Contacts of the helix formed by residues 75 - 80 (chain A) in PDB entry 2KWI
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 TYR 75 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LYS* 4.9 22.8 - - - -
70A ALA* 3.4 29.0 - - + +
72A LEU* 3.7 18.6 - - + +
73A GLU 3.6 0.6 - - - -
74A ASP* 1.3 89.5 - - + +
76A ALA* 1.3 56.1 + - - +
77A ALA 3.0 6.3 - - - +
78A ILE* 3.0 44.9 + - + +
413B HIS* 5.3 5.4 - - + -
414B ARG* 6.4 0.4 - - + -
417B GLN* 3.3 29.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU 6.3 0.4 - - - +
73A GLU* 3.7 19.2 + - - +
74A ASP 2.7 10.1 + - - +
75A TYR* 1.3 68.6 - - - +
77A ALA* 1.3 56.5 + - - +
78A ILE 3.0 5.6 - - - -
79A ARG* 3.8 9.4 - - - +
80A ASP* 2.8 48.0 + - + +
81A ASN* 3.2 10.7 + - - +
417B GLN* 5.5 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TYR 3.0 0.8 - - - -
76A ALA* 1.3 78.7 - - - +
78A ILE* 1.3 58.1 + - + +
81A ASN* 3.1 32.4 - - - +
82A TYR* 2.9 21.8 - - - -
412B LEU 4.5 0.2 - - - +
413B HIS* 3.3 35.0 - - + +
416B LEU* 3.7 7.2 - - + -
417B GLN* 3.5 17.4 - - + +
429B LEU* 3.9 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LYS* 3.2 37.7 - - + +
48A ALA* 4.3 9.2 - - + -
67A LEU* 6.0 1.1 - - + -
69A THR* 3.1 24.4 - - + +
70A ALA* 3.7 14.4 - - + +
75A TYR* 3.0 42.7 + - + +
77A ALA* 1.3 81.1 - - + +
79A ARG* 1.3 59.7 + - - +
82A TYR* 3.1 33.2 - - + +
413B HIS* 3.7 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 4.8 7.2 - - + -
21A GLY 5.9 1.8 - - - -
69A THR* 4.1 13.1 + - - +
70A ALA 3.2 16.4 + - - +
71A GLY* 3.8 25.2 - - - -
72A LEU 4.7 9.5 + - - +
73A GLU* 5.6 6.4 + - - +
75A TYR 3.5 3.6 + - - +
76A ALA* 3.3 7.9 + - - +
78A ILE* 1.3 82.4 - - - +
80A ASP* 1.3 103.7 + - - +
82A TYR* 4.0 0.7 - - - +
83A PHE* 3.1 50.5 + - + -
107A PHE* 4.9 21.2 - - - -
110A GLN* 4.7 10.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ALA* 2.8 28.5 + - + +
79A ARG* 1.3 115.6 + - - +
81A ASN* 1.3 63.7 + - - +
82A TYR 3.1 4.0 - - - -
83A PHE* 3.0 35.3 + - + +
84A ARG 4.5 1.0 + - - -
110A GLN* 3.4 23.6 - - - +
114A VAL* 4.4 14.9 - - + +
426B GLU* 5.3 1.0 - - - +
----------------------------------------------------------
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