Contacts of the helix formed by residues 744 - 757 (chain A) in PDB entry 2KLQ
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 LYS 744 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743A LEU* 1.3 75.7 - - + +
745A ARG* 1.3 71.3 + - + +
746A SER* 3.7 29.8 - - - +
747A GLU* 3.0 32.9 + - + +
748A LEU* 3.5 7.8 - - - +
794A GLY 4.9 1.8 + - - -
796A LYS 5.2 0.6 + - - -
797A GLY* 4.1 25.9 + - - -
802A SER* 5.8 1.0 + - - -
810A TYR* 4.1 24.4 - - + -
811A LEU* 5.2 3.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 745 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A ALA 5.7 0.2 - - - -
743A LEU 3.2 6.8 + - - -
744A LYS* 1.3 72.7 - - + +
746A SER* 1.3 73.7 + - - +
748A LEU* 3.1 31.7 + - + +
749A VAL* 3.7 7.2 + - - +
777A ILE* 4.0 37.3 - - + +
778A HIS* 6.3 0.6 - - - +
781A THR* 5.0 13.9 + - - +
787A LEU* 6.0 0.7 - - + -
795A LEU 4.8 5.5 + - - -
796A LYS* 4.9 11.1 + - - +
811A LEU* 3.9 38.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 746 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A LYS* 3.1 21.8 - - - +
745A ARG* 1.3 86.0 + - - +
747A GLU* 1.3 56.7 + - - +
749A VAL* 3.2 13.5 + - - +
750A ASN* 2.9 26.8 + - - +
777A ILE* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 747 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730A HIS* 5.4 5.7 + - - -
743A LEU* 5.4 6.6 - - - +
744A LYS* 3.0 28.4 + - + +
746A SER* 1.3 75.7 - - - +
748A LEU* 1.3 62.4 + - + +
750A ASN* 3.1 16.5 - - - +
751A TRP* 2.9 44.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 748 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A LEU* 4.4 12.0 - - + +
727A ILE* 4.1 25.1 - - + -
730A HIS* 3.7 42.0 - - + +
741A SER* 4.0 10.3 - - - +
742A ALA 4.7 7.0 - - - +
743A LEU* 6.3 0.2 - - + -
744A LYS 3.5 18.6 - - - +
745A ARG* 3.1 19.3 + - + +
747A GLU* 1.3 82.4 - - + +
749A VAL* 1.3 62.0 + - + +
751A TRP* 3.5 14.7 + - - +
752A TYR* 3.0 24.8 + - - +
773A ILE* 5.5 0.7 - - + -
777A ILE* 5.5 4.5 - - + -
813A VAL* 5.3 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 749 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745A ARG 4.1 3.4 - - - +
746A SER* 3.2 12.5 + - - +
748A LEU* 1.3 73.0 - - - +
750A ASN* 1.3 56.6 + - - +
752A TYR* 3.0 6.7 + - - +
753A LEU* 2.8 56.3 + - + +
770A LYS* 5.3 2.5 - - + +
773A ILE* 3.7 32.5 - - + -
774A GLU* 5.5 2.7 - - + +
777A ILE* 3.4 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 750 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746A SER 2.9 14.4 + - - +
747A GLU* 3.1 22.1 + - - +
749A VAL* 1.3 78.1 - - - +
751A TRP* 1.3 64.0 + - - +
753A LEU* 3.3 10.5 + - - +
754A LYS* 3.0 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 751 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A LEU* 3.2 33.7 - - + -
729A LEU* 5.8 3.6 - - + -
730A HIS* 3.5 43.1 + + + -
747A GLU* 2.9 41.8 + - + +
748A LEU* 3.5 17.9 - - + +
750A ASN* 1.3 74.5 - - - +
752A TYR* 1.3 59.6 + - - +
754A LYS* 3.1 13.7 + - + +
755A GLU* 2.9 55.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 752 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A ARG* 3.3 28.0 + - - +
723A ILE* 3.4 29.0 - - + +
726A LEU* 3.5 34.5 - - + -
748A LEU 3.0 21.6 + - - +
749A VAL* 3.0 7.7 + - - +
751A TRP* 1.3 82.3 - - - +
753A LEU* 1.3 59.5 + - + +
755A GLU* 3.0 22.7 - - + +
756A ILE* 2.9 48.7 + - + +
769A LYS* 3.6 30.3 - - + +
773A ILE* 4.2 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 753 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749A VAL* 2.8 41.9 + - + +
750A ASN* 3.6 8.3 - - - +
752A TYR* 1.3 79.5 - - + +
754A LYS* 1.3 61.0 + - + +
756A ILE* 3.6 20.6 - - + +
757A GLU* 3.0 33.9 + - - +
766A LEU* 4.9 6.5 - - + +
769A LYS* 4.8 0.2 - - + -
770A LYS* 3.5 47.1 - - + +
773A ILE* 4.7 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 754 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750A ASN* 3.0 33.0 - - - +
751A TRP* 3.1 17.7 + - + +
753A LEU* 1.3 81.3 - - + +
755A GLU* 1.3 56.1 + - - +
757A GLU* 3.1 35.0 + - - +
758A SER* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 755 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A LEU* 5.8 0.3 - - - +
729A LEU* 5.8 3.8 - - - +
751A TRP* 2.9 39.5 + - + +
752A TYR* 3.0 40.6 + - + +
754A LYS* 1.3 77.3 - - - +
756A ILE* 1.3 68.6 + - + +
757A GLU 3.0 8.6 + - - -
758A SER* 3.3 19.1 + - - -
759A GLU* 4.6 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 756 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752A TYR* 2.9 56.3 + - + +
753A LEU* 3.6 18.4 - - + +
755A GLU* 1.3 80.1 - - - +
757A GLU* 1.3 63.0 + - - +
758A SER 3.0 2.9 - - - -
759A GLU* 2.9 47.1 + - + +
760A ILE* 3.1 22.6 - - + +
766A LEU* 4.1 12.3 - - + -
769A LYS* 3.6 40.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 757 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753A LEU 3.0 13.3 + - - +
754A LYS* 3.1 49.6 + - - +
755A GLU 3.0 1.0 - - - +
756A ILE* 1.3 79.7 - - + +
758A SER* 1.3 63.3 + - - +
759A GLU 3.5 0.2 + - - -
760A ILE* 3.5 26.1 + - + +
766A LEU* 5.4 4.5 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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