Contacts of the helix formed by residues 975 - 986 (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 THR 975 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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687B ARG* 4.9 15.8 + - - -
971B GLY* 3.6 4.7 - - - -
972B ARG* 3.0 31.2 + - - +
974B SER* 1.3 82.9 + - - +
976B TYR* 1.3 72.0 + - - +
977B ALA 3.4 2.0 - - - -
978B THR* 3.0 17.9 + - - -
979B ILE* 3.1 39.4 + - + +
1026B GLU* 5.1 2.2 - - - +
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Residues in contact with TYR 976 (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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776B THR* 4.1 9.9 - - + -
777B GLU* 4.4 20.0 - - + +
780B LEU* 3.9 18.6 - - + -
813B ASP* 5.8 2.1 - - - +
962B ILE* 4.5 15.5 - - + -
965B MET* 4.4 23.8 - - + +
966B LYS* 4.0 26.8 - - + +
970B ILE 3.9 9.6 - - - -
971B GLY* 3.6 25.4 + - - -
972B ARG* 2.9 38.5 + - - -
973B PRO* 3.5 25.0 + - + +
975B THR* 1.3 78.0 - - - +
977B ALA* 1.3 64.3 + - - +
979B ILE* 3.3 8.4 + - - +
980B VAL* 3.1 19.0 + - - +
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Residues in contact with ALA 977 (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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780B LEU* 4.8 1.9 - - + +
791B VAL* 3.6 30.9 - - + +
792B LYS* 3.5 15.5 - - + +
795B MET* 3.8 30.1 - - + -
973B PRO 5.0 1.6 + - - -
974B SER 5.6 0.2 - - - -
975B THR 3.4 0.6 - - - +
976B TYR* 1.3 78.6 - - - +
978B THR* 1.3 58.3 + - - +
980B VAL* 3.5 0.5 - - - +
981B ASP* 2.8 34.5 + - - +
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Residues in contact with THR 978 (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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792B LYS* 3.3 17.4 + - - +
974B SER 3.7 15.8 + - - -
975B THR* 3.0 11.7 + - - -
977B ALA* 1.3 78.0 - - - +
979B ILE* 1.3 61.4 + - + +
981B ASP* 3.9 0.5 - - - +
982B ARG* 2.8 37.5 + - + +
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Residues in contact with ILE 979 (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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716B ALA* 3.8 41.5 - - + +
717B GLN* 4.0 12.6 - - + +
720B VAL* 4.0 17.3 - - + -
965B MET* 4.6 13.2 - - - -
970B ILE* 4.7 3.1 - - + -
971B GLY* 4.4 10.5 - - - -
975B THR* 3.1 35.9 + - + +
976B TYR 3.7 5.8 - - - +
978B THR* 1.3 80.3 - - + +
980B VAL* 1.3 66.0 + - - +
982B ARG* 3.2 17.1 + - - +
983B LEU* 3.5 13.3 + - + +
1026B GLU* 5.7 0.4 - - - +
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Residues in contact with VAL 980 (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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720B VAL* 5.6 0.7 - - + -
791B VAL* 3.3 29.2 - - + -
958B GLN* 4.0 20.4 - - + +
961B ILE* 4.6 3.8 - - + -
962B ILE* 4.7 4.9 - - + -
965B MET* 4.6 13.2 - - + -
976B TYR 3.1 18.6 + - - +
977B ALA* 3.5 1.3 - - - +
979B ILE* 1.3 78.1 - - - +
981B ASP* 1.3 64.0 + - - +
983B LEU* 3.0 27.5 + - - +
984B PHE* 3.4 11.2 - - + -
996B MET* 3.5 31.0 - - + -
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Residues in contact with ASP 981 (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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791B VAL* 4.9 2.5 - - + -
792B LYS* 3.2 41.4 + - + +
958B GLN* 6.1 0.9 - - - +
977B ALA 2.8 23.8 + - - +
978B THR 3.9 2.0 - - - +
980B VAL* 1.3 79.1 - - - +
982B ARG* 1.3 64.5 + - - +
984B PHE* 3.1 20.5 + - - +
985B MET* 3.3 20.8 + - - +
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Residues in contact with ARG 982 (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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712B SER* 3.7 27.7 + - - +
713B ALA 3.3 18.4 + - - +
714B GLY* 3.2 18.6 - - - -
717B GLN* 3.0 48.3 - - - +
978B THR* 2.8 23.1 + - + +
979B ILE* 3.2 8.1 + - - +
981B ASP* 1.3 78.3 + - - +
983B LEU* 1.3 63.0 + - - +
985B MET* 3.5 12.1 - - + +
986B ARG* 3.3 31.2 + - - +
988B TYR* 5.1 1.1 - - - -
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Residues in contact with LEU 983 (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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717B GLN* 3.4 45.3 - - + +
720B VAL* 4.1 27.4 - - + -
721B LEU* 4.3 13.7 - - + +
724B ILE* 4.1 17.7 - - + -
979B ILE* 3.5 13.5 - - + +
980B VAL* 3.0 14.5 + - - +
982B ARG* 1.3 75.5 - - - +
984B PHE* 1.3 64.5 + - + +
986B ARG 3.4 1.2 + - - -
987B ASN 3.4 2.1 + - - -
988B TYR* 3.0 40.4 + - + +
989B VAL* 3.5 17.5 + - + -
996B MET* 5.2 0.9 - - + -
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Residues in contact with PHE 984 (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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958B GLN* 4.6 11.2 - - - -
980B VAL* 3.4 21.5 - - + -
981B ASP* 3.1 12.0 + - - +
983B LEU* 1.3 73.0 - - + +
985B MET* 1.3 55.2 + - - +
986B ARG 2.9 4.3 - - - -
987B ASN* 2.5 33.1 + - - +
989B VAL* 3.7 25.8 - - + +
990B VAL* 4.1 4.5 - - - -
991B GLU* 3.8 37.5 - - + -
996B MET* 3.4 41.7 - - + -
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Residues in contact with MET 985 (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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981B ASP* 3.3 14.5 + - - +
982B ARG* 3.5 21.8 - - - +
984B PHE* 1.3 78.0 - - - +
986B ARG* 1.3 96.9 + - - +
987B ASN* 3.2 9.7 + - - +
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Residues in contact with ARG 986 (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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710B ASN* 4.0 23.2 + - - +
711B LEU* 5.5 1.4 - - - +
712B SER* 2.9 37.3 + - - +
982B ARG* 3.3 21.2 + - - +
983B LEU 3.8 0.7 - - - +
984B PHE 2.8 1.4 + - - -
985B MET* 1.3 122.0 - - - +
987B ASN* 1.3 67.8 + - - +
988B TYR* 2.9 47.0 + - + +
1001B LEU* 4.4 3.1 - - - +
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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