Contacts of the helix formed by residues 59 - 75 (chain A) in PDB entry 2KSO
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 GLY 59 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU 3.2 0.8 - - - -
58A PRO* 1.3 84.8 - - - +
60A HIS* 1.3 55.8 + - - +
61A GLN 3.0 0.2 - - - -
62A LYS* 3.1 19.6 + - - +
63A ARG* 3.1 15.9 + - - +
47B HIS* 3.2 14.2 + - - +
48B ASN* 3.2 33.6 + - - +
66B GLU* 5.0 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A MET* 3.3 14.6 - - + +
26A GLN* 3.9 23.8 - - - -
27A TYR* 2.8 43.1 + + + +
55A VAL* 3.8 8.5 - - + -
57A LEU* 3.2 25.4 + - + +
59A GLY* 1.3 70.9 - - - +
61A GLN* 1.3 56.1 + - - +
62A LYS 3.0 9.3 + - - -
63A ARG* 3.8 4.9 - - - -
64A ILE* 3.2 30.7 + - - +
46B VAL 3.5 9.5 + - - -
47B HIS 3.0 21.4 + - - -
48B ASN 3.2 15.7 - - - -
49B GLY* 3.1 18.0 + - - -
51B ASP* 5.2 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASN* 4.4 5.5 + - - -
50A ILE* 4.5 8.5 - - + +
51A LYS* 2.9 47.4 + - + +
55A VAL* 2.9 35.4 + - + -
56A ARG* 3.5 14.1 + - - +
57A LEU 3.1 16.3 + - - +
58A PRO* 3.1 19.3 + - - +
59A GLY 3.0 0.6 - - - -
60A HIS* 1.3 76.7 - - - +
62A LYS* 1.3 56.5 + - - +
65A ALA* 3.2 22.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PRO 3.5 6.7 + - - +
59A GLY* 3.1 8.9 + - - +
60A HIS 3.0 0.4 - - - -
61A GLN* 1.3 80.3 - - - +
63A ARG* 1.3 59.9 + - - +
64A ILE 3.2 1.6 - - - -
65A ALA* 3.8 3.6 - - + -
66A TYR* 2.8 58.5 + - + +
62B GLU* 3.2 16.2 + - - +
63B ASP* 4.2 2.0 + - - +
65B GLU* 2.7 26.9 + - - +
66B GLU* 2.8 43.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 3.1 45.8 - - + +
24A MET* 3.9 10.8 - - + -
59A GLY 3.1 9.6 + - - +
60A HIS* 4.0 7.4 - - - +
62A LYS* 1.3 78.9 - - - +
64A ILE* 1.3 56.5 + - - +
66A TYR* 4.5 4.4 - - - +
67A SER* 2.7 30.2 + - - -
48B ASN* 2.9 31.7 + - - +
49B GLY* 5.0 1.1 - - - -
50B TRP* 3.1 31.5 - - - +
63B ASP* 2.7 23.4 + - - -
66B GLU* 2.6 46.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TRP* 3.9 21.6 - - + -
22A ILE* 4.6 3.1 - - + -
24A MET* 4.0 18.6 - - + -
27A TYR* 3.8 26.7 - - + -
31A PHE* 4.0 17.5 - - + -
50A ILE* 3.8 27.4 - - + -
55A VAL* 3.9 20.2 - - + -
60A HIS 3.2 17.8 + - - +
62A LYS 3.2 0.4 - - - -
63A ARG* 1.3 75.6 - - - +
65A ALA* 1.3 54.7 + - - +
67A SER* 3.4 2.4 + - - -
68A LEU* 2.7 48.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASN* 3.5 25.8 - - - +
50A ILE* 3.9 12.7 - - + +
61A GLN 3.2 23.6 + - - +
62A LYS* 3.4 4.3 + - + +
64A ILE* 1.3 78.5 - - - +
66A TYR* 1.3 63.4 + - - +
68A LEU* 3.1 4.9 + - - +
69A LEU* 3.0 33.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS* 2.8 43.7 + - + +
63A ARG* 4.5 4.9 - - - +
65A ALA* 1.3 73.1 - - - +
67A SER* 1.3 64.7 + - - +
69A LEU* 3.2 35.4 + - + +
70A GLY* 3.4 4.0 + - - -
62B GLU* 3.5 29.4 + - + -
63B ASP* 4.3 24.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TRP* 3.2 28.3 - - - -
22A ILE* 3.5 15.6 - - - +
63A ARG* 2.7 24.9 + - - -
64A ILE 3.4 1.3 + - - -
65A ALA 3.3 0.4 - - - -
66A TYR* 1.3 82.3 - - - +
68A LEU* 1.3 61.8 + - - +
70A GLY* 3.1 5.1 + - - +
71A LEU* 3.1 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TRP* 4.0 9.8 - - + -
42A VAL* 3.4 38.8 - - + +
43A VAL* 4.6 1.8 - - - -
45A MET* 3.8 23.1 - - - +
46A THR 5.3 0.2 - - - -
50A ILE* 3.2 40.2 - - + -
64A ILE* 2.7 28.0 + - + +
65A ALA* 3.3 6.1 - - - +
67A SER* 1.3 73.7 - - - +
69A LEU* 1.3 58.5 + - + +
71A LEU* 3.1 11.0 + - + +
72A LYS* 2.8 48.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASN* 5.6 5.4 - - - +
65A ALA* 3.0 24.4 + - + +
66A TYR* 3.2 25.5 + - + +
68A LEU* 1.3 76.1 - - + +
70A GLY* 1.3 63.4 + - - +
72A LYS* 3.4 18.8 + - + +
73A ASP* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TYR 3.4 4.8 + - - -
67A SER* 3.1 8.0 + - - -
69A LEU* 1.3 79.5 - - - +
71A LEU* 1.3 51.5 + - - +
73A ASP* 3.1 6.9 + - - +
74A GLN* 2.7 44.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TRP* 3.8 48.7 - - + +
39A ILE* 4.9 14.8 - - + -
42A VAL* 4.8 5.8 - - + -
43A VAL* 3.8 18.4 - - + +
67A SER 3.1 13.0 + - - +
68A LEU* 3.5 18.6 - - + +
70A GLY* 1.3 75.0 - - - +
72A LYS* 1.3 65.0 + - - +
74A GLN* 3.5 11.4 - - + +
75A VAL* 3.1 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL* 2.8 47.5 + - + +
44A GLN 3.4 7.1 + - - -
45A MET 3.0 25.5 + - - -
46A THR* 4.1 6.9 - - - +
68A LEU* 2.8 46.1 + - - +
69A LEU* 3.7 18.6 - - + +
71A LEU* 1.3 72.1 - - - +
73A ASP* 1.3 59.3 + - - +
75A VAL* 3.3 8.7 - - - +
76A ASN* 2.8 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU 3.0 16.5 + - - +
70A GLY* 3.6 6.1 - - - +
72A LYS* 1.3 75.4 - - - +
74A GLN* 1.3 65.1 + - - +
76A ASN* 2.9 19.0 + - - +
77A THR* 2.8 27.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLY* 2.7 31.1 + - - +
71A LEU* 3.5 14.8 - - + +
73A ASP* 1.3 74.6 - - + +
75A VAL* 1.3 60.9 + - - +
77A THR* 3.1 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 6.0 6.1 - - + -
40A GLU* 6.3 2.5 - - - -
43A VAL* 4.6 19.1 - - + -
71A LEU 3.1 14.5 + - - +
72A LYS* 3.3 18.8 - - - +
74A GLN* 1.3 76.3 - - - +
76A ASN* 1.3 68.7 - - - +
77A THR 3.3 2.9 - - - -
78A VAL* 4.7 7.8 - - - +
----------------------------------------------------------
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