Contacts of the helix formed by residues 782 - 795 (chain A) in PDB entry 4KXA
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 LEU 782 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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733A TRP* 3.5 51.4 - - + +
734A ASN 3.6 2.9 - - - +
735A ASP* 4.8 5.6 - - - +
745A ARG* 4.3 15.7 - - + -
746A SER* 5.5 0.9 - - - +
749A LEU* 3.9 26.7 - - + -
767A LEU* 4.5 5.8 - - + -
778A LEU* 5.6 0.4 - - + -
779A PRO* 2.9 34.3 + - + +
781A ASN* 1.3 86.3 - - + +
783A ARG* 1.3 66.4 + - - +
784A LEU 3.4 2.7 - - - -
785A LEU* 3.1 14.1 + - + +
786A VAL* 2.9 29.4 + - + +
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Residues in contact with ARG 783 (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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377A LYS 3.9 2.8 + - - -
378A GLU* 2.8 61.4 + - - +
771A TRP* 6.5 0.2 - - - -
777A SER* 2.9 24.2 + - - +
778A LEU* 3.2 39.2 + - + +
779A PRO 3.3 7.4 + - - +
780A VAL* 3.9 13.7 - - - +
781A ASN 3.7 0.8 - - - -
782A LEU* 1.3 75.3 - - - +
784A LEU* 1.3 64.6 + - - +
786A VAL* 3.0 8.1 + - - +
787A TYR* 2.8 47.2 + - + +
815A GLU* 2.9 36.6 + - - -
818A LYS* 4.1 7.6 - - + -
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Residues in contact with LEU 784 (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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780A VAL 5.1 0.4 + - - -
781A ASN 5.4 1.0 - - - +
782A LEU 3.4 0.4 - - - -
783A ARG* 1.3 79.2 - - - +
785A LEU* 1.3 61.2 + - + +
787A TYR* 3.2 5.0 + - - -
788A ARG* 2.9 45.4 + - + +
818A LYS* 3.9 38.1 - - + +
821A TYR* 3.8 45.8 - - + -
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Residues in contact with LEU 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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733A TRP* 4.5 17.0 - - + -
746A SER* 3.4 29.8 - - - +
749A LEU* 3.8 16.6 - - + -
750A GLY* 3.5 31.2 - - - +
753A CYS* 5.5 0.2 - - - -
764A ALA* 4.4 2.3 - - - +
781A ASN 5.1 5.6 - - - +
782A LEU* 3.1 13.5 + - + +
784A LEU* 1.3 80.5 - - + +
786A VAL* 1.3 58.4 + - - +
788A ARG* 4.4 11.4 - - - +
789A TYR* 2.8 55.5 + - + +
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Residues in contact with VAL 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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733A TRP* 4.2 10.1 - - + -
764A ALA* 3.9 7.4 - - - +
767A LEU* 3.8 31.6 - - + -
768A PHE* 3.4 38.3 - - + +
778A LEU* 3.7 26.2 - - + -
782A LEU* 2.9 21.9 + - + +
783A ARG 3.0 7.1 + - - +
785A LEU* 1.3 76.8 - - - +
787A TYR* 1.3 57.2 + - + +
790A GLY* 2.8 30.7 + - - +
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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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768A PHE* 4.4 8.9 - + + -
771A TRP* 3.6 37.2 + + - -
778A LEU* 3.7 21.1 - - + +
783A ARG* 2.8 48.9 + - + +
784A LEU* 3.8 3.1 - - - +
786A VAL* 1.3 74.8 - - + +
788A ARG* 1.3 58.4 + - + +
791A MET* 3.0 33.1 + - - +
803A THR* 6.1 1.8 - - + -
815A GLU* 2.6 31.4 + - - -
818A LYS* 3.8 35.2 - - + +
819A LEU* 4.0 16.4 - - + -
822A GLY* 3.7 19.1 - - - -
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Residues in contact with ARG 788 (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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750A GLY* 5.5 1.8 + - - -
784A LEU* 2.9 37.6 + - + +
785A LEU* 3.8 13.2 - - - +
787A TYR* 1.3 76.2 - - - +
789A TYR* 1.3 97.8 + - + +
792A GLN* 2.9 31.2 + - - +
821A TYR* 3.3 59.1 + - + -
822A GLY* 4.5 1.1 - - - -
825A SER* 3.3 21.2 + - - +
859A TYR* 6.0 1.0 - - - +
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Residues in contact with TYR 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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750A GLY 3.5 12.2 + - - -
753A CYS* 3.6 43.5 - - + -
754A LYS* 3.6 18.3 + - - +
761A LEU* 3.9 13.7 - - + -
764A ALA* 3.9 17.0 - - + -
785A LEU* 2.8 37.6 + - + +
788A ARG* 1.3 108.9 + - + +
790A GLY* 1.3 61.2 + - - +
792A GLN* 3.6 32.8 - - - -
793A ASN* 3.0 37.5 + - - +
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Residues in contact with GLY 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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764A ALA* 4.2 10.5 - - - +
765A SER* 4.5 1.3 - - - -
768A PHE* 3.5 26.5 - - - -
785A LEU 4.0 0.2 + - - -
786A VAL 2.8 20.2 + - - -
789A TYR* 1.3 77.6 - - - +
791A MET* 1.3 55.3 + - - +
794A SER* 2.9 36.2 + - - -
795A GLY 3.5 1.9 + - - -
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Residues in contact with MET 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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768A PHE* 3.9 17.9 - - + -
787A TYR* 3.0 22.8 + - + +
788A ARG 3.9 1.3 - - - +
790A GLY* 1.3 74.8 - - - +
792A GLN* 1.3 61.1 + - - +
795A GLY* 2.8 45.5 + - - +
799A SER* 3.9 10.8 - - - +
800A TRP* 4.0 24.2 - - + -
803A THR* 3.2 38.8 - - + +
822A GLY* 3.2 25.4 - - - +
823A LEU 4.7 0.2 - - - +
825A SER* 4.3 0.2 - - - -
826A VAL* 3.6 24.2 - - + +
827A LYS 4.7 0.3 + - - -
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Residues in contact with GLN 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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753A CYS 5.7 0.4 + - - -
761A LEU* 5.1 3.6 - - - +
788A ARG* 2.9 19.4 + - - +
789A TYR* 3.6 34.9 - - - +
791A MET* 1.3 79.7 - - - +
793A ASN* 1.3 73.8 + - - +
795A GLY 4.8 0.3 + - - +
825A SER* 3.5 21.9 + - - +
826A VAL* 4.8 0.2 - - - +
827A LYS* 3.8 50.3 + - + +
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Residues in contact with ASN 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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761A LEU* 3.3 51.5 + - - +
765A SER* 3.8 13.2 + - - +
789A TYR* 3.0 21.8 + - - +
792A GLN* 1.3 98.1 + - - +
794A SER* 1.3 59.4 + - - +
795A GLY 3.8 0.2 - - - -
827A LYS* 5.3 2.6 + - - -
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Residues in contact with SER 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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765A SER* 3.0 27.3 + - - -
768A PHE* 4.2 11.7 - - - -
772A LEU* 6.0 0.9 - - - +
790A GLY 2.9 12.3 + - - -
793A ASN* 1.3 77.4 - - - +
795A GLY* 1.3 66.0 + - - +
796A ASN* 3.7 10.2 + - - +
799A SER* 4.2 4.0 + - - -
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Residues in contact with GLY 795 (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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768A PHE* 4.5 1.6 - - - -
790A GLY 3.5 1.6 + - - -
791A MET* 2.8 37.3 + - - +
792A GLN 5.6 0.2 - - - +
793A ASN 3.8 0.8 - - - -
794A SER* 1.3 81.6 - - - +
796A ASN* 1.3 59.9 + - - +
799A SER* 3.5 9.4 - - - -
826A VAL* 4.4 10.9 - - - +
827A LYS 5.8 0.2 + - - -
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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