Contacts of the helix formed by residues 1015 - 1035 (chain B) in PDB entry 5W0N
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 THR1015 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1013B SER 5.2 0.4 - - - +
1014B PRO* 1.3 76.4 - - - +
1016B ILE* 1.3 61.2 + - - +
1017B ILE* 3.4 10.1 + - - +
1018B GLU* 2.8 40.8 + - - +
1019B ASP* 2.9 28.7 + - - +
1055B LYS* 4.0 11.2 - - - +
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Residues in contact with ILE1016 (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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1015B THR* 1.3 74.1 - - - +
1017B ILE* 1.3 74.7 + - + +
1019B ASP* 3.4 11.8 + - - +
1020B GLN* 3.0 28.1 + - - +
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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
----------------------------------------------------------
1015B THR* 3.1 8.8 + - - +
1016B ILE* 1.3 93.2 - - + +
1018B GLU* 1.3 61.7 + - + +
1020B GLN* 3.4 18.0 + - - +
1021B ALA* 3.1 23.0 + - + +
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Residues in contact with GLU1018 (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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1014B PRO* 3.2 12.6 - - + +
1015B THR* 2.8 40.9 + - - +
1017B ILE* 1.3 77.3 - - + +
1019B ASP* 1.3 64.0 + - - +
1021B ALA* 3.4 9.6 + - - +
1022B ARG* 3.4 25.7 + - - +
1055B LYS* 2.9 39.0 + - - +
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Residues in contact with ASP1019 (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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1014B PRO* 3.5 26.5 - - - +
1015B THR 2.9 19.6 + - - +
1016B ILE* 3.6 13.5 - - - +
1018B GLU* 1.3 75.4 - - - +
1020B GLN* 1.3 65.4 + - - +
1022B ARG* 3.0 25.4 + - - +
1023B GLU* 3.2 10.7 + - - +
1048B SER* 4.9 9.1 - - - +
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Residues in contact with GLN1020 (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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1016B ILE 3.0 17.1 + - - +
1017B ILE* 3.4 18.5 + - + +
1019B ASP* 1.3 75.5 - - - +
1021B ALA* 1.3 57.1 + - - +
1023B GLU* 3.1 11.0 + - + +
1024B HIS* 2.9 60.1 + - + +
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Residues in contact with ALA1021 (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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1017B ILE* 3.1 14.9 + - + +
1018B GLU* 3.5 13.2 - - - +
1019B ASP 3.2 0.4 - - - -
1020B GLN* 1.3 77.0 + - - +
1022B ARG* 1.3 57.1 + - + +
1024B HIS* 3.2 12.8 + - - +
1025B ILE* 3.0 36.8 + - + +
1114B SER* 6.0 3.6 - - - -
1116B LEU* 6.5 0.2 - - + -
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Residues in contact with ARG1022 (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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1014B PRO* 5.2 6.6 - - - +
1018B GLU* 3.4 14.6 + - - +
1019B ASP* 3.0 21.2 + - - +
1021B ALA* 1.3 78.9 - - + +
1023B GLU* 1.3 61.2 + - - +
1025B ILE* 3.3 9.8 + - - +
1026B ARG 3.1 17.2 + - - -
1044B LEU* 3.9 14.6 - - + +
1048B SER* 2.9 34.1 + - - +
1054B PHE 3.4 13.4 + - - -
1055B LYS 3.1 25.5 + - - -
1057B SER* 2.6 24.9 + - - +
1058B ASP 3.1 19.2 + - - -
1059B LEU* 3.6 24.4 - - + +
1116B LEU* 3.7 22.2 - - + +
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Residues in contact with GLU1023 (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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1019B ASP 3.2 7.1 + - - +
1020B GLN* 3.1 14.4 + - + +
1022B ARG* 1.3 78.5 - - - +
1024B HIS* 1.3 66.0 + - + +
1026B ARG* 3.0 44.5 + - - +
1027B GLN* 2.9 32.0 + - - +
1044B LEU* 4.2 11.5 - - + +
1049B LYS* 4.9 13.0 + - - +
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Residues in contact with HIS1024 (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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1020B GLN* 2.9 55.5 + - + -
1021B ALA* 3.5 12.1 - - - +
1023B GLU* 1.3 77.7 - - + +
1025B ILE* 1.3 60.0 + - - +
1027B GLN* 3.1 21.8 + - - +
1028B ASN* 2.8 30.2 + - - +
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Residues in contact with ILE1025 (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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1021B ALA* 3.0 22.4 + - + +
1022B ARG* 3.3 10.7 + - - +
1024B HIS* 1.3 75.6 - - + +
1026B ARG* 1.3 61.8 + - - +
1028B ASN* 3.0 7.2 + - + +
1029B LEU* 2.8 40.8 + - + +
1059B LEU* 3.5 21.1 - - + -
1111B HIS* 3.8 32.5 - - + +
1114B SER* 3.5 34.5 - - - +
1116B LEU* 4.2 15.0 - - + -
1118B VAL* 4.8 2.9 - - + -
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Residues in contact with ARG1026 (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 ARG 3.1 10.3 + - - +
1023B GLU* 3.0 41.0 + - - +
1025B ILE* 1.3 79.4 - - - +
1027B GLN* 1.3 75.2 + - - +
1029B LEU* 3.8 7.1 - - - +
1030B GLU* 2.9 66.3 + - - +
1042B LEU* 2.9 45.4 + - + +
1043B SER* 4.2 1.3 - - - +
1044B LEU* 4.0 34.3 - - + +
1059B LEU* 4.6 1.3 - - - +
1061B VAL* 5.0 3.1 - - + -
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Residues in contact with GLN1027 (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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1023B GLU* 2.9 22.0 + - - +
1024B HIS* 3.3 31.0 + - - +
1026B ARG* 1.3 94.8 - - - +
1028B ASN* 1.3 61.6 + - - +
1030B GLU* 3.5 6.1 + - - +
1031B SER* 3.2 28.7 + - - +
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Residues in contact with ASN1028 (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 HIS 2.8 16.3 + - - +
1025B ILE* 3.0 6.9 + - - +
1027B GLN* 1.3 74.8 - - - +
1029B LEU* 1.3 70.2 + - - +
1031B SER* 3.2 7.5 + - - -
1032B PHE* 2.9 23.1 + - - +
1090B HIS* 3.0 31.5 + - - -
1111B HIS* 5.2 7.7 + - - +
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Residues in contact with LEU1029 (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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1025B ILE* 2.8 43.9 + - + +
1026B ARG* 3.9 3.4 - - - +
1028B ASN* 1.3 77.7 - - - +
1030B GLU* 1.3 58.8 + - - +
1032B PHE* 4.4 2.9 - - - -
1033B ILE* 2.8 40.2 + - + +
1042B LEU* 3.6 16.6 - - + -
1059B LEU* 5.0 1.6 - - + -
1061B VAL* 5.0 3.4 - - + -
1087B LEU* 4.6 7.6 - - + -
1090B HIS* 4.5 10.8 - - + -
1093B LEU* 4.3 19.3 - - + -
1109B PHE* 4.0 35.9 - - + -
1111B HIS* 5.5 1.8 - - + -
1118B VAL* 4.1 11.9 - - + -
1120B ILE* 4.8 5.8 - - + -
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Residues in contact with GLU1030 (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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1026B ARG* 2.9 43.8 + - - +
1027B GLN* 3.8 6.2 - - - +
1029B LEU* 1.3 77.4 - - - +
1031B SER* 1.3 62.2 + - - +
1033B ILE* 3.9 2.4 - - - +
1034B ARG* 3.0 57.7 + - - +
1040B THR* 3.7 15.1 - - - +
1041B LYS* 3.4 11.1 - - - +
1042B LEU* 3.0 40.2 + - + +
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Residues in contact with SER1031 (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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1027B GLN* 3.2 15.9 + - - +
1028B ASN* 3.2 9.2 + - - -
1030B GLU* 1.3 78.6 + - - +
1032B PHE* 1.3 64.6 + - - +
1034B ARG* 3.3 24.4 + - - +
1035B GLN* 3.6 12.6 + - - +
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Residues in contact with PHE1032 (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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1028B ASN* 2.9 18.1 + - - +
1029B LEU* 3.8 4.0 - - + +
1031B SER* 1.3 77.8 - - - +
1033B ILE* 1.3 66.7 + - + +
1035B GLN* 3.2 44.9 + - - +
1036B ASP* 4.3 3.4 + - - +
1086B VAL* 3.3 40.2 - - + -
1087B LEU* 4.1 12.6 - - + -
1089B LYS* 3.8 14.8 - - + -
1090B HIS* 3.5 58.6 - + + +
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Residues in contact with ILE1033 (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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1029B LEU* 2.8 26.4 + - + +
1030B GLU 4.2 2.2 - - - +
1032B PHE* 1.3 77.7 - - + +
1034B ARG* 1.3 59.0 + - - +
1035B GLN 3.1 0.9 + - - -
1036B ASP* 3.2 4.9 + - - +
1037B PHE* 2.8 40.7 + - + -
1040B THR* 3.6 26.9 - - + +
1042B LEU* 4.1 16.6 - - + -
1063B MET* 4.1 3.4 - - + -
1083B LEU* 3.8 26.0 - - + -
1086B VAL* 4.8 7.2 - - + -
1087B LEU* 4.1 20.2 - - + -
1120B ILE* 4.1 22.0 - - + -
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Residues in contact with ARG1034 (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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1030B GLU* 3.0 50.3 + - - +
1031B SER* 3.6 13.4 + - - +
1032B PHE 3.2 0.4 - - - -
1033B ILE* 1.3 77.3 - - - +
1035B GLN* 1.3 62.9 - - - +
1037B PHE 3.5 7.4 - - - +
1038B PRO* 3.3 23.2 - - + +
1039B GLY* 4.2 8.8 - - - +
1040B THR* 3.0 40.4 + - - +
1041B LYS* 5.0 2.6 - - - +
1066B ASN* 4.9 10.5 - - - +
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Residues in contact with GLN1035 (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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1031B SER 3.8 7.8 + - - +
1032B PHE* 3.4 44.3 - - - +
1033B ILE 3.1 0.6 - - - -
1034B ARG* 1.3 79.1 - - - +
1036B ASP* 1.3 67.5 + - - +
1038B PRO* 4.8 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
------------------------------------------------------------
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