Contacts of the strand formed by residues 1061 - 1067 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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937A TYR* 3.4 16.6 - - - -
943A VAL* 3.6 3.5 - - - -
944A TYR* 2.8 35.6 + - - +
1059A VAL* 3.6 5.2 - - - +
1060A GLN* 1.3 80.7 - - - +
1062A ARG* 1.3 61.7 + - - -
1359A ARG* 6.0 1.1 - - - -
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Residues in contact with ARG1062 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935A VAL* 4.7 10.2 - - + +
936A VAL* 3.1 43.1 + - - +
937A TYR* 3.5 23.9 + - + -
938A ARG* 5.9 3.7 - - - +
941A ASP* 4.0 21.9 + - + -
942A SER 3.3 17.9 - - - +
944A TYR* 3.9 9.0 - - - -
1061A GLY* 1.3 74.7 - - - -
1063A CYS* 1.3 73.8 + - - +
1064A THR* 5.4 4.2 + - - -
1084A ASP* 4.2 9.5 - - - +
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Residues in contact with CYS1063 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941A ASP* 5.3 0.9 - - - +
942A SER* 3.1 48.0 + - - +
943A VAL 4.2 1.1 - - - -
944A TYR* 3.5 38.8 - - + +
997A ILE* 3.9 17.3 - - - -
1061A GLY 4.0 0.2 + - - -
1062A ARG* 1.3 84.4 - - - +
1064A THR* 1.3 64.1 + - - +
1065A VAL* 4.2 7.2 - - - -
1084A ASP* 3.3 17.7 - - + +
1086A PHE* 4.4 3.4 - - + -
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Residues in contact with THR1064 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1062A ARG* 5.4 4.5 + - - -
1063A CYS* 1.3 78.0 + - - +
1065A VAL* 1.3 62.4 + - - +
1066A GLU* 3.6 22.0 - - + +
1078A TYR* 3.2 22.7 - - + +
1083A PRO 5.5 1.2 + - - -
1084A ASP* 3.0 10.3 + - - +
1085A ARG* 4.5 9.0 - - + +
1086A PHE* 2.7 33.3 + - - +
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Residues in contact with VAL1065 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942A SER* 3.8 27.5 + - - +
997A ILE* 4.2 10.1 - - + -
999A ARG* 4.5 15.0 + - - +
1024A PHE* 3.4 29.8 - - + -
1045A LEU* 4.0 17.0 - - + -
1063A CYS* 4.1 4.6 + - - -
1064A THR* 1.3 80.5 - - - +
1066A GLU* 1.3 72.3 + - - +
1086A PHE* 3.5 24.0 - - + +
1087A TYR* 4.5 1.3 - - - -
1088A PHE* 3.5 19.6 - - + -
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Residues in contact with GLU1066 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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999A ARG* 5.6 1.7 + - - -
1064A THR* 3.6 16.8 - - + +
1065A VAL* 1.3 90.0 + - - +
1067A TYR* 1.3 72.1 + - - +
1068A GLY 3.3 0.2 + - - -
1070A ASP* 4.8 9.9 - - + +
1071A LEU* 5.5 7.6 - - + +
1078A TYR* 3.5 33.2 - - + +
1086A PHE 3.3 6.3 + - - -
1087A TYR* 3.2 7.4 - - + +
1088A PHE* 3.2 23.6 + - - -
1108A SER* 5.2 4.9 + - - -
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Residues in contact with TYR1067 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066A GLU* 1.3 74.2 + - - +
1068A GLY* 1.3 76.3 + - - +
1069A GLU* 3.3 35.0 - - + +
1070A ASP* 3.2 44.2 + - + +
1071A LEU* 3.5 7.4 + - - +
1088A PHE* 3.2 39.2 - + + -
1089A LEU* 3.6 12.8 + - - -
1101A ASP* 5.0 3.6 - - - +
1102A PRO* 3.3 31.2 + - + +
1106A ALA 5.1 0.8 + - - +
1107A ARG* 4.4 27.8 - - + -
1114A LYS* 3.9 19.2 + - - -
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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