Contacts of the strand formed by residues 1044 - 1055 (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 MET1044 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1027A PRO* 3.1 33.5 - - - +
1040A THR* 4.3 10.8 - - + -
1041A ASP* 3.0 29.2 + - + +
1042A ILE 3.4 2.5 - - - +
1043A ASN* 1.3 79.6 + - - +
1045A LEU* 1.3 71.0 + - - +
1046A TYR* 4.5 28.9 - - - +
1087A TYR* 3.3 50.3 - - + +
1088A PHE* 4.9 0.9 - - - -
1089A LEU* 5.1 11.7 - - + +
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Residues in contact with LEU1045 (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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997A ILE* 3.8 31.2 - - + -
1024A PHE* 4.0 22.7 - - + -
1025A TYR 3.6 15.5 - - - +
1026A ARG* 3.7 25.8 - - + -
1027A PRO* 4.6 0.2 - - - -
1042A ILE 5.9 0.9 - - - +
1044A MET* 1.3 85.4 - - - +
1046A TYR* 1.3 70.3 + - - +
1065A VAL* 4.0 14.8 - - + -
1086A PHE* 3.8 30.3 - - + -
1087A TYR 2.6 14.5 + - - +
1088A PHE* 2.9 26.2 - - + +
1089A LEU 4.0 0.9 + - - -
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Residues in contact with TYR1046 (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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1024A PHE* 3.6 5.0 - - - -
1025A TYR* 2.8 51.9 + - + +
1027A PRO* 4.2 29.4 - - + -
1030A THR* 3.9 14.6 - - + -
1040A THR* 6.0 2.0 - - + +
1044A MET* 4.5 20.5 - - - +
1045A LEU* 1.3 77.6 - - - +
1047A TRP* 1.3 62.3 + - - +
1089A LEU* 5.5 1.6 - - + -
1090A GLU* 3.7 41.4 + - + -
1092A TYR* 4.4 9.6 - - + -
1099A PHE* 3.2 41.1 - + - -
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Residues in contact with TRP1047 (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* 3.1 34.3 - - + -
1022A TYR* 3.7 43.7 - + + -
1023A LYS 5.5 0.4 - - - -
1024A PHE* 3.7 33.9 - + + -
1045A LEU 4.1 1.2 + - - -
1046A TYR* 1.3 72.7 - - - +
1048A SER* 1.3 90.5 + - - +
1049A ASP* 3.4 11.3 + - - -
1088A PHE* 4.1 15.6 - + + +
1090A GLU 3.3 16.2 + - - +
1091A ALA* 3.0 16.7 - - + +
1092A TYR* 2.6 33.5 + - - +
1102A PRO* 5.0 0.9 - - + -
1103A PRO* 4.1 12.1 - - + +
1105A HIS* 3.9 19.3 - + - -
1106A ALA* 3.6 30.7 - - + -
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Residues in contact with SER1048 (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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1022A TYR* 4.2 4.3 - - - +
1023A LYS* 2.5 41.9 + - - +
1025A TYR* 3.7 28.1 - - - -
1046A TYR 3.7 0.2 + - - -
1047A TRP* 1.3 106.7 + - - +
1049A ASP* 1.3 58.6 + - - +
1050A GLU* 3.3 15.7 + - - +
1091A ALA* 5.2 0.7 - - - -
1092A TYR 4.1 11.4 - - - -
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Residues in contact with ASP1049 (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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1022A TYR* 3.8 11.9 - - - -
1047A TRP* 3.4 12.0 + - - -
1048A SER* 1.3 72.3 - - - +
1050A GLU* 1.3 63.1 + - - +
1051A GLU* 3.4 13.0 + - - +
1092A TYR 4.9 2.0 + - - -
1100A GLU* 5.2 2.8 - - - +
1103A PRO* 3.6 19.1 - - - +
1105A HIS* 3.1 29.0 + - - -
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Residues in contact with GLU1050 (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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953A ASN* 3.0 45.9 + - + +
1022A TYR* 3.7 0.7 - - - -
1023A LYS* 2.7 53.5 + - + +
1025A TYR* 2.8 34.7 + - - -
1048A SER* 3.3 11.0 - - - +
1049A ASP* 1.3 76.9 - - - +
1051A GLU* 1.3 56.2 + - - +
1092A TYR 5.4 0.8 - - - +
1094A SER* 3.0 21.3 + - - +
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Residues in contact with GLU1051 (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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953A ASN* 5.0 5.8 + - - +
1001A LYS* 3.1 37.3 + - + +
1020A ARG* 3.6 27.6 + - - +
1021A LEU 3.1 13.7 - - - +
1022A TYR* 3.7 17.3 - - + -
1023A LYS* 4.0 8.3 + - - -
1049A ASP 3.4 10.5 + - - +
1050A GLU* 1.3 78.4 - - - +
1052A ALA* 1.3 66.9 + - - +
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Residues in contact with ALA1052 (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* 4.1 24.9 - - + -
1019A LEU 3.3 1.4 - - - +
1020A ARG* 3.7 3.4 - - - +
1021A LEU* 2.9 36.2 + - + +
1023A LYS* 4.1 18.8 - - + -
1051A GLU* 1.3 79.4 - - - +
1053A VAL* 1.3 68.5 + - - +
1054A VAL* 5.2 1.1 - - + -
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Residues in contact with VAL1053 (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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949A ALA 4.9 2.9 - - - +
1004A HIS* 4.7 10.3 - - + +
1018A LYS* 4.0 29.8 - - + -
1019A LEU 3.1 11.9 - - - +
1020A ARG* 3.3 42.6 - - - +
1052A ALA* 1.3 75.7 - - - +
1054A VAL* 1.3 70.9 + - - +
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Residues in contact with VAL1054 (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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945A LEU* 3.7 43.1 - - + -
949A ALA* 3.9 22.9 - - + +
950A PHE* 4.5 7.2 - - + -
1018A LYS* 3.3 10.0 - - - +
1019A LEU* 2.8 36.4 + - + +
1021A LEU* 3.9 17.5 - - + -
1052A ALA 5.2 0.7 - - - +
1053A VAL* 1.3 80.5 - - - +
1055A ASN* 1.3 75.3 + - - +
1056A PHE 4.6 0.2 - - - +
1058A ASP* 4.7 3.1 - - + +
1059A VAL* 4.8 4.0 - - + -
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Residues in contact with ASN1055 (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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1015A ALA 4.9 8.8 - - - +
1016A ASP* 4.6 5.6 + - - +
1017A ILE 3.7 9.1 + - - +
1018A LYS* 3.5 27.6 - - - +
1054A VAL* 1.3 80.5 - - - +
1056A PHE* 1.3 56.2 + - - +
1057A SER* 2.9 24.9 + - - +
1058A ASP* 2.7 43.3 + - - +
1059A VAL 3.9 0.5 + - - -
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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