Contacts of the strand formed by residues 1044 - 1055 (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 MET1044 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1026B ARG* 5.2 0.2 - - - +
1027B PRO* 3.1 49.3 - - + +
1040B THR* 4.2 15.9 - - + -
1041B ASP* 2.8 18.9 + - + +
1042B ILE 4.5 3.1 - - - +
1043B ASN* 1.3 79.3 + - - +
1045B LEU* 1.3 75.1 + - - +
1046B TYR* 3.7 33.2 - - + +
1087B TYR* 3.3 45.5 - - + +
1088B PHE* 4.9 1.3 - - - -
1089B LEU* 5.6 9.6 - - - -
1090B GLU* 6.0 0.2 - - - +
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Residues in contact with LEU1045 (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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997B ILE* 4.3 14.6 - - + -
1024B PHE* 4.2 30.1 - - + +
1025B TYR 3.6 4.3 - - - +
1026B ARG* 3.8 32.3 - - + +
1027B PRO* 4.6 0.4 - - - -
1042B ILE 5.9 0.2 - - - +
1044B MET* 1.3 88.1 - - - +
1046B TYR* 1.3 66.9 + - - +
1065B VAL* 3.9 18.6 - - + -
1086B PHE* 3.5 41.3 - - + -
1087B TYR 2.8 9.8 + - - +
1088B PHE* 2.8 26.7 - - + +
1089B LEU 4.2 2.6 + - - -
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Residues in contact with TYR1046 (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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1024B PHE* 3.5 6.3 - - - -
1025B TYR* 2.7 51.8 + - + +
1027B PRO* 3.9 29.6 - - + -
1030B THR* 4.0 8.1 - - + -
1032B ARG* 5.4 5.1 + - + -
1040B THR* 5.0 5.5 - - - +
1044B MET* 3.7 28.3 - - + +
1045B LEU* 1.3 74.6 - - - +
1047B TRP* 1.3 61.2 + - - +
1089B LEU 5.9 0.4 - - - -
1090B GLU* 3.2 44.7 + - + +
1092B TYR* 4.2 11.4 - - + -
1099B PHE* 3.5 40.4 - + - -
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Residues in contact with TRP1047 (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* 3.3 35.0 - - + -
1022B TYR* 3.8 43.7 - + + -
1023B LYS 5.4 0.2 - - - -
1024B PHE* 3.5 33.1 - + + -
1045B LEU 4.1 1.4 + - - -
1046B TYR* 1.3 74.0 - - - +
1048B SER* 1.3 87.1 + - - +
1049B ASP* 3.6 14.2 + - - -
1088B PHE* 3.7 25.9 - + + +
1090B GLU 3.3 7.1 + - - -
1091B ALA* 3.1 22.4 - - + -
1092B TYR* 2.4 36.2 + - - +
1103B PRO* 3.9 10.8 - - + +
1105B HIS* 4.1 11.9 - + - -
1106B ALA* 3.4 33.7 - - + -
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Residues in contact with SER1048 (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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1022B TYR* 4.0 7.1 - - - +
1023B LYS* 3.1 36.3 + - - +
1025B TYR* 3.4 35.3 - - - -
1047B TRP* 1.3 98.2 + - - +
1049B ASP* 1.3 61.3 + - - +
1050B GLU* 3.8 9.3 + - - +
1092B TYR 3.8 15.7 - - - -
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Residues in contact with ASP1049 (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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1022B TYR* 4.0 14.5 - - + -
1047B TRP* 3.6 15.7 + - - -
1048B SER* 1.3 73.5 - - - +
1050B GLU* 1.3 66.6 + - - +
1051B GLU* 2.9 19.2 + - - +
1092B TYR 4.7 2.4 + - - -
1103B PRO* 3.6 14.2 - - - +
1105B HIS* 3.0 31.7 + - - -
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Residues in contact with GLU1050 (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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953B ASN* 3.0 43.4 + - + +
1023B LYS* 2.9 58.2 + - + +
1025B TYR* 2.5 25.9 + - - -
1048B SER* 3.4 9.3 - - - +
1049B ASP* 1.3 74.8 - - - +
1051B GLU* 1.3 61.2 + - - +
1094B SER* 2.5 29.4 + - - +
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Residues in contact with GLU1051 (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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1001B LYS* 3.5 31.5 + - - +
1020B ARG* 3.4 40.1 + - + +
1021B LEU 3.1 11.0 - - - +
1022B TYR* 3.7 13.0 - - + +
1023B LYS* 4.0 5.0 - - - -
1049B ASP 3.3 11.5 - - - +
1050B GLU* 1.3 75.7 - - - +
1052B ALA* 1.3 63.3 + - - +
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Residues in contact with ALA1052 (chain B).
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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950B PHE* 4.2 25.8 - - + -
1019B LEU 3.5 1.2 - - - +
1020B ARG* 4.9 0.9 - - - +
1021B LEU* 3.0 36.9 + - + +
1023B LYS* 3.8 24.0 - - + -
1051B GLU* 1.3 78.9 - - - +
1053B VAL* 1.3 67.2 + - - +
1054B VAL* 5.5 0.2 - - - -
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Residues in contact with VAL1053 (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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949B ALA 4.4 8.7 - - - +
950B PHE* 5.6 0.2 - - - +
1004B HIS* 5.0 7.2 - - + +
1018B LYS* 4.1 28.0 - - + +
1019B LEU 3.3 12.8 - - - +
1020B ARG* 3.5 37.9 - - - +
1052B ALA* 1.3 78.7 - - - +
1054B VAL* 1.3 72.0 + - - +
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Residues in contact with VAL1054 (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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945B LEU* 4.0 33.7 - - + -
949B ALA* 4.6 13.7 - - + +
950B PHE* 5.6 1.6 - - + -
1018B LYS* 3.6 7.6 - - - +
1019B LEU* 3.0 33.0 + - + +
1021B LEU* 4.2 9.9 - - + -
1052B ALA 3.9 0.2 + - - -
1053B VAL* 1.3 77.4 - - - +
1055B ASN* 1.3 63.2 + - - +
1058B ASP* 6.0 0.4 - - + -
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Residues in contact with ASN1055 (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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945B LEU* 4.9 0.7 - - - +
1015B ALA 4.9 7.6 - - - +
1016B ASP* 4.4 5.8 + - - +
1017B ILE 4.2 4.7 + - - +
1018B LYS* 3.3 35.2 - - - +
1019B LEU* 5.4 1.3 - - - -
1054B VAL* 1.3 77.6 - - - +
1056B PHE* 1.3 55.3 + - - +
1057B SER* 3.0 26.9 + - - +
1058B ASP* 2.7 42.4 + - + +
1059B VAL* 3.8 2.6 + - - +
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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