Contacts of the helix formed by residues 999 - 1012 (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 999 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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987B ASN* 2.7 32.5 + - + +
988B TYR 3.2 5.1 + - - -
989B VAL* 3.5 19.7 - - - +
990B VAL* 3.7 24.0 - - + -
998B PRO* 1.3 75.6 - - - +
1000B LYS* 1.3 64.9 + - - +
1001B LEU* 3.3 5.3 + - - +
1002B GLY 2.8 16.8 + - - -
1003B ILE* 2.9 24.8 + - - +
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Residues in contact with LYS1000 (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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999B THR* 1.3 72.1 - - - +
1001B LEU* 1.3 63.8 + - - +
1003B ILE* 2.9 23.3 - - + +
1004B ASP* 3.2 24.5 + - - +
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Residues in contact with LEU1001 (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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706B PHE* 4.8 20.6 - - + -
711B LEU* 3.9 17.7 - - + -
986B ARG 4.4 4.7 - - - +
987B ASN* 4.5 6.5 - - + +
988B TYR* 3.1 39.0 - - + -
999B THR* 3.2 7.3 + - - +
1000B LYS* 1.3 79.7 - - - +
1002B GLY* 1.3 59.7 + - - +
1004B ASP* 3.5 3.0 + - + -
1005B VAL* 2.9 40.9 + - + +
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Residues in contact with GLY1002 (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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721B LEU* 3.8 8.1 - - - +
725B ILE* 4.5 1.8 - - - -
988B TYR* 3.5 38.6 - - - -
999B THR* 2.8 11.6 + - - -
1001B LEU* 1.3 78.1 - - - +
1003B ILE* 1.3 63.3 + - - +
1005B VAL* 3.1 4.3 + - - +
1006B PHE* 3.0 24.6 + - - +
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Residues in contact with ILE1003 (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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725B ILE* 3.7 31.9 - - + +
998B PRO* 4.9 5.8 - - + +
999B THR 2.9 15.2 + - - +
1000B LYS* 2.9 27.8 - - + +
1002B GLY* 1.3 72.3 - - - +
1004B ASP* 1.3 62.1 + - - +
1006B PHE* 3.9 1.2 - - - +
1007B ARG* 2.7 57.1 + - + +
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Residues in contact with ASP1004 (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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706B PHE* 3.6 22.7 - - + -
1000B LYS* 3.2 28.7 + - - +
1001B LEU* 4.2 4.0 - - + +
1003B ILE* 1.3 82.4 - - - +
1005B VAL* 1.3 57.7 + - - +
1007B ARG* 3.6 15.5 + - - +
1008B PHE* 2.7 35.3 + - - +
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Residues in contact with VAL1005 (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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702B LEU* 3.5 25.1 - - + -
706B PHE* 4.2 11.2 - - + -
711B LEU* 4.7 4.0 - - + -
713B ALA* 5.8 0.2 - - + -
717B GLN* 5.0 8.3 - - - +
718B THR* 6.2 0.2 - - - +
721B LEU* 5.1 2.0 - - + -
988B TYR* 3.9 19.1 - - + +
1001B LEU* 2.9 47.4 + - + +
1002B GLY* 3.5 4.5 - - - +
1004B ASP* 1.3 76.2 - - - +
1006B PHE* 1.3 53.4 + - - +
1008B PHE* 3.0 2.4 + - - +
1009B LEU* 2.7 57.1 + - + +
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Residues in contact with PHE1006 (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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718B THR* 3.3 47.1 - - + -
719B LEU* 4.8 2.9 - - + -
721B LEU* 4.2 8.0 - - + +
722B GLY* 3.4 22.0 - - - -
725B ILE* 3.6 34.3 - - + -
726B ASP* 4.5 16.4 - - - -
1002B GLY 3.0 9.8 + - - +
1003B ILE 3.9 1.1 - - - +
1005B VAL* 1.3 79.4 - - - +
1007B ARG* 1.3 58.7 + - + +
1009B LEU* 3.1 5.6 + - - +
1010B VAL* 2.7 64.1 + - + +
1017B VAL* 5.7 0.2 - - + -
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Residues in contact with ARG1007 (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* 2.7 52.7 + - + +
1004B ASP* 3.6 16.3 + - - +
1005B VAL 3.2 0.2 - - - -
1006B PHE* 1.3 80.3 - - + +
1008B PHE* 1.3 64.0 + - - +
1010B VAL* 3.6 10.3 - - + +
1011B ARG* 2.9 68.8 + - - +
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Residues in contact with PHE1008 (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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701B LYS* 3.2 40.2 - - + -
702B LEU* 3.8 9.4 - - + -
704B GLU* 4.0 3.1 - - - -
705B ARG* 3.4 36.1 - - + +
706B PHE* 3.8 16.4 - + + -
1004B ASP 2.7 21.8 + - - +
1005B VAL 3.3 2.5 - - - +
1007B ARG* 1.3 72.7 - - - +
1009B LEU* 1.3 79.7 + - + +
1011B ARG* 3.0 8.4 + - + +
1012B ARG* 2.8 69.6 + - + +
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Residues in contact with LEU1009 (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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698B LEU* 4.6 30.1 - - + +
701B LYS* 5.4 2.9 - - + -
702B LEU* 3.4 37.2 - - + -
713B ALA* 4.9 2.9 - - + -
718B THR* 4.4 25.4 - - + +
1005B VAL* 2.7 43.8 + - + +
1006B PHE* 3.7 3.1 - - - +
1008B PHE* 1.3 90.8 - - + +
1010B VAL* 1.3 58.6 + - - +
1011B ARG 3.1 4.2 + - - -
1012B ARG* 3.8 4.9 + - + +
1013B TYR 3.3 22.6 - - - +
1014B ALA* 3.8 1.7 - - - +
1017B VAL* 5.4 8.8 - - + +
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Residues in contact with VAL1010 (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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718B THR* 5.3 3.3 - - + +
1006B PHE* 2.7 55.3 + - + +
1007B ARG* 3.6 12.8 - - - +
1009B LEU* 1.3 72.9 - - - +
1011B ARG* 1.3 60.9 + - + +
1014B ALA* 3.3 28.7 + - + +
1017B VAL* 5.9 1.6 - - + -
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Residues in contact with ARG1011 (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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1007B ARG* 2.9 65.4 + - - +
1008B PHE* 3.5 5.9 - - + +
1009B LEU 3.0 0.6 - - - -
1010B VAL* 1.3 79.9 - - + +
1012B ARG* 1.3 54.7 + - - +
1013B TYR* 2.6 19.2 + - - -
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Residues in contact with ARG1012 (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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701B LYS* 5.4 14.7 - - - +
704B GLU* 4.1 13.4 + - - -
1008B PHE* 2.8 55.7 + - + +
1009B LEU* 4.1 4.1 - - + +
1011B ARG* 1.3 70.4 - - + +
1013B TYR* 1.3 73.1 + - - +
1016B PHE* 5.0 0.7 - - - -
1053B ILE* 5.8 6.5 - - - +
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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