Contacts of the helix formed by residues 957 - 969 (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 957 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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784B ASN* 4.0 7.6 - - - -
956B PHE* 1.3 73.7 - - - +
958B GLN* 1.3 65.3 + - - +
959B SER* 3.0 9.5 + - - -
960B GLU* 3.0 43.9 + - - +
961B ILE* 3.2 10.4 + - - +
994B GLY 3.0 25.6 - - - +
995B ARG* 3.5 24.7 - - - +
996B MET* 4.0 6.3 - - - -
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Residues in contact with GLN 958 (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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784B ASN* 3.3 18.8 - - - +
790B SER* 3.4 23.5 - - - -
791B VAL* 3.4 42.1 - - + +
957B THR* 1.3 74.1 - - - +
959B SER* 1.3 59.5 + - - +
961B ILE* 2.8 26.2 - - - +
962B ILE* 3.0 13.7 - - - +
980B VAL* 4.0 22.4 - - + +
981B ASP* 6.1 0.8 - - - +
984B PHE* 4.6 11.8 - - - -
991B GLU* 3.0 29.8 + - - +
996B MET* 3.9 12.9 - - + +
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Residues in contact with SER 959 (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 5.0 0.4 - - - -
781B SER* 3.3 50.7 + - - +
784B ASN* 2.6 26.9 - - - +
785B ARG* 4.5 11.5 - - - +
957B THR* 3.0 8.0 - - - -
958B GLN* 1.3 73.6 - - - +
960B GLU* 1.3 63.9 + - - +
962B ILE* 3.1 13.7 + - - +
963B GLN* 3.4 11.4 + - - +
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Residues in contact with GLU 960 (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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727B ARG* 3.1 19.6 + - - -
956B PHE* 2.9 31.9 - - + -
957B THR* 3.0 40.5 + - - +
959B SER* 1.3 74.6 + - - +
961B ILE* 1.3 64.8 + - - +
963B GLN* 3.4 16.2 + - - +
964B MET* 3.1 22.7 + - - +
995B ARG* 2.8 28.0 + - - -
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Residues in contact with ILE 961 (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* 3.7 24.0 - - + -
723B TRP* 4.5 13.9 - - + -
724B ILE* 4.0 8.5 - - + -
956B PHE* 3.9 31.2 - - + -
957B THR 3.2 9.5 + - - +
958B GLN* 2.8 34.5 - - + +
960B GLU* 1.3 77.3 - - - +
962B ILE* 1.3 71.6 + - + +
964B MET* 3.4 5.4 + - + +
965B MET* 3.1 44.0 + - + +
980B VAL* 4.6 6.5 - - + -
996B MET* 4.1 15.7 - - + -
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Residues in contact with ILE 962 (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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777B GLU* 3.7 31.4 - - + +
780B LEU* 4.1 21.1 - - + -
781B SER* 3.5 17.3 - - - +
791B VAL* 3.4 26.5 - - + -
958B GLN 3.0 22.0 - - - +
959B SER* 3.1 9.7 + - - +
961B ILE* 1.3 89.1 - - + +
963B GLN* 1.3 67.8 + - - +
965B MET* 3.0 16.0 + - + +
966B LYS* 2.9 21.2 + - + +
976B TYR* 4.5 17.2 - - + -
980B VAL* 4.7 4.7 - - + -
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Residues in contact with GLN 963 (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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777B GLU* 4.6 9.6 - - - +
781B SER* 3.7 14.8 + - - +
959B SER* 3.5 27.5 + - - +
960B GLU* 3.4 14.7 + - - +
962B ILE* 1.3 77.4 - - - +
964B MET* 1.3 53.4 + - - +
966B LYS* 3.2 5.8 + - - +
967B GLU* 2.7 58.3 + - - +
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Residues in contact with MET 964 (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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723B TRP* 3.8 22.4 - - + -
727B ARG* 5.1 5.6 - - - +
956B PHE* 3.7 30.7 - - + -
960B GLU 3.1 13.1 + - - +
961B ILE* 3.6 12.3 - - + +
962B ILE 3.1 0.2 - - - -
963B GLN* 1.3 76.7 - - - +
965B MET* 1.3 52.3 - - - +
967B GLU* 4.2 15.9 - - - +
968B ARG* 2.7 75.9 + - + +
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Residues in contact with MET 965 (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* 3.9 30.5 - - + -
723B TRP* 4.0 11.7 - - + -
961B ILE* 3.1 52.5 + - + +
962B ILE* 3.0 18.7 + - + +
964B MET* 1.3 76.7 - - - +
966B LYS* 1.3 56.6 + - - +
968B ARG 3.6 0.3 + - - -
969B GLY 2.9 6.8 + - - -
970B ILE* 2.7 51.0 + - + +
976B TYR* 4.4 24.5 - - + +
979B ILE* 4.6 17.3 - - + -
980B VAL* 4.6 12.1 - - + -
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Residues in contact with LYS 966 (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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777B GLU* 3.2 47.6 - - + +
962B ILE 2.9 12.6 + - - +
963B GLN 3.6 5.4 - - - +
965B MET* 1.3 72.7 - - - +
967B GLU* 1.3 78.0 + - - +
969B GLY* 2.9 14.6 + - - -
976B TYR* 4.0 23.0 - - + +
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Residues in contact with GLU 967 (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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963B GLN* 2.7 48.0 + - - +
964B MET* 3.6 17.4 + - - +
966B LYS* 1.3 85.3 - - - +
968B ARG* 1.3 66.9 + - + +
969B GLY 3.4 0.5 + - - -
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Residues in contact with ARG 968 (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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723B TRP* 3.5 39.8 - - + +
964B MET* 2.7 62.2 + - + +
965B MET 4.3 0.7 - - - +
967B GLU* 1.3 77.6 - - - +
969B GLY* 1.3 58.2 + - - +
970B ILE* 3.0 16.3 - - + +
1019B GLU* 3.0 44.1 + - - +
1023B ARG* 3.6 10.9 - - - +
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Residues in contact with GLY 969 (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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965B MET 2.9 5.2 + - - -
966B LYS 2.9 11.9 + - - -
967B GLU 3.2 1.2 + - - -
968B ARG* 1.3 80.0 - - - +
970B ILE* 1.3 64.0 - - - +
971B GLY 4.3 2.5 - - - -
1023B ARG* 3.5 24.4 + - - +
1026B GLU* 4.1 12.2 - - - +
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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