Contacts of the helix formed by residues 1020 - 1038 (chain B) in PDB entry 5DSG
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 ALA1020 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A PRO* 6.6 0.2 - - + -
1018B ASP* 3.0 10.5 - - + +
1019B GLU* 1.3 75.5 - - - +
1021B GLU* 1.3 56.3 + - - +
1022B LYS* 2.9 6.3 - - - +
1023B LEU* 2.9 32.2 + - + +
1024B PHE* 3.8 2.8 + - - +
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Residues in contact with GLU1021 (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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1004B PHE* 3.5 45.5 - - + +
1005B GLU* 4.9 3.7 - - - +
1008B ARG* 4.4 7.7 - - - +
1017B GLY* 4.7 11.8 - - - -
1018B ASP 3.5 17.8 + - - +
1019B GLU* 2.9 2.7 - - - +
1020B ALA* 1.3 78.3 - - - +
1022B LYS* 1.3 58.0 + - + +
1024B PHE* 2.9 26.5 + - + +
1025B ASN* 2.9 30.9 + - - +
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Residues in contact with LYS1022 (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 GLU* 3.0 39.6 + - + +
1020B ALA* 4.9 0.7 - - - -
1021B GLU* 1.3 77.1 - - + +
1023B LEU* 1.3 64.1 + - - +
1025B ASN* 2.9 44.3 + - - +
1026B GLN* 3.1 7.4 + - - +
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Residues in contact with LEU1023 (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 ALA* 2.9 23.6 + - + +
1022B LYS* 1.3 77.6 - - - +
1024B PHE* 1.3 64.0 + - + +
1026B GLN* 2.9 23.3 + - - +
1027B ASP* 3.3 11.8 + - - +
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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
----------------------------------------------------------
1004B PHE* 3.5 22.4 - + + -
1007B LEU* 4.6 16.2 - - + -
1008B ARG* 4.6 21.1 - - + -
1011B GLU* 5.5 7.2 - - + -
1020B ALA 3.8 1.8 + - - -
1021B GLU* 2.9 39.7 + - - +
1023B LEU* 1.3 80.6 - - + +
1025B ASN* 1.3 55.0 + - - +
1027B ASP* 2.9 13.5 + - - +
1028B VAL* 2.7 37.5 + - + +
1061B PHE* 4.5 22.2 - + - -
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Residues in contact with ASN1025 (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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1004B PHE* 3.1 34.7 - - - -
1021B GLU* 2.9 31.9 + - - +
1022B LYS* 2.9 44.5 + - - +
1024B PHE* 1.3 75.3 - - - +
1026B GLN* 1.3 58.4 + - - +
1029B ASP* 2.8 36.8 + - - +
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Residues in contact with GLN1026 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022B LYS 3.1 6.9 + - - +
1023B LEU* 2.9 13.2 + - - +
1025B ASN* 1.3 77.1 - - - +
1027B ASP* 1.3 69.6 + - - +
1029B ASP* 3.0 9.1 + - - +
1030B ALA* 2.9 21.0 + - - +
1033B ARG* 5.6 0.3 + - - -
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Residues in contact with ASP1027 (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 LEU* 3.3 11.7 + - - +
1024B PHE* 2.9 17.4 + - - +
1026B GLN* 1.3 82.6 - - - +
1028B VAL* 1.3 57.3 + - - +
1030B ALA* 3.0 10.9 + - - +
1031B ALA* 2.8 28.6 + - - +
1061B PHE* 3.7 25.2 - - + -
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Residues in contact with VAL1028 (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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1003B ILE* 4.7 12.1 - - + -
1004B PHE* 3.6 29.4 - - + -
1007B LEU* 3.7 29.4 - - + -
1024B PHE* 2.7 23.5 + - + +
1025B ASN 4.2 1.3 - - - +
1027B ASP* 1.3 71.6 - - - +
1029B ASP* 1.3 57.7 + - - +
1031B ALA* 3.0 10.6 + - - +
1032B VAL* 2.7 49.3 + - + +
1057B ILE* 4.4 14.1 - - + -
1061B PHE* 4.5 5.8 - - + -
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Residues in contact with ASP1029 (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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1004B PHE* 5.4 1.0 - - - -
1025B ASN* 2.8 23.1 + - - +
1026B GLN* 3.0 11.5 + - - +
1028B VAL* 1.3 81.4 - - - +
1030B ALA* 1.3 51.8 + - - +
1032B VAL* 3.0 10.8 + - - +
1033B ARG* 2.6 50.9 + - - +
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Residues in contact with ALA1030 (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 GLN 2.9 12.6 + - - +
1027B ASP* 3.0 14.6 + - - +
1029B ASP* 1.3 74.4 - - - +
1031B ALA* 1.3 52.1 + - - +
1033B ARG* 3.0 27.2 + - - +
1034B GLY* 2.8 31.9 + - - -
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Residues in contact with ALA1031 (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 ASP 2.8 11.3 + - - +
1028B VAL* 3.2 12.3 - - - +
1030B ALA* 1.3 75.9 - - - +
1032B VAL* 1.3 57.6 + - - +
1034B GLY* 2.9 4.1 + - - -
1035B ILE* 2.8 33.5 + - + +
1057B ILE* 4.6 13.5 - - + +
1060B VAL* 4.3 21.0 - - + +
1061B PHE* 4.5 16.8 - - + +
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Residues in contact with VAL1032 (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 VAL* 2.7 29.9 + - + +
1029B ASP* 3.3 11.2 - - - +
1031B ALA* 1.3 70.9 - - - +
1033B ARG* 1.3 58.6 + - - +
1035B ILE* 2.9 10.7 + - - +
1036B LEU* 2.8 45.3 + - + +
1045B TYR* 4.1 21.1 - - + +
1057B ILE* 3.7 30.1 - - + -
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Residues in contact with ARG1033 (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 GLN 5.6 0.2 + - - -
1029B ASP* 2.6 32.4 + - - +
1030B ALA* 3.2 38.0 - - - +
1032B VAL* 1.3 73.6 - - - +
1034B GLY* 1.3 51.9 + - - +
1036B LEU* 3.0 12.8 + - + +
1037B ARG* 2.6 37.4 + - + +
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Residues in contact with GLY1034 (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 ALA 2.8 13.6 + - - -
1031B ALA* 2.9 4.2 + - - -
1033B ARG* 1.3 75.2 - - - +
1035B ILE* 1.3 52.3 + - - +
1037B ARG* 2.9 7.4 + - - +
1038B ASN* 2.7 32.8 + - - +
1060B VAL* 5.9 0.7 - - - -
1065B GLU* 3.1 30.9 - - - +
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Residues in contact with ILE1035 (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 ALA 2.8 18.8 + - - +
1032B VAL* 3.2 12.1 - - - +
1034B GLY* 1.3 76.7 - - - +
1036B LEU* 1.3 62.0 + - + +
1038B ASN* 3.3 17.9 + - - +
1041B LEU* 3.9 20.6 - - + +
1042B LYS* 3.5 9.0 + - - -
1045B TYR* 3.5 44.2 - - + -
1056B LEU* 4.5 4.9 - - + -
1057B ILE* 3.7 33.9 - - + +
1060B VAL* 3.8 31.9 - - + -
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Residues in contact with LEU1036 (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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1032B VAL* 2.8 29.1 + - + +
1033B ARG* 3.5 11.2 - - + +
1035B ILE* 1.3 78.2 - - - +
1037B ARG* 1.3 61.0 + - - +
1038B ASN 4.1 3.3 - - - +
1042B LYS* 3.7 37.0 - - + +
1045B TYR* 4.3 25.4 - - + -
1046B ASP* 5.0 1.3 - - - +
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Residues in contact with ARG1037 (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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1033B ARG* 2.6 19.1 + - + +
1034B GLY* 2.9 14.1 + - - +
1036B LEU* 1.3 75.2 - - - +
1038B ASN* 1.3 63.1 + - - +
1039B ALA* 3.6 3.5 + - - +
1065B GLU* 4.4 5.4 - - - +
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Residues in contact with ASN1038 (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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1034B GLY 2.7 18.0 + - - +
1035B ILE 3.3 1.5 + - - +
1036B LEU 4.1 0.4 - - - +
1037B ARG* 1.3 74.4 - - - +
1039B ALA* 1.3 58.9 + - - +
1040B LYS* 2.7 32.6 + - - +
1041B LEU* 2.8 32.3 + - + +
1042B LYS* 3.2 28.4 + - - +
1065B GLU* 3.8 23.5 + - - +
1066B THR* 5.0 1.8 - - - +
1069B ALA* 4.1 15.8 - - - +
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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