Contacts of the helix formed by residues 66 - 79 (chain A) in PDB entry 5TKM
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 HIS 66 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLN 3.3 18.4 - - - +
59A VAL 3.6 13.3 + - - -
60A TYR* 3.0 14.2 + - - -
61A PHE 2.9 24.4 + - - -
62A LYS 3.3 12.1 + - - -
63A PRO* 2.9 23.1 + - + +
65A TYR* 1.3 80.8 - - - +
67A ALA* 1.3 65.9 + - - +
68A GLU* 3.5 13.7 + - - +
69A MET* 3.2 3.1 + - - -
70A CYS* 2.9 24.7 + - - -
97A CYS* 3.5 13.0 - - + -
100A CYS* 3.6 4.8 - - - -
401A ZN 2.0 35.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A THR* 3.6 41.0 - - + +
35A LEU* 3.9 20.7 - - + +
55A PHE* 4.4 4.8 - - + +
56A ARG 4.4 2.2 - - - -
57A GLY* 3.7 16.4 - - - +
58A GLN 4.3 2.4 + - - -
66A HIS* 1.3 73.7 - - - +
68A GLU* 1.3 59.6 + - - +
70A CYS* 3.2 8.7 + - - +
71A PHE* 2.8 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A THR* 4.1 16.4 + - - +
35A LEU* 4.0 10.3 - - + +
58A GLN 5.2 0.9 - - - +
66A HIS* 3.5 18.5 - - - +
67A ALA* 1.3 85.6 + - - +
69A MET* 1.3 71.1 + - + +
71A PHE* 3.5 2.9 + - - +
72A LEU* 3.0 26.2 + - - +
90A TRP* 3.5 34.8 - - + -
92A VAL* 5.5 2.0 - - + +
94A TRP 4.2 1.6 - - - +
95A THR 4.0 4.7 - - - +
96A PRO* 3.4 38.2 - - + +
97A CYS 5.0 0.7 - - - -
100A CYS* 4.1 8.3 - - + -
104A LEU* 4.3 2.1 - - + +
401A ZN 4.0 3.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PRO* 3.2 34.5 - - + +
64A GLN* 4.6 8.7 - - - +
66A HIS 3.2 3.5 + - - +
68A GLU* 1.3 85.6 - - + +
70A CYS* 1.3 61.0 + - - +
71A PHE 3.2 0.4 - - - -
72A LEU* 3.9 24.5 - - + +
73A SER* 2.9 32.7 + - - -
100A CYS* 3.7 31.9 - - + +
103A LYS* 3.9 33.9 - - + -
104A LEU* 4.4 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASN* 4.8 4.5 + - - +
55A PHE* 3.7 24.5 - - + -
56A ARG 4.4 13.5 - - - -
64A GLN 4.7 8.7 + - - -
65A TYR* 4.6 7.2 - - - -
66A HIS 2.9 22.0 + - - -
67A ALA* 3.3 12.1 - - - +
69A MET* 1.3 76.2 - - - +
71A PHE* 1.3 62.2 + - - +
73A SER* 4.0 3.8 - - - -
74A TRP* 3.1 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 4.2 4.7 - - + -
37A TYR* 3.5 47.3 - + + -
39A VAL* 4.3 2.5 - - + -
55A PHE* 3.8 17.4 - + + -
67A ALA 2.8 18.1 + - - +
68A GLU 3.7 4.5 - - - +
70A CYS* 1.3 77.7 - - - +
72A LEU* 1.3 69.3 + - + +
74A TRP* 3.3 10.1 + + - +
75A PHE* 2.8 52.6 + + + +
88A ILE* 3.7 32.3 - - + -
90A TRP* 3.5 34.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLU 3.0 16.0 + - - +
69A MET* 3.3 30.0 + - + +
71A PHE* 1.3 87.2 - - + +
73A SER* 1.3 59.4 + - - +
75A PHE* 3.8 2.6 - - + +
76A CYS* 3.0 39.7 + - - -
103A LYS* 4.3 18.6 - - + +
104A LEU* 4.1 19.1 - - + -
107A PHE* 3.8 45.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A MET 2.9 18.4 + - - -
70A CYS* 4.0 4.3 - - - -
72A LEU* 1.3 76.7 - - - +
74A TRP* 1.3 61.9 + - - +
76A CYS* 3.6 3.8 + - - +
77A GLY* 3.1 19.8 + - - -
78A ASN* 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASN* 4.4 13.8 - - + +
8A PRO* 3.9 23.2 - - + +
37A TYR* 3.6 39.5 - + - -
39A VAL* 4.4 2.5 - - + -
51A ASP* 4.1 13.0 - - + -
55A PHE* 3.5 20.0 - + + -
70A CYS 3.1 17.9 + - - +
71A PHE* 3.7 20.9 - + - +
73A SER* 1.3 76.8 - - - +
75A PHE* 1.3 80.0 + + + +
77A GLY 3.3 0.2 + - - -
78A ASN* 2.9 68.1 + - + +
79A GLN* 3.5 39.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 4.2 16.4 - - + -
71A PHE* 2.8 46.2 + + + +
72A LEU* 3.8 4.7 - - + +
74A TRP* 1.3 82.4 - + + +
76A CYS* 1.3 61.3 + - - +
79A GLN* 2.8 55.3 + - + +
80A LEU* 3.2 31.8 + - + -
86A PHE* 4.0 25.8 - + + -
88A ILE* 3.9 20.2 - - + -
107A PHE* 3.8 28.3 - + - -
114A VAL* 4.5 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 3.0 25.2 + - - +
73A SER* 4.2 4.3 - - - +
75A PHE* 1.3 76.4 - - - +
77A GLY* 1.3 57.8 + - - +
80A LEU* 3.0 38.3 - - + +
81A PRO* 5.1 0.2 - - - +
107A PHE* 4.0 30.1 - - - -
111A HIS* 5.6 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A SER 3.1 15.4 + - - -
74A TRP 3.8 2.2 - - - -
75A PHE 3.2 0.2 - - - -
76A CYS* 1.3 77.8 - - - +
78A ASN* 1.3 67.9 + - - +
80A LEU 4.0 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A SER 4.9 0.2 + - - -
74A TRP* 2.9 62.4 + - + +
77A GLY* 1.3 86.3 - - - +
79A GLN* 1.3 67.2 + - - +
80A LEU 3.7 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 4.6 4.0 - - + -
50A TRP* 3.6 23.0 + - - -
51A ASP* 2.4 39.9 + - - -
74A TRP* 3.5 21.6 - - + -
75A PHE* 2.8 48.5 + - + +
78A ASN* 1.3 83.3 + - - +
80A LEU* 1.3 63.4 + - - +
81A PRO 4.1 0.9 - - - +
82A ALA* 3.4 21.3 - - - +
86A PHE* 3.8 11.5 - - + -
----------------------------------------------------------
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