Contacts of the helix formed by residues 662 - 671 (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 662 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470B ASP* 4.5 3.5 + - - -
523B PHE* 3.4 10.5 - - - -
660B GLU* 2.7 34.5 + - - +
661B VAL* 1.3 76.5 - - - +
663B ARG* 1.3 60.3 + - - +
664B ARG* 3.5 12.6 + - + +
665B ALA* 2.9 28.2 + - + +
666B ILE* 2.8 29.5 + - - +
805B GLY 5.3 0.2 - - - -
850B THR* 5.3 3.8 - - - -
851B ARG* 3.8 27.5 + - - +
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Residues in contact with ARG 663 (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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250B THR* 4.8 12.9 + - - -
251B VAL* 5.3 5.3 - - - +
252B ARG* 5.4 2.4 - - - +
469B TYR* 4.0 12.7 + - - +
470B ASP* 3.8 26.9 + - - +
471B ILE* 3.5 37.2 - - - +
523B PHE* 3.4 62.2 + - + +
524B PHE* 4.2 9.8 - - + -
662B THR* 1.3 75.5 + - - +
664B ARG* 1.3 62.2 + - - +
666B ILE* 3.5 3.6 + - - +
667B LEU* 3.1 43.6 + - + +
851B ARG* 5.6 0.4 - - - +
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Residues in contact with ARG 664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B ASP* 4.6 25.2 + - + +
473B PHE* 4.3 26.8 - - - -
662B THR* 3.1 11.4 + - + +
663B ARG* 1.3 78.2 - - - +
665B ALA* 1.3 66.8 + - - +
667B LEU* 3.5 7.3 + - - +
668B GLU* 3.0 44.3 + - + +
820B VAL* 5.1 21.9 - - + +
823B ARG* 5.9 2.8 - - - +
824B ILE* 6.0 3.2 - - - +
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Residues in contact with ALA 665 (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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658B PHE* 4.1 10.9 - - + +
659B HIS 5.2 0.7 - - - +
660B GLU* 3.1 39.7 - - + +
662B THR* 2.9 20.3 + - + +
664B ARG* 1.3 76.4 - - - +
666B ILE* 1.3 66.1 + - - +
668B GLU* 3.2 12.3 + - - +
669B ALA* 2.8 25.2 + - - +
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Residues in contact with ILE 666 (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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509B PHE* 4.5 16.2 - - + -
520B ILE* 4.1 26.2 - - + -
523B PHE* 3.8 15.3 - - + -
524B PHE* 4.0 21.5 - - + -
547B LEU* 5.6 1.1 - - + -
658B PHE* 4.0 26.7 - - + -
661B VAL* 4.5 0.9 - - - -
662B THR 2.8 29.4 + - - +
663B ARG* 3.9 6.5 - - - +
665B ALA* 1.3 77.5 - - - +
667B LEU* 1.3 58.3 + - - +
669B ALA* 3.0 8.7 + - - +
670B LEU* 2.8 49.3 + - + +
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Residues in contact with LEU 667 (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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471B ILE* 6.2 1.3 - - + -
524B PHE* 4.0 14.8 - - + -
542B MET* 3.9 28.0 - - + -
543B GLN* 4.4 13.7 - - - +
544B LYS* 3.9 21.1 - - - +
663B ARG* 3.1 44.9 + - + +
664B ARG* 3.9 6.1 - - - +
666B ILE* 1.3 72.2 - - - +
668B GLU* 1.3 68.7 + - + +
670B LEU* 3.3 9.8 + - + +
671B GLU* 3.1 26.4 + - - +
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Residues in contact with GLU 668 (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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664B ARG* 3.0 43.4 + - + +
665B ALA* 3.6 7.9 - - - +
667B LEU* 1.3 74.8 - - + +
669B ALA* 1.3 59.4 + - - +
671B GLU* 2.9 28.0 + - - +
672B SER* 3.1 12.9 + - - -
820B VAL* 4.7 13.5 - - - +
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Residues in contact with ALA 669 (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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509B PHE* 6.3 0.9 - - + -
656B ALA* 4.4 6.6 - - + +
657B GLU 3.8 29.8 + - - +
658B PHE* 4.1 18.6 - - + -
665B ALA 2.8 13.4 + - - +
666B ILE* 3.4 9.2 - - + +
668B GLU* 1.3 72.7 - - - +
670B LEU* 1.3 58.3 + - + +
671B GLU 2.9 5.2 - - - -
672B SER* 2.9 24.8 + - - +
673B LEU* 3.3 14.5 - - - +
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Residues in contact with LEU 670 (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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509B PHE* 4.3 19.7 - - + -
542B MET* 3.9 26.9 - - + -
544B LYS* 3.9 20.4 - - + +
545B TYR* 4.1 20.3 + - + -
547B LEU* 5.0 6.5 - - + -
627B ILE* 3.8 29.2 - - + -
656B ALA* 5.4 0.9 - - + -
666B ILE* 2.8 40.1 + - + +
667B LEU* 3.3 4.9 + - + +
669B ALA* 1.3 72.6 - - + +
671B GLU* 1.3 65.0 + - - +
672B SER 3.3 0.6 + - - -
673B LEU* 3.7 22.9 - - + +
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Residues in contact with GLU 671 (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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544B LYS* 2.8 37.8 + - - +
667B LEU 3.1 9.8 + - - +
668B GLU* 3.0 15.9 - - - +
669B ALA 2.9 0.6 - - - -
670B LEU* 1.3 84.1 - - - +
672B SER* 1.3 59.6 + - - +
673B LEU 3.8 0.8 + - - -
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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