Contacts of the helix formed by residues 784 - 794 (chain A) in PDB entry 2KFZ
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 ALA 784 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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770A ALA 3.1 25.8 - - - +
773A LEU* 3.5 20.2 - - + +
774A ALA* 3.8 20.2 - - + -
779A ILE* 3.7 13.2 - - + -
780A PRO 3.3 2.7 + - - +
782A LYS 4.7 1.8 - - - +
783A GLU* 1.3 78.6 - - - +
785A GLN* 1.3 64.0 + - - +
786A LYS 3.1 0.4 - - - -
787A TYR* 3.1 14.6 + - - +
788A MET* 3.2 18.6 + - - +
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Residues in contact with GLN 785 (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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770A ALA* 3.1 30.8 + - + +
771A PHE* 5.1 7.0 - - + -
782A LYS* 3.4 34.2 - - + +
784A ALA* 1.3 81.2 - - - +
786A LYS* 1.3 58.8 + - - +
788A MET* 3.5 4.1 + - - +
789A ASP* 2.8 66.4 + - - +
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Residues in contact with LYS 786 (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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782A LYS 3.3 14.0 + - - +
783A GLU* 3.3 26.2 - - - +
784A ALA 3.1 0.6 - - - -
785A GLN* 1.3 80.7 - - - +
787A TYR* 1.3 66.7 + - + +
789A ASP* 4.1 6.6 - - - +
790A LEU* 3.3 42.3 + - + +
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Residues in contact with TYR 787 (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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741A VAL* 4.0 6.7 - - + +
742A PHE* 3.7 38.6 - + - -
756A SER* 4.2 6.2 + - - -
760A ILE* 3.7 22.1 - - + +
773A LEU* 4.9 1.6 - - + -
777A LEU* 4.1 16.2 - - + -
779A ILE* 3.6 30.7 - - + +
783A GLU* 3.0 38.6 + - - -
784A ALA* 3.1 7.5 + - - +
786A LYS* 1.3 86.4 - - + +
788A MET* 1.3 60.3 + - - +
790A LEU* 3.3 14.2 + - + +
791A TYR* 2.9 27.4 + - - +
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Residues in contact with MET 788 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760A ILE* 5.0 13.7 - - + +
763A GLY* 5.8 1.1 - - - -
764A LEU* 4.3 26.5 - - + +
768A MET* 3.7 23.1 - - + +
769A SER 4.8 0.4 - - - -
770A ALA* 3.4 36.6 - - + +
773A LEU* 4.5 19.5 - - + -
784A ALA 3.2 12.6 + - - +
785A GLN* 4.1 6.7 - - - +
786A LYS 3.5 0.2 - - - -
787A TYR* 1.3 74.5 - - + +
789A ASP* 1.3 64.8 + - - +
791A TYR* 3.5 6.5 - - - +
792A PHE* 3.0 50.9 + - + -
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Residues in contact with ASP 789 (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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785A GLN* 2.8 52.1 + - - +
786A LYS* 4.1 6.4 - - - +
788A MET* 1.3 77.4 - - - +
790A LEU* 1.3 64.6 + - - +
792A PHE* 3.5 9.1 + - - +
793A GLU* 3.1 26.5 + - - +
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Residues in contact with LEU 790 (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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741A VAL* 3.6 35.7 - - + +
742A PHE* 5.7 4.0 - - + -
786A LYS* 3.3 42.8 + - + +
787A TYR* 3.3 17.2 + - + +
789A ASP* 1.3 79.4 - - + +
791A TYR* 1.3 59.6 + - - +
793A GLU* 3.7 11.8 + - - +
794A ARG* 3.3 40.7 + - - +
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Residues in contact with TYR 791 (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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321A MG 1.9 35.4 - - - -
714A MET* 3.8 6.9 - - - +
723A LEU* 4.2 4.7 - - - +
737A THR* 3.5 23.1 - - + -
741A VAL* 3.9 15.0 - - + +
760A ILE* 3.5 23.8 - - + -
761A ASN* 3.1 11.9 + - - -
764A LEU* 3.4 27.1 - - + +
787A TYR 2.9 15.8 + - - +
788A MET* 3.5 9.6 - - - +
790A LEU* 1.3 76.4 - - - +
792A PHE* 1.3 67.3 + + + +
794A ARG* 3.1 2.6 + - - -
795A TYR* 2.7 56.5 + + + +
798A VAL* 4.2 9.9 - - + -
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Residues in contact with PHE 792 (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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764A LEU* 3.7 28.7 - - + -
788A MET* 3.0 40.9 + - + +
789A ASP* 3.5 9.4 + - - +
791A TYR* 1.3 83.9 - + - +
793A GLU* 1.3 57.0 + - - +
795A TYR 3.8 4.3 - - - -
796A PRO* 3.1 29.1 - - - +
798A VAL* 4.0 10.8 - - + -
799A LEU* 3.7 47.3 - - + +
802A MET* 3.8 25.4 - - + -
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Residues in contact with GLU 793 (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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789A ASP 3.1 18.8 + - - +
790A LEU* 3.9 15.4 - - - +
791A TYR 3.1 0.4 - - - -
792A PHE* 1.3 78.1 - - - +
794A ARG* 1.3 92.8 + - - +
796A PRO* 4.0 8.4 - - - +
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Residues in contact with ARG 794 (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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720A ASP* 4.7 0.7 - - - +
722A GLY* 6.0 0.2 - - - -
740A GLU* 3.2 70.3 + - + +
741A VAL* 5.1 0.7 - - - +
790A LEU* 3.3 30.6 + - - +
791A TYR* 3.1 4.8 + - - +
793A GLU* 1.3 119.2 + - - +
795A TYR* 1.3 71.2 + - + +
796A PRO* 3.3 8.3 - - - +
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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