Contacts of the helix formed by residues 790 - 804 (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 SER 790 (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* 5.8 0.4 - - - -
788B LYS 3.8 1.4 + - - -
789B PHE* 1.3 75.0 - - - +
791B VAL* 1.3 63.9 + - - +
792B LYS* 4.0 5.4 + - - +
793B GLN* 3.3 27.6 + - - +
794B THR* 3.0 23.4 + - - -
958B GLN* 3.4 27.1 - - - +
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Residues in contact with VAL 791 (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* 3.8 23.1 - - + +
784B ASN* 6.0 0.9 - - + -
790B SER* 1.3 71.6 - - - +
792B LYS* 1.3 76.8 + - + +
794B THR* 3.1 4.5 + - - -
795B MET* 3.1 26.7 + - - +
958B GLN* 3.4 28.0 - - + +
962B ILE* 3.4 33.7 - - + -
977B ALA* 3.6 21.3 - - + +
980B VAL* 3.3 27.8 - - + -
981B ASP* 4.7 3.1 - - + +
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Residues in contact with LYS 792 (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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790B SER* 3.4 5.5 + - - +
791B VAL* 1.3 84.7 - - + +
793B GLN* 1.3 61.8 + - - +
795B MET* 3.3 5.9 + - + +
796B GLN* 3.2 24.2 + - + +
977B ALA* 3.5 10.3 + - + +
978B THR* 3.3 44.1 + - - +
981B ASP* 3.2 42.5 + - + +
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Residues in contact with GLN 793 (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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788B LYS 4.4 1.7 - - - +
789B PHE* 3.3 41.9 - - + -
790B SER* 3.3 21.9 + - - +
791B VAL 3.2 0.2 - - - -
792B LYS* 1.3 80.9 - - - +
794B THR* 1.3 58.5 + - - +
796B GLN* 3.4 7.0 + - - +
797B ILE* 2.9 41.0 + - + +
875B GLU* 5.4 8.2 - - + +
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Residues in contact with THR 794 (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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779B MET* 3.9 16.6 - - + +
780B LEU* 3.7 23.3 + - + -
783B ALA* 3.5 23.7 - - + +
789B PHE* 3.1 22.6 + - - +
790B SER 3.0 14.9 + - - -
791B VAL* 3.1 8.6 + - - -
793B GLN* 1.3 75.4 - - - +
795B MET* 1.3 59.7 + - - +
797B ILE* 3.3 7.7 + - - +
798B ALA* 2.9 27.0 + - - +
879B LEU* 3.8 11.3 - - + +
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Residues in contact with MET 795 (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* 3.7 15.7 - - + -
779B MET* 4.5 8.1 - - - -
780B LEU* 3.5 23.1 - - + -
791B VAL 3.1 14.2 + - - +
792B LYS* 3.7 9.0 - - + +
794B THR* 1.3 76.0 - - - +
796B GLN* 1.3 57.5 + - - +
798B ALA* 3.8 4.4 - - - +
799B GLN* 3.0 29.9 + - - +
810B HIS* 4.1 12.8 - - + +
811B ARG* 3.5 35.7 - - + -
973B PRO 3.7 16.2 - - - +
974B SER* 5.2 1.1 - - - -
977B ALA* 3.8 20.4 - - + -
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Residues in contact with GLN 796 (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* 3.2 14.4 + - + +
793B GLN* 3.6 11.9 - - + +
795B MET* 1.3 75.3 - - - +
797B ILE* 1.3 67.3 + - + +
799B GLN* 3.1 28.6 + - - +
800B GLU* 2.4 55.3 + - - +
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Residues in contact with ILE 797 (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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789B PHE* 4.8 6.5 - - + -
793B GLN* 2.9 31.8 + - + +
794B THR* 3.3 7.6 + - - +
796B GLN* 1.3 79.0 - - + +
798B ALA* 1.3 63.3 + - - +
800B GLU* 3.2 3.6 + - - +
801B LEU* 3.1 22.1 + - + +
875B GLU* 3.9 27.8 - - + +
876B HIS* 3.5 52.0 + - + +
879B LEU* 3.4 25.4 - - + -
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Residues in contact with ALA 798 (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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779B MET* 4.2 20.0 - - + -
794B THR 2.9 18.2 + - - +
795B MET* 3.8 6.5 - - - +
796B GLN 3.3 0.2 - - - -
797B ILE* 1.3 78.6 - - - +
799B GLN* 1.3 57.8 + - - +
801B LEU* 3.2 2.2 + - - -
802B PHE* 3.0 24.6 + - - +
807B ILE* 3.2 19.3 - - + +
810B HIS* 3.6 24.6 + - + -
879B LEU* 4.1 10.1 - - + -
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Residues in contact with GLN 799 (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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631B ASP* 5.3 5.5 - - - +
795B MET 3.0 16.8 + - - +
796B GLN* 3.1 34.4 + - - +
797B ILE 3.3 0.2 - - - -
798B ALA* 1.3 76.7 - - - +
800B GLU* 1.3 59.3 + - - +
802B PHE* 3.2 3.4 + - + +
803B GLU* 2.9 46.1 + - + +
810B HIS* 3.4 32.0 + - + +
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Residues in contact with GLU 800 (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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796B GLN* 2.4 39.4 + - - +
797B ILE* 3.2 3.6 + - - +
799B GLN* 1.3 76.5 - - + +
801B LEU* 1.3 64.2 + - - +
802B PHE 3.3 0.2 - - - -
803B GLU* 3.5 18.8 - - - +
804B ASN* 3.1 31.8 + - - +
870B GLU 5.7 1.1 - - - +
871B GLY 4.6 2.9 - - - +
872B LEU* 4.1 7.7 - - + +
873B ARG* 4.3 6.9 + - - -
876B HIS* 2.8 36.5 + - + -
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Residues in contact with LEU 801 (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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797B ILE* 3.1 14.6 + - + +
798B ALA* 3.4 11.0 - - - +
799B GLN 3.2 0.2 - - - -
800B GLU* 1.3 77.1 - - - +
802B PHE* 1.3 63.2 + - - +
804B ASN* 3.4 5.7 + - - -
806B LEU* 3.1 46.8 + - + +
807B ILE* 3.7 23.8 - - + -
872B LEU* 4.1 9.2 - - + -
876B HIS* 3.6 48.0 - - + +
877B PHE* 5.9 1.3 - - + -
879B LEU* 4.2 21.1 - - + -
880B TYR* 4.3 16.4 - - + +
883B ILE* 4.6 3.1 - - + -
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Residues in contact with PHE 802 (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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516B LYS* 4.7 5.6 - - + -
631B ASP* 3.5 24.7 - - - -
632B PRO* 4.7 2.2 - - + -
658B PHE* 4.6 8.5 - + - -
659B HIS 3.6 15.9 - - - -
660B GLU* 3.6 11.9 - - - -
661B VAL* 3.3 32.9 - - + +
798B ALA 3.0 12.9 + - - +
799B GLN* 3.5 7.9 - - + +
801B LEU* 1.3 76.2 - - - +
803B GLU* 1.3 70.7 + - + +
805B GLY* 3.0 12.1 + - - -
807B ILE* 3.2 29.5 - - + +
808B THR 4.3 0.2 - - - +
809B TYR* 3.5 40.4 - + + -
810B HIS* 3.8 24.0 - + - +
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Residues in contact with GLU 803 (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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513B SER* 2.4 37.9 + - - +
515B THR* 4.0 14.9 + - + -
516B LYS* 3.9 14.3 - - + +
519B GLN* 3.5 19.8 - - - +
661B VAL* 3.9 13.2 - - - +
799B GLN* 2.9 31.9 + - + +
800B GLU* 3.5 27.9 - - - +
801B LEU 3.4 0.2 - - - -
802B PHE* 1.3 82.0 - - + +
804B ASN* 1.3 68.7 + - - +
805B GLY 3.3 1.1 + - - -
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Residues in contact with ASN 804 (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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515B THR* 2.9 28.5 - - - +
519B GLN* 3.0 27.7 + - - +
800B GLU* 3.1 21.9 + - - +
801B LEU 4.1 3.1 - - - +
802B PHE 3.1 1.0 - - - -
803B GLU* 1.3 79.8 + - - +
805B GLY* 1.3 60.7 + - - +
806B LEU* 3.4 5.3 + - + +
869B VAL* 3.6 23.3 - - + +
870B GLU 2.7 40.8 + - - +
872B LEU* 3.6 10.5 - - + +
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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