Contacts of the helix formed by residues 70 - 85 (chain A) in PDB entry 6CV8
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 GLU 70 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ALA* 4.1 9.6 - - - +
29A MET* 3.8 22.5 - - + +
32A LEU* 3.3 38.3 - - + +
58A LEU* 3.5 21.9 - - + +
61A ARG* 3.1 27.9 + - - +
67A LYS* 5.1 1.0 - - - -
68A SER* 4.1 0.4 - - - +
69A GLY* 1.3 84.4 - - - +
71A LEU* 1.3 60.7 + - - +
72A LYS 3.4 1.3 - - - -
73A THR* 3.2 9.0 + - - -
74A TRP* 3.0 26.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
55A THR* 5.2 4.5 - - + +
58A LEU* 3.8 26.4 - - + +
59A SER* 3.6 31.2 - - - +
62A ALA* 3.7 16.4 - - + -
68A SER* 3.1 20.9 + - - +
70A GLU* 1.3 74.7 - - - +
72A LYS* 1.3 68.6 + - - +
73A THR 2.9 2.3 + - - -
74A TRP* 2.9 11.5 + - + -
75A GLY* 2.8 33.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
25A GLU* 4.8 12.8 - - - +
68A SER* 3.1 23.6 + - - +
69A GLY* 5.0 3.6 - - - +
71A LEU* 1.3 78.8 - - - +
73A THR* 1.3 60.9 + - - +
75A GLY* 4.3 0.8 - - - -
76A LEU* 3.2 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PRO* 4.5 1.3 - - + -
25A GLU* 3.6 30.4 + - - +
26A ILE* 3.7 40.6 - - + +
29A MET* 3.7 21.2 - - + +
69A GLY 3.6 17.5 + - - -
70A GLU 3.2 6.6 + - - -
71A LEU 2.9 0.6 - - - -
72A LYS* 1.3 78.7 - - - +
74A TRP* 1.3 59.6 + - - +
76A LEU* 3.3 3.6 + - - +
77A VAL* 2.9 34.7 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
29A MET* 3.6 17.4 - - + -
33A LEU* 4.1 8.3 - - + -
45A LEU* 3.5 36.8 - - + -
51A TRP* 3.2 34.3 - + + -
54A ILE* 3.4 25.1 + - + -
55A THR* 2.7 36.3 + - + +
58A LEU* 3.2 35.4 - - + -
70A GLU 3.0 7.4 + - - +
71A LEU* 2.9 12.0 + - + +
73A THR* 1.3 76.9 - - - +
75A GLY* 1.3 54.3 + - - +
77A VAL* 3.2 5.7 + - + -
78A LEU* 2.7 63.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 2.8 22.3 + - - +
72A LYS* 4.7 0.9 - - - -
74A TRP* 1.3 76.2 - - - +
76A LEU* 1.3 56.8 + - - +
78A LEU* 3.7 6.4 - - - +
79A GLY* 2.8 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A CYS* 5.3 0.4 - - - +
16A CYS* 4.2 18.7 - - - -
19A THR* 3.5 33.4 - - - +
20A SER* 3.9 4.0 - - - -
21A PRO* 3.7 35.4 - - + -
25A GLU* 4.6 4.5 - - - +
72A LYS* 3.2 23.6 + - + +
73A THR 3.3 6.8 + - - +
74A TRP 3.1 0.4 - - - -
75A GLY* 1.3 72.8 - - - +
77A VAL* 1.3 63.5 + - - +
78A LEU 2.9 5.0 + - - -
79A GLY* 3.1 11.4 + - - -
80A ALA* 3.3 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 3.8 24.1 - - + +
12A CYS* 5.7 1.8 - - + -
21A PRO* 4.2 7.9 - - + -
26A ILE* 3.9 34.8 - - + -
29A MET* 4.6 8.7 - - + -
30A LEU* 6.4 0.2 - - + -
45A LEU* 3.6 29.4 - - + -
73A THR* 2.9 25.7 + - + +
74A TRP* 3.9 9.6 - - + +
76A LEU* 1.3 74.3 - - - +
78A LEU* 1.3 58.1 + - - +
80A ALA* 4.0 5.0 + - - +
81A LEU* 3.5 22.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 5.5 0.4 - - + -
51A TRP* 3.2 39.5 - - + -
55A THR* 3.9 22.2 - - + +
74A TRP* 2.7 47.7 + - + +
75A GLY* 3.7 6.1 - - - +
77A VAL* 1.3 75.3 - - - +
79A GLY* 1.3 60.9 + - - +
80A ALA 2.9 2.4 + - - -
81A LEU* 3.1 2.3 + - - -
82A LYS* 2.8 65.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A TYR* 5.0 2.1 - - - +
16A CYS* 5.4 3.8 - - - -
75A GLY 2.8 21.2 + - - -
76A LEU* 3.1 3.1 + - - -
78A LEU* 1.3 72.4 - - - +
80A ALA* 1.3 59.6 + - - +
82A LYS* 4.2 9.5 - - - +
83A ALA* 3.9 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 5.7 2.9 - - + -
11A ALA* 4.8 3.4 - - + -
12A CYS* 4.0 24.9 - - + +
15A TYR* 3.8 35.6 - - + -
16A CYS* 4.4 3.3 - - - -
76A LEU 3.3 12.6 + - - +
77A VAL* 4.2 5.2 - - - +
78A LEU 2.9 1.4 + - - -
79A GLY* 1.3 76.1 - - - +
81A LEU* 1.3 66.5 + - - +
83A ALA* 2.9 15.6 + - - +
84A ALA* 3.0 9.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 4.9 19.7 - - + -
45A LEU* 3.1 55.4 - - + +
46A TYR* 5.4 7.4 - - + -
51A TRP* 3.5 18.6 - - + -
77A VAL* 3.5 12.6 + - + +
78A LEU* 3.1 2.8 + - - +
80A ALA* 1.3 78.3 - - - +
82A LYS* 1.3 56.4 + - - +
84A ALA* 2.7 34.5 + - + +
85A ARG* 2.9 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TRP* 3.6 28.6 - - + -
78A LEU* 2.8 52.0 + - + +
79A GLY* 4.2 8.5 - - - +
81A LEU* 1.3 72.3 - - - +
83A ALA* 1.3 58.7 + - - +
85A ARG* 3.8 4.0 + - - +
86A GLU* 3.2 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A TYR* 4.1 25.4 + - + -
79A GLY 3.9 10.1 + - - +
80A ALA 2.9 10.1 + - - +
82A LYS* 1.3 76.1 - - - +
84A ALA* 1.3 64.5 + - - +
85A ARG 3.2 1.8 - - - -
86A GLU* 3.3 17.8 + - - +
87A GLU* 3.6 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA* 6.4 1.8 - - + -
15A TYR* 4.0 23.3 - - + +
80A ALA 3.0 10.1 + - - +
81A LEU* 2.7 24.3 + - + +
83A ALA* 1.3 76.9 - - - +
85A ARG* 1.3 58.2 + - + +
86A GLU 3.3 2.9 + - - -
87A GLU* 4.3 10.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A TYR* 2.8 32.1 + - - +
48A PRO* 3.3 45.5 - - + +
51A TRP* 3.7 15.9 - - + -
81A LEU* 2.9 23.2 + - + +
82A LYS* 4.0 5.4 - - - +
83A ALA 3.2 0.4 - - - -
84A ALA* 1.3 79.7 - - + +
86A GLU* 1.3 61.3 + - - +
87A GLU* 3.8 2.7 - - - -
----------------------------------------------------------
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