Contacts of the helix formed by residues 817 - 829 (chain A) in PDB entry 1KEK
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 GLU 817 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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815A CYS* 3.4 6.8 - - - -
816A GLY* 1.3 80.5 - - - +
818A THR* 1.4 65.2 + - - +
819A PRO* 3.5 0.4 - - - -
820A TYR* 3.3 21.5 + - - +
821A VAL* 3.5 9.5 + - - +
840A CYS* 3.5 9.7 - - - +
841A SER 3.7 1.2 + - - -
844A TRP* 2.9 26.1 + - + +
989A MET* 3.3 47.6 - - + +
991A THR* 3.4 13.2 - - - +
1069A ALA* 4.2 7.2 - - + -
2235A SF4 3.5 20.6 - - - -
2236A HTL 2.6 24.1 + - - -
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Residues in contact with THR 818 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700A PRO* 2.8 32.5 + - - +
806A MET* 3.8 13.9 - - + -
809A SER* 3.8 20.4 - - - +
811A ALA* 3.8 11.4 - - + -
815A CYS* 3.6 6.7 + - - +
817A GLU* 1.4 74.8 - - - +
819A PRO* 1.3 75.3 - - - +
821A VAL* 3.2 7.9 - - - +
822A ARG* 3.0 25.4 + - - +
844A TRP* 3.7 26.2 - - + +
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Residues in contact with PRO 819 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697A PHE 4.3 2.1 - - - +
698A VAL 3.4 28.5 - - - +
699A CYS 4.1 9.9 - - - +
700A PRO* 3.7 11.4 - - + -
815A CYS 3.2 15.9 - - - +
816A GLY* 4.0 6.3 - - - +
817A GLU 3.5 4.5 - - - -
818A THR* 1.3 97.3 - - - +
820A TYR* 1.4 64.0 + - + +
822A ARG* 3.5 3.8 + - + +
823A VAL* 3.1 27.5 + - - +
1042A MET* 3.6 23.6 - - + -
1084A GLN* 4.9 4.5 - - - +
1087A MET* 5.8 2.2 - - + -
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Residues in contact with TYR 820 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816A GLY 3.0 29.2 - - - -
817A GLU* 3.3 8.7 + - - +
818A THR 3.2 0.8 - - - -
819A PRO* 1.4 80.5 - - + +
821A VAL* 1.3 63.0 + - - +
823A VAL* 3.2 2.8 + - - -
824A ILE* 3.0 26.5 + - - +
987A PHE* 3.6 24.0 - + + -
989A MET* 5.1 2.2 - - + -
1040A VAL* 4.0 8.7 - - + -
1041A SER* 3.6 6.6 - - - -
1042A MET* 3.0 50.6 + - + +
1049A PHE* 3.6 27.7 - + - -
1067A ALA* 3.7 19.1 - - + -
1068A TYR 2.7 28.5 + - - -
1069A ALA* 4.5 0.7 - - - -
1087A MET* 3.6 11.0 - - + +
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Residues in contact with VAL 821 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806A MET* 3.3 24.2 - - + -
817A GLU 3.5 1.5 + - - +
818A THR* 3.2 17.5 - - - +
820A TYR* 1.3 75.0 - - - +
822A ARG* 1.3 63.4 + - - +
824A ILE* 3.2 9.6 + - - +
825A THR* 3.0 27.3 + - - +
844A TRP* 3.4 20.4 - - + -
853A TYR* 4.5 4.9 - - + +
960A PHE* 3.7 29.8 - - + -
987A PHE* 4.6 6.5 - - + -
989A MET* 3.8 28.3 - - - -
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Residues in contact with ARG 822 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696A ALA* 2.8 28.6 + - - +
697A PHE* 4.0 7.5 + - - +
699A CYS 4.1 11.4 + - - -
700A PRO 5.9 0.4 - - - -
701A HIS 5.2 0.7 - - - +
702A SER* 2.9 43.7 + - - +
704A ILE 4.2 14.5 + - - -
706A PRO* 5.3 3.0 - - - +
800A GLN* 2.8 27.6 + - - +
804A PRO* 3.4 19.2 - - + +
806A MET* 4.0 19.1 - - + +
818A THR 3.0 17.8 + - - +
819A PRO* 3.7 4.5 - - - +
821A VAL* 1.3 77.4 - - - +
823A VAL* 1.3 61.4 + - - +
825A THR* 2.6 25.5 + - - -
826A GLN* 3.2 26.9 + - - +
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Residues in contact with VAL 823 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697A PHE* 3.9 37.0 - - + +
799A SER* 5.2 0.4 - - - -
800A GLN* 4.5 1.3 - - - +
819A PRO 3.1 18.6 + - - +
820A TYR 3.2 0.2 + - - -
822A ARG* 1.3 71.7 - - - +
824A ILE* 1.3 67.9 + - - +
826A GLN* 2.9 30.9 + - + +
827A LEU* 3.2 14.1 + - + +
1042A MET* 4.1 2.7 - - + -
1049A PHE* 3.5 27.6 - - + -
1050A LEU* 3.7 26.7 - - + -
1053A LEU* 4.1 4.3 - - + -
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Residues in contact with ILE 824 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820A TYR 3.0 19.5 + - - +
821A VAL* 3.5 8.5 - - - +
823A VAL* 1.3 77.1 - - - +
825A THR* 1.3 62.3 + - - +
827A LEU* 3.1 3.0 + - - -
828A PHE* 3.0 36.4 + - + -
829A GLY 4.0 0.2 + - - -
832A MET* 3.7 27.1 - - + -
958A TRP* 4.4 10.5 - - + -
960A PHE* 4.2 15.3 - - + -
987A PHE* 3.7 44.6 - - + -
1049A PHE* 4.3 1.1 - - + -
1053A LEU* 3.7 29.4 - - + -
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Residues in contact with THR 825 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793A ARG* 4.2 2.9 + - - -
803A GLU 4.4 2.0 - - - +
805A LEU* 2.9 44.5 + - + +
806A MET* 3.9 5.0 + - + -
821A VAL* 3.0 14.7 + - + +
822A ARG 2.6 18.7 + - - -
824A ILE* 1.3 78.2 - - + +
826A GLN* 1.3 56.8 + - - +
827A LEU 3.0 0.4 - - - -
829A GLY* 2.8 30.4 + - - +
832A MET* 4.4 9.0 - - + -
834A ILE* 5.4 0.7 - - + -
853A TYR* 4.3 16.4 - - + -
862A PRO* 4.1 20.0 - - + -
960A PHE* 6.0 1.3 - - + -
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Residues in contact with GLN 826 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793A ARG* 2.9 28.8 + - - +
799A SER* 3.3 25.2 + - - +
800A GLN* 2.7 41.0 + - - +
802A GLN* 3.4 23.6 + - + +
803A GLU 3.7 20.4 - - - +
804A PRO* 3.7 8.6 - - + +
822A ARG* 3.2 31.7 + - - +
823A VAL* 2.9 23.2 + - - +
825A THR* 1.3 74.8 - - - +
827A LEU* 1.3 63.1 + - + +
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Residues in contact with LEU 827 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793A ARG* 3.3 49.2 + - + +
794A ASP* 4.4 16.2 - - + -
799A SER* 4.3 7.6 - - - -
823A VAL* 3.2 13.7 + - + +
824A ILE* 3.1 7.7 + - - +
825A THR 3.0 0.4 - - - -
826A GLN* 1.3 84.7 - - + +
828A PHE* 1.3 85.7 + - + +
830A GLU* 4.6 0.7 - - - +
831A ARG* 5.5 0.7 + - - -
1050A LEU* 3.9 29.4 - - + +
1053A LEU* 3.9 32.8 - - + -
1054A LYS* 4.7 2.9 - - + +
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Residues in contact with PHE 828 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824A ILE* 3.0 20.9 + - + +
827A LEU* 1.3 107.5 - - + +
829A GLY* 1.3 64.1 + - - +
830A GLU* 3.3 10.5 - - - -
831A ARG* 3.0 33.7 + - - +
832A MET* 3.4 16.7 + - - +
956A SER* 4.5 12.3 - - - +
958A TRP* 3.6 27.4 - + - +
1053A LEU* 3.7 27.6 - - + -
1054A LYS* 4.4 5.8 - - + -
1057A GLU* 3.5 39.0 - - + -
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Residues in contact with GLY 829 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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805A LEU* 3.7 15.5 - - - -
825A THR* 2.8 30.3 + - - -
828A PHE* 1.3 70.3 - - - +
830A GLU* 1.3 62.2 + - - +
831A ARG 3.2 1.4 + - - -
832A MET* 3.4 23.0 + - - +
861A GLY 3.3 0.9 - - - -
862A PRO* 3.2 25.0 - - - -
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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