Contacts of the helix formed by residues 1018 - 1035 (chain B) in PDB entry 1GKU
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 SER1018 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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719B LEU* 4.4 0.4 - - - -
1014B ALA 3.6 8.4 + - - -
1015B LYS* 3.1 19.0 + - - -
1017B VAL* 1.3 80.3 - - - +
1019B GLU* 1.3 54.8 + - - +
1020B ASP* 2.6 37.8 + - - +
1021B ARG* 2.8 22.9 + - - +
1022B THR* 2.9 14.0 + - - -
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Residues in contact with GLU1019 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719B LEU* 3.4 35.5 - - + +
723B TRP* 4.1 7.4 + - - -
968B ARG* 3.0 59.5 + - - +
970B ILE* 4.1 15.0 - - + -
1018B SER* 1.3 71.1 - - - +
1020B ASP* 1.3 62.3 + - - +
1023B ARG* 2.9 26.5 - - + +
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Residues in contact with ASP1020 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1018B SER* 2.6 24.3 + - - +
1019B GLU* 1.3 83.3 + - - +
1021B ARG* 1.3 59.8 + - - +
1023B ARG* 3.7 2.0 - - - +
1024B ASP* 3.1 26.7 + - - +
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Residues in contact with ARG1021 (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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715B ARG* 2.9 30.7 - - - +
1015B LYS* 2.9 51.1 + - - +
1016B PHE* 3.3 23.4 - - - +
1017B VAL 4.9 0.4 - - - +
1018B SER* 2.8 21.7 + - - +
1020B ASP* 1.3 72.3 - - - +
1022B THR* 1.3 60.7 + - - +
1023B ARG 3.1 1.8 - - - -
1024B ASP* 3.0 8.9 + - + +
1025B LEU* 2.8 34.7 + - + +
1049B GLU* 3.5 17.8 + - - +
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Residues in contact with THR1022 (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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715B ARG* 3.0 45.8 + - + +
716B ALA* 4.1 7.9 - - + -
719B LEU* 3.8 24.4 - - + +
970B ILE* 4.0 11.4 - - + +
1017B VAL* 4.0 12.6 + - - -
1018B SER 2.9 15.1 + - - -
1021B ARG* 1.3 77.6 - - - +
1023B ARG* 1.3 60.0 + - - +
1025B LEU* 3.7 6.1 + - - +
1026B GLU* 3.3 25.0 + - - +
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Residues in contact with ARG1023 (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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968B ARG 3.6 23.8 - - - +
969B GLY* 3.5 18.1 + - - +
970B ILE* 3.9 8.9 - - + +
1019B GLU* 2.9 23.2 + - + +
1020B ASP* 3.7 3.8 - - - +
1021B ARG 3.1 0.4 - - - -
1022B THR* 1.3 76.0 - - - +
1024B ASP* 1.3 69.7 + - - +
1026B GLU* 3.1 18.2 + - - +
1027B SER* 2.8 49.5 + - - +
1030B ASP* 4.8 4.8 + - - -
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Residues in contact with ASP1024 (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 ASP 3.1 15.7 + - - +
1021B ARG* 3.0 12.8 + - - +
1023B ARG* 1.3 80.0 - - - +
1025B LEU* 1.3 61.5 + - - +
1027B SER* 3.0 9.8 + - - -
1028B ARG* 2.7 62.3 + - - +
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Residues in contact with LEU1025 (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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690B GLU* 4.1 13.7 - - - +
715B ARG* 3.2 48.7 - - + +
1021B ARG* 2.8 22.1 + - + +
1022B THR* 4.0 5.8 - - - +
1024B ASP* 1.3 76.9 - - - +
1026B GLU* 1.3 63.9 + - - +
1028B ARG* 3.0 34.7 + - + +
1029B MET* 3.0 38.3 + - + +
1045B ASP* 5.0 3.8 - - - +
1046B MET* 4.7 16.8 - - + -
1049B GLU* 4.9 4.3 - - - +
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Residues in contact with GLU1026 (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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687B ARG* 5.4 1.4 - - - -
716B ALA* 5.6 3.1 - - - +
969B GLY 4.1 10.5 - - - +
970B ILE* 4.3 3.6 - - - +
971B GLY* 2.8 45.1 + - - +
972B ARG* 3.3 43.7 + - + +
975B THR* 5.1 2.3 - - - +
1022B THR* 3.3 15.6 + - - +
1023B ARG* 3.1 18.5 + - - +
1025B LEU* 1.3 78.1 - - - +
1027B SER* 1.3 61.4 + - - +
1029B MET* 3.7 18.6 - - - +
1030B ASP* 3.4 9.7 + - - +
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Residues in contact with SER1027 (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 ARG* 2.8 39.7 + - - +
1024B ASP* 3.0 10.4 + - - -
1026B GLU* 1.3 77.8 - - - +
1028B ARG* 1.3 64.2 + - - +
1030B ASP* 3.2 10.4 + - - +
1031B ALA* 3.1 21.0 + - - +
1034B ARG* 4.5 6.6 + - - -
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Residues in contact with ARG1028 (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 ASP* 2.7 43.1 + - - +
1025B LEU* 3.0 27.7 + - + +
1027B SER* 1.3 77.0 - - - +
1029B MET* 1.3 63.1 + - + +
1030B ASP 3.1 2.1 + - - -
1031B ALA* 3.3 15.8 + - - +
1032B ILE* 3.3 12.6 + - - +
1037B LEU* 4.0 27.2 - - + +
1042B ALA* 5.2 13.7 - - + +
1045B ASP* 3.1 34.1 + - - +
1046B MET* 6.5 1.1 - - - -
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Residues in contact with MET1029 (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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683B ALA* 4.0 8.4 - - + +
686B VAL* 4.2 15.9 - - + -
687B ARG* 3.3 55.4 - - + -
690B GLU* 4.3 16.6 - - + +
972B ARG* 2.9 27.0 + - - +
1025B LEU* 3.0 25.4 + - + +
1026B GLU* 3.6 20.4 + - - +
1027B SER 3.3 0.2 - - - -
1028B ARG* 1.3 80.7 - - + +
1030B ASP* 1.3 56.1 + - - +
1032B ILE* 2.8 29.3 - - + +
1033B GLU* 3.6 6.9 + - - +
1046B MET* 4.9 4.3 - - + -
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Residues in contact with ASP1030 (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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972B ARG* 2.6 34.5 + - - +
1023B ARG* 4.8 4.0 + - - -
1026B GLU* 3.4 14.2 - - - +
1027B SER* 3.2 16.1 + - - +
1028B ARG 3.1 0.6 - - - -
1029B MET* 1.3 79.0 - - - +
1031B ALA* 1.3 63.6 + - - +
1032B ILE 3.3 0.2 - - - -
1033B GLU* 3.3 16.5 - - - +
1034B ARG* 3.3 44.0 + - - +
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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 SER 3.1 12.3 + - - +
1028B ARG* 3.6 10.8 - - - +
1030B ASP* 1.3 76.0 - - - +
1032B ILE* 1.3 66.6 + - - +
1034B ARG* 2.8 25.5 + - - +
1036B GLU* 2.9 33.1 + - + +
1037B LEU* 3.6 22.7 - - + +
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Residues in contact with ILE1032 (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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679B ASN* 3.3 26.6 - - - +
682B LYS* 3.3 27.1 - - + +
683B ALA* 3.4 20.0 - - + +
686B VAL* 5.2 6.5 - - + -
1028B ARG 3.3 7.8 + - - +
1029B MET* 2.8 37.7 - - + +
1031B ALA* 1.3 78.6 - - - +
1033B GLU* 1.3 59.3 + - - +
1035B GLY* 2.7 25.1 + - - -
1037B LEU* 3.7 28.1 - - + +
1039B TYR* 3.9 18.6 - - + -
1042B ALA* 5.7 0.4 - - + -
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Residues in contact with GLU1033 (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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634B THR* 3.3 26.2 - - + +
679B ASN* 3.4 21.5 + - - +
680B LEU* 4.1 20.4 - - + +
683B ALA* 3.6 20.4 - - + +
972B ARG* 4.3 14.6 + - - -
1029B MET 3.8 8.2 - - - +
1030B ASP* 3.3 20.5 + - - +
1031B ALA 3.1 0.2 - - - -
1032B ILE* 1.3 82.2 - - - +
1034B ARG* 1.3 60.9 + - - +
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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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679B ASN* 4.5 5.5 + - - -
1027B SER* 4.5 7.3 + - - -
1030B ASP* 3.3 35.1 + - - +
1031B ALA* 2.8 22.2 + - - +
1033B GLU* 1.3 79.7 - - - +
1035B GLY* 1.3 58.4 + - - +
1036B GLU* 3.0 41.2 + - + +
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Residues in contact with GLY1035 (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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679B ASN* 3.8 20.2 - - - -
1032B ILE 2.7 15.4 + - - -
1033B GLU 3.2 0.8 + - - -
1034B ARG* 1.3 79.2 - - - +
1036B GLU* 1.3 64.9 + - - +
1037B LEU 4.0 2.2 - - - -
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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