - - +
1062B ARG 3.7 22.4 - - - -
1063B CYS* 3.6 16.8 - - + -
1084B ASP* 2.9 29.8 + - - +
1086B PHE* 3.2 33.9 - + - -
1359B ARG* 4.0 15.0 - - - -
1364B PRO* 3.4 18.1 - - + +
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Residues in contact with LEU 945 (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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943B VAL* 4.6 10.5 - - + +
944B TYR* 1.3 82.1 - - - +
946B PRO* 1.3 69.5 - - + +
949B ALA* 3.6 18.8 - - + -
950B PHE* 4.2 10.5 - - + -
995B TYR* 3.2 13.1 - - - +
996B ARG* 2.6 44.6 + - + +
998B GLY 5.3 1.3 - - - +
1019B LEU* 6.1 0.4 - - + -
1021B LEU* 3.3 34.5 - - + -
1054B VAL* 4.0 19.3 - - + -
1055B ASN 4.9 1.3 - - - +
1058B ASP* 3.8 21.1 - - + +
1059B VAL* 3.9 15.7 - - + +
1060B GLN* 4.3 0.2 - - - -
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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