Contacts of the helix formed by residues 748 - 756 (chain A) in PDB entry 3K5M
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 ASP 748 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732A TRP* 3.0 16.4 + - - +
733A THR 3.6 24.3 - - - +
734A THR* 3.9 12.1 - - + +
746A PRO 3.7 0.8 + - - -
747A LEU* 1.3 72.6 - - - +
749A TYR* 1.3 56.6 + - - +
750A GLU* 3.2 13.5 + - - +
751A HIS* 3.1 39.6 + - + +
752A TYR* 3.1 21.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 749 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A LEU* 3.2 37.4 - - + +
674A MET* 3.6 42.8 - - + -
675A ALA 5.2 0.2 - - - -
676A GLY* 3.3 14.6 - - - -
678A LEU 6.0 0.2 - - - -
679A ASP* 2.7 36.7 + - - -
682A LEU* 3.8 17.0 - - + -
747A LEU* 3.5 26.2 + - + +
748A ASP* 1.3 69.4 + - - +
750A GLU* 1.3 61.3 + - - +
751A HIS 3.1 1.6 - - - -
752A TYR* 3.3 6.8 + + - +
753A LEU* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 750 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A MET* 4.4 11.4 - - + +
748A ASP* 3.2 10.4 + - - +
749A TYR* 1.3 78.3 - - - +
751A HIS* 1.3 60.9 + - - +
753A LEU* 3.6 24.9 - - - +
754A THR* 2.9 45.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 751 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A TYR* 2.7 37.3 + + - -
732A TRP* 3.2 56.3 - + + +
748A ASP* 3.1 34.5 + - + +
750A GLU* 1.3 77.7 - - - +
752A TYR* 1.3 66.3 + + - +
754A THR* 3.8 4.5 - - - -
755A ARG* 2.8 50.4 + - + +
812T A 3.5 13.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
642A THR* 3.8 6.7 - - + -
644A LEU* 4.2 6.5 - - + -
673A LEU* 4.0 17.0 - - + -
682A LEU* 2.8 64.4 + - + +
684A TYR* 3.7 18.6 - + - -
731A VAL* 3.5 6.8 - - - +
732A TRP* 2.9 46.0 + - + -
747A LEU* 4.5 4.3 - - + -
748A ASP 3.1 22.4 - - - -
749A TYR* 3.3 8.5 + + - +
751A HIS* 1.3 80.1 - - - +
753A LEU* 1.3 60.7 + - - +
756A GLN* 2.9 42.0 + - + +
757A LEU* 3.0 11.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
670A ILE* 4.5 31.0 - - + -
673A LEU* 3.9 14.3 - - + +
674A MET* 4.6 11.9 - - - -
749A TYR 2.9 17.4 + - - +
750A GLU* 3.6 30.5 - - - +
751A HIS 3.3 0.2 - - - -
752A TYR* 1.3 78.1 - - - +
754A THR* 1.3 61.8 + - + +
757A LEU* 3.6 11.1 + - + -
758A GLN* 3.0 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 754 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A ARG* 4.7 4.3 + - - -
750A GLU* 2.9 43.7 + - + +
751A HIS* 3.4 5.7 + - - -
753A LEU* 1.3 82.6 - - + +
755A ARG* 1.3 83.2 + - - +
758A GLN* 3.7 9.2 - - - +
759A PRO* 3.4 16.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 755 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A ARG* 6.2 0.2 - - - +
641A TRP* 3.7 7.1 - - - -
684A TYR* 4.6 1.8 - - - +
751A HIS* 2.8 47.9 + - + +
754A THR* 1.3 92.2 + - - +
756A GLN* 1.3 72.8 + - - +
759A PRO* 3.5 15.0 - - - +
811T T 4.8 7.5 + - - +
812T A 3.3 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 756 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A TRP* 3.2 25.1 - - - +
642A THR* 2.7 49.3 + - + +
644A LEU* 4.6 6.7 - - + -
645A ALA* 3.3 18.0 - - + +
684A TYR* 3.4 32.3 + - - +
752A TYR* 2.9 27.7 + - + +
755A ARG* 1.3 92.7 - - - +
757A LEU* 1.3 65.2 + - - +
758A GLN 3.4 0.9 - - - -
759A PRO* 3.4 7.2 - - - +
760A VAL* 3.5 19.8 + - - +
811T T 5.8 1.6 - - - +
----------------------------------------------------------
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