Contacts of the strand formed by residues 1011 - 1025 (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 LYS1011 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1007B LYS* 3.5 3.3 - - - -
1008B LYS 2.6 42.3 + - - +
1009B LYS 3.2 6.5 - - - +
1010B GLY* 1.3 77.9 - - - +
1012B VAL* 1.3 61.7 + - - +
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Residues in contact with VAL1012 (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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914B VAL* 4.5 15.9 - - + -
917B GLN* 4.6 17.5 - - + +
925B VAL* 4.8 7.6 - - + -
1005B CYS* 3.9 21.1 - - - -
1006B GLY 3.9 3.6 - - - -
1007B LYS* 4.3 3.8 - - - +
1008B LYS* 4.5 3.1 - - - +
1011B LYS* 1.3 81.7 - - - +
1013B ASN* 1.3 60.5 + - - +
1014B GLU* 4.1 6.4 + - + +
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Residues in contact with ASN1013 (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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1005B CYS* 3.5 11.1 - - - +
1006B GLY* 2.5 24.2 + - - +
1008B LYS* 3.4 42.0 + - + +
1012B VAL* 1.3 74.1 + - - +
1014B GLU* 1.3 64.1 + - - +
1015B ALA* 3.7 18.6 - - - +
1016B ASP* 3.2 40.0 + - - +
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Residues in contact with GLU1014 (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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912B PRO* 3.0 42.6 - - - +
913B LYS* 3.6 10.9 - - - +
914B VAL* 3.4 39.5 + - + +
1012B VAL* 4.1 7.5 + - + +
1013B ASN* 1.3 75.3 - - - +
1015B ALA* 1.3 61.1 + - - +
1016B ASP 2.9 6.6 + - - -
1017B ILE* 3.6 23.6 + - + +
1056B PHE* 5.7 0.3 - - - -
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Residues in contact with ALA1015 (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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912B PRO* 5.7 2.5 - - - -
1013B ASN* 3.4 17.8 - - - +
1014B GLU* 1.3 77.2 - - - +
1016B ASP* 1.3 58.3 + - - +
1017B ILE 3.9 0.8 + - - -
1055B ASN* 4.9 6.6 - - - +
1057B SER* 5.8 3.1 - - - -
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Residues in contact with ASP1016 (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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924B ARG* 2.8 36.9 + - - +
1005B CYS* 3.3 14.9 - - - +
1006B GLY* 3.3 5.7 + - - +
1013B ASN* 3.2 28.3 + - + +
1014B GLU 2.9 0.8 - - - -
1015B ALA* 1.3 81.0 - - - +
1017B ILE* 1.3 60.5 + - - +
1018B LYS* 3.8 20.4 - - - +
1055B ASN* 4.4 5.8 + - - -
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Residues in contact with ILE1017 (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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912B PRO* 4.8 3.1 - - + -
913B LYS 4.6 11.9 - - - +
914B VAL* 4.5 13.9 - - + -
927B CYS* 6.0 0.2 - - - -
930B ILE* 3.8 28.5 - - + -
1003B ILE* 4.0 12.1 - - + -
1004B HIS 4.0 4.7 - - - +
1005B CYS* 3.6 16.4 - - + -
1014B GLU* 3.6 33.7 + - + +
1015B ALA 3.9 0.6 - - - -
1016B ASP* 1.3 77.0 - - - +
1018B LYS* 1.3 74.3 + - - +
1019B LEU* 4.5 0.2 - - + -
1055B ASN* 4.2 4.1 + - - +
1056B PHE* 3.0 47.4 + - + +
1057B SER 4.7 0.2 + - - -
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Residues in contact with LYS1018 (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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924B ARG* 4.1 16.0 - - - +
1003B ILE* 3.8 0.5 - - - -
1004B HIS* 3.1 50.9 + - + +
1016B ASP* 3.8 15.7 - - - +
1017B ILE* 1.3 77.3 - - - +
1019B LEU* 1.3 73.9 + - - +
1020B ARG 4.3 0.4 + - - -
1053B VAL* 4.1 18.4 - - + +
1054B VAL 3.6 8.3 - - - +
1055B ASN* 3.3 28.3 - - - +
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Residues in contact with LEU1019 (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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930B ILE* 4.3 12.3 - - + -
937B TYR* 6.0 3.4 - - + -
943B VAL* 5.1 1.8 - - + -
945B LEU* 6.1 0.4 - - + -
1000B ILE* 4.2 18.6 - - + -
1002B GLU 3.7 2.2 - - - +
1003B ILE* 3.9 30.3 - - + -
1004B HIS* 5.5 0.9 - - - -
1017B ILE* 4.5 2.2 - - + -
1018B LYS* 1.3 86.9 - - - +
1020B ARG* 1.3 61.7 - - - +
1021B LEU* 3.5 20.2 + - + +
1052B ALA 3.5 1.9 - - - +
1053B VAL* 3.3 9.0 - - - -
1054B VAL* 3.0 35.3 + - + +
1055B ASN 5.5 0.4 - - - -
1056B PHE* 3.9 18.6 - - + +
1059B VAL* 3.9 28.9 - - + -
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Residues in contact with ARG1020 (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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1000B ILE* 3.5 1.4 - - - -
1001B LYS* 2.5 47.3 + - + +
1002B GLU* 3.0 55.0 + - + -
1004B HIS* 4.8 14.9 - - + -
1018B LYS 4.3 0.2 - - - -
1019B LEU* 1.3 70.3 - - - +
1021B LEU* 1.3 53.2 + - - +
1051B GLU* 3.4 36.7 + - + +
1052B ALA* 4.1 4.1 - - - +
1053B VAL* 3.5 30.0 - - + +
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Residues in contact with LEU1021 (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* 5.1 3.4 - - + -
945B LEU* 3.3 34.8 - - + -
950B PHE* 4.6 12.8 - - + -
998B GLY* 4.4 11.0 - - - +
999B ARG 3.0 7.9 - - - +
1000B ILE* 3.3 38.8 - - + +
1001B LYS* 4.8 1.3 - - - -
1019B LEU* 3.8 22.2 - - + +
1020B ARG* 1.3 75.3 - - - +
1022B TYR* 1.3 68.6 + - - +
1023B LYS* 5.0 0.4 - - + +
1051B GLU* 3.1 10.4 - - - +
1052B ALA* 3.0 39.6 + - + +
1054B VAL* 4.2 11.7 - - + -
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Residues in contact with TYR1022 (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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998B GLY* 3.0 8.0 - - - -
999B ARG* 2.7 47.8 + - + +
1001B LYS* 2.6 57.5 + - + +
1021B LEU* 1.3 75.0 - - - +
1023B LYS* 1.3 63.5 + - - +
1024B PHE* 4.4 1.2 - - - -
1047B TRP* 3.8 34.3 - + + -
1048B SER 4.0 9.0 - - - +
1049B ASP* 4.0 29.4 - - - -
1050B GLU 3.9 2.0 - - - -
1051B GLU* 3.7 18.4 - - - -
1105B HIS* 4.3 19.0 + + - +
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Residues in contact with LYS1023 (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* 3.7 26.0 - - + -
951B THR* 2.5 32.3 + - - +
952B PHE* 3.7 9.6 - - + +
953B ASN* 3.6 18.6 + - - +
997B ILE 4.2 3.6 - - - -
998B GLY* 4.6 0.4 - - - -
1021B LEU* 3.9 0.8 + - + -
1022B TYR* 1.3 74.8 - - - +
1024B PHE* 1.3 61.4 + - - +
1047B TRP* 5.2 0.2 - - - -
1048B SER* 3.1 39.6 + - - +
1050B GLU* 2.9 57.9 + - + +
1051B GLU 4.0 4.7 + - - -
1052B ALA* 3.8 27.1 - - + -
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Residues in contact with PHE1024 (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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942B SER* 3.6 11.0 - - - -
950B PHE* 4.8 0.2 - - - -
952B PHE* 3.5 18.9 - - - -
997B ILE* 3.0 47.0 + - + +
998B GLY* 3.9 7.2 - - - -
999B ARG* 4.0 12.8 - - + -
1022B TYR 4.4 1.6 - - - -
1023B LYS* 1.3 74.0 - - - +
1025B TYR* 1.3 61.9 + - - +
1026B ARG* 3.6 2.9 + - - +
1029B ASN* 4.7 0.2 - - - +
1045B LEU* 4.2 23.6 - - + +
1046B TYR 3.5 16.4 - - - +
1047B TRP* 3.5 46.4 - + + -
1065B VAL* 3.4 34.5 - - + -
1088B PHE* 4.2 14.4 - + + -
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Residues in contact with TYR1025 (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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952B PHE* 3.4 34.4 - + + +
953B ASN 3.5 4.5 + - - -
954B ILE* 4.2 3.8 - - + +
1024B PHE* 1.3 72.1 - - - +
1026B ARG* 1.3 64.6 + - - +
1029B ASN* 2.8 36.8 - - + -
1030B THR* 3.9 3.8 - - + -
1045B LEU* 3.6 3.5 - - - -
1046B TYR* 2.7 54.2 + - + +
1048B SER* 3.4 29.6 - - - -
1050B GLU* 2.5 37.4 + - - -
1092B TYR* 3.6 32.8 - + + -
1094B SER* 3.3 9.6 + - - -
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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