Contacts of the strand formed by residues 1011 - 1025 (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 LYS1011 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1007A LYS* 3.1 8.5 - - - +
1008A LYS 2.7 38.9 + - - +
1009A LYS* 3.0 6.3 - - + +
1010A GLY* 1.3 80.2 - - - +
1012A VAL* 1.3 65.9 + - - +
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Residues in contact with VAL1012 (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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914A VAL* 4.7 18.6 - - + -
917A GLN* 3.1 33.7 - - - +
925A VAL* 4.0 20.2 - - + -
927A CYS* 5.5 2.0 - - - -
1005A CYS* 3.8 25.4 - - + -
1006A GLY 3.7 5.6 - - - +
1007A LYS* 4.4 1.6 - - - +
1008A LYS 5.2 0.4 - - - +
1011A LYS* 1.3 78.9 - - - +
1013A ASN* 1.3 62.2 + - - +
1014A GLU* 3.5 12.2 + - + +
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Residues in contact with ASN1013 (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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1005A CYS* 3.7 7.8 - - - +
1006A GLY 2.8 25.7 + - - +
1007A LYS 3.9 13.8 - - - +
1008A LYS* 4.0 15.2 - - + +
1011A LYS 3.4 1.0 + - - -
1012A VAL* 1.3 71.6 - - - +
1014A GLU* 1.3 58.4 + - - +
1015A ALA* 3.1 23.2 - - - +
1016A ASP* 3.0 46.1 + - - +
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Residues in contact with GLU1014 (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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911A MET* 4.9 10.6 - - + +
912A PRO* 3.6 31.4 - - - +
913A LYS* 3.6 16.9 - - - +
914A VAL* 3.3 40.5 + - + +
1012A VAL* 3.5 13.9 + - + +
1013A ASN* 1.3 69.2 - - - +
1015A ALA* 1.3 57.2 + - - +
1016A ASP 3.0 8.5 + - - -
1017A ILE* 3.3 27.9 + - + +
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Residues in contact with ALA1015 (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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912A PRO* 5.5 5.4 - - - -
1013A ASN* 3.1 17.2 - - - +
1014A GLU* 1.3 77.1 - - - +
1016A ASP* 1.3 59.1 + - - +
1017A ILE 3.8 1.6 - - - -
1055A ASN* 4.9 6.5 - - - +
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Residues in contact with ASP1016 (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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924A ARG* 2.9 32.2 + - - -
1005A CYS* 3.2 2.4 - - - -
1006A GLY* 3.0 25.6 + - - +
1013A ASN* 3.0 30.4 + - + +
1015A ALA* 1.3 79.7 - - - +
1017A ILE* 1.3 59.2 + - - +
1018A LYS* 3.9 15.2 - - - +
1055A ASN* 4.6 5.4 + - - -
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Residues in contact with ILE1017 (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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912A PRO* 4.4 2.5 - - + -
913A LYS 3.9 21.1 - - - +
914A VAL* 5.0 3.4 - - + -
927A CYS* 6.3 0.7 - - - -
930A ILE* 3.7 20.6 - - + -
1003A ILE* 3.5 30.3 - - + -
1004A HIS 3.9 5.6 - - - +
1005A CYS* 4.0 13.9 - - + +
1014A GLU* 3.3 28.0 + - + +
1015A ALA 3.8 1.4 - - - -
1016A ASP* 1.3 75.9 - - - +
1018A LYS* 1.3 67.7 + - - +
1019A LEU* 4.8 0.2 - - + -
1055A ASN* 3.7 6.5 + - - +
1056A PHE* 3.0 50.9 + - + +
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Residues in contact with LYS1018 (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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924A ARG* 4.0 21.0 - - - +
1002A GLU 3.8 0.3 - - - +
1003A ILE* 3.5 1.6 - - - +
1004A HIS* 3.1 50.8 + - - +
1016A ASP* 3.9 14.8 + - - +
1017A ILE* 1.3 80.0 - - - +
1019A LEU* 1.3 71.0 + - - +
1020A ARG 4.3 0.2 - - - -
1053A VAL* 4.0 16.2 - - + -
1054A VAL 3.3 11.2 - - - +
1055A ASN* 3.5 23.8 - - - +
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Residues in contact with LEU1019 (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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930A ILE* 4.4 6.3 - - + -
937A TYR* 6.0 1.3 - - + -
943A VAL* 4.6 5.8 - - + -
1000A ILE* 3.7 24.5 - - + -
1002A GLU 3.9 1.6 - - - +
1003A ILE* 3.4 37.9 - - + -
1017A ILE* 4.8 0.2 - - + -
1018A LYS* 1.3 85.6 - - - +
1020A ARG* 1.3 59.5 - - - +
1021A LEU* 3.6 20.4 + - + +
1052A ALA 3.3 2.6 - - - +
1053A VAL* 3.1 9.9 - - - -
1054A VAL* 2.8 42.3 + - + +
1056A PHE* 4.2 15.7 - - + -
1059A VAL* 4.0 27.8 - - + -
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Residues in contact with ARG1020 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1000A ILE* 3.6 1.4 - - - -
1001A LYS* 2.6 56.4 + - + +
1002A GLU* 2.8 43.6 + - + +
1004A HIS* 5.0 12.7 - - + -
1018A LYS 4.3 0.2 - - - -
1019A LEU* 1.3 69.9 - - - +
1021A LEU* 1.3 55.4 + - - +
1051A GLU* 3.6 35.4 + - - +
1052A ALA* 3.7 4.8 - - - +
1053A VAL* 3.3 31.7 - - - +
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Residues in contact with LEU1021 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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943A VAL* 4.9 5.4 - - + -
945A LEU* 3.4 33.0 - - + -
950A PHE* 4.7 10.8 - - + -
998A GLY* 4.6 9.6 - - - +
999A ARG 3.2 8.3 - - - +
1000A ILE* 3.4 42.2 - - + +
1001A LYS* 4.7 0.9 - - - -
1019A LEU* 3.7 20.9 - - + +
1020A ARG* 1.3 75.2 - - - +
1022A TYR* 1.3 67.0 + - - +
1023A LYS* 3.6 1.2 + - + +
1051A GLU* 3.1 12.1 - - - +
1052A ALA* 2.9 34.5 + - + +
1054A VAL* 3.9 19.5 - - + -
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Residues in contact with TYR1022 (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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998A GLY* 3.2 4.9 - - - -
999A ARG* 2.8 45.3 + - + +
1001A LYS* 3.0 49.6 + - + +
1021A LEU* 1.3 71.9 - - - +
1023A LYS* 1.3 65.6 + - - +
1024A PHE* 4.1 2.6 - - - -
1047A TRP* 3.7 36.3 - + + -
1048A SER 4.2 7.9 - - - +
1049A ASP* 3.8 24.2 - - - -
1050A GLU 3.8 2.2 - - - -
1051A GLU* 3.7 24.7 - - + -
1105A HIS* 3.6 22.5 + + - -
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Residues in contact with LYS1023 (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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950A PHE* 3.5 36.6 - - + -
951A THR 2.6 30.8 + - - +
952A PHE* 4.4 10.5 - - + -
953A ASN* 3.4 34.4 + - - +
997A ILE 4.3 0.2 - - - -
998A GLY* 4.7 0.7 - - - -
1021A LEU* 3.6 2.9 + - + +
1022A TYR* 1.3 75.3 - - - +
1024A PHE* 1.3 60.8 + - - +
1047A TRP* 5.5 0.3 - - - -
1048A SER* 2.5 35.8 + - - +
1050A GLU* 2.7 40.2 + - + +
1051A GLU 4.0 17.9 - - - -
1052A ALA* 4.1 8.7 - - + -
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Residues in contact with PHE1024 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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942A SER* 4.0 10.3 - - - -
950A PHE* 4.7 0.9 - - - -
952A PHE* 3.7 18.0 - - - -
996A ARG* 5.8 0.2 - - - -
997A ILE* 3.0 35.3 + - + +
998A GLY* 3.8 20.0 - - - -
999A ARG* 4.0 21.3 - - + -
1022A TYR 4.1 2.0 - - - -
1023A LYS* 1.3 73.9 - - - +
1025A TYR* 1.3 62.1 + - - +
1026A ARG* 3.7 2.8 + - - +
1045A LEU* 4.0 23.5 - - + +
1046A TYR 3.6 15.9 - - - -
1047A TRP* 3.7 41.1 - + - -
1065A VAL* 3.4 27.1 - - + -
1088A PHE* 3.9 18.8 - + + -
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Residues in contact with TYR1025 (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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952A PHE* 3.3 34.9 - + + +
954A ILE* 3.4 23.1 + - + +
1023A LYS* 5.5 0.4 - - + -
1024A PHE* 1.3 72.3 - - - +
1026A ARG* 1.3 63.0 + - - +
1029A ASN* 3.5 36.6 - - + -
1030A THR* 3.9 6.7 - - + -
1045A LEU* 3.6 5.3 - - - +
1046A TYR* 2.8 54.6 + - + +
1048A SER* 3.7 22.7 - - - -
1050A GLU* 2.8 41.2 + - - -
1092A TYR* 3.9 30.3 - + + -
1094A SER* 3.5 0.6 - - - -
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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