Contacts of the helix formed by residues 58 - 80 (chain A) in PDB entry 2VXX
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 58 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLU 5.1 2.1 + - - -
56A GLY 3.2 0.4 - - - -
57A ALA* 1.3 94.0 + - - +
59A PHE* 1.3 66.1 + - - +
60A TYR 3.4 2.5 - - - -
61A PRO* 3.2 14.8 - - + +
62A LEU* 3.2 40.6 + - + +
114A CYS* 4.6 12.9 - - - -
168A PHE* 5.6 2.2 - - + -
57D ALA* 3.2 41.1 - - - +
58D GLU* 4.2 8.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PHE 6.1 0.4 - - - -
54A VAL* 3.3 32.8 - - + +
55A GLU* 4.0 8.9 - - + +
56A GLY 3.0 26.8 + - - +
57A ALA 3.4 1.6 + - - -
58A GLU* 1.3 77.9 - - - +
60A TYR* 1.3 74.6 + + + +
62A LEU* 3.7 0.9 - - - +
63A HIS* 2.8 71.5 + + - +
82B GLU* 5.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PHE* 1.3 94.0 - + + +
61A PRO* 1.4 73.3 - - + +
63A HIS* 3.2 14.9 - + - +
64A GLN* 3.0 63.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA 5.3 1.1 - - - +
58A GLU* 3.2 24.7 - - + +
60A TYR* 1.4 97.9 - - + +
62A LEU* 1.3 54.8 + - - +
64A GLN* 3.3 14.8 + - - +
65A PHE* 2.8 29.7 + - - +
168A PHE* 4.7 5.6 - - + -
60D TYR* 3.9 14.4 - - + -
61D PRO* 3.6 39.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 3.8 14.8 - - + -
58A GLU* 3.2 38.4 + - + +
59A PHE 3.8 1.8 - - - +
61A PRO* 1.3 73.6 - - - +
63A HIS* 1.3 59.3 + - - +
65A PHE* 3.7 3.5 - - + +
66A PHE* 2.9 47.7 + - + -
114A CYS* 3.7 34.5 - - + -
118A LEU* 3.8 30.5 - - + -
168A PHE* 3.7 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A HIS* 2.7 76.6 + + - -
52A PHE 5.3 1.3 - - - -
54A VAL* 3.8 10.1 - - + +
59A PHE* 2.8 46.1 + + + +
60A TYR* 3.2 17.0 - + - +
62A LEU* 1.3 72.7 - - - +
64A GLN* 1.3 65.7 + - + +
66A PHE* 3.7 1.9 + - - +
67A GLN 3.4 5.5 + - - -
202A ZN 2.1 35.7 - - - -
82B GLU* 3.1 14.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A HIS* 5.4 0.4 - - - -
60A TYR* 3.0 63.2 + - + -
61A PRO* 3.6 12.5 - - - +
62A LEU 3.2 0.2 - - - -
63A HIS* 1.3 79.5 - - + +
65A PHE* 1.3 65.3 + - - +
67A GLN* 3.2 8.1 + - - +
68A ASP* 3.0 33.2 + - - +
60D TYR* 4.9 8.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A TYR* 5.0 1.3 - + - -
61A PRO 2.8 19.7 + - - +
62A LEU* 3.7 4.9 - - + +
64A GLN* 1.3 71.9 - - - +
66A PHE* 1.3 71.0 + + - +
68A ASP* 3.3 5.9 + - + +
69A CYS* 3.0 53.5 + - - -
118A LEU* 4.1 15.0 - - + -
161A ARG* 4.3 3.8 - - + -
164A HIS* 4.0 28.0 - + + -
165A ILE* 3.7 31.6 - - + -
168A PHE* 3.7 26.5 - + + -
60D TYR* 3.6 38.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A TYR* 3.6 25.3 - + - +
50A HIS* 3.5 39.0 - - + -
51A HIS* 3.7 11.0 - - + +
54A VAL* 3.9 18.4 - - + -
62A LEU* 2.9 41.6 + - + +
63A HIS 4.0 0.4 - - - +
65A PHE* 1.3 79.7 - + - +
67A GLN* 1.3 57.6 + - - +
69A CYS* 3.3 5.9 + - - +
70A TYR* 2.9 31.8 + - - -
114A CYS 5.1 1.1 - - - -
117A MET* 4.4 13.0 - - + -
118A LEU* 3.9 30.1 - - + -
121A ASP* 3.4 24.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A HIS* 3.1 32.2 + - + +
63A HIS 3.4 2.9 + - - +
64A GLN* 3.2 10.8 + - - +
66A PHE* 1.3 75.7 - - - +
68A ASP* 1.3 68.3 + - - +
69A CYS 3.1 1.3 - - - -
70A TYR* 3.4 31.9 + - + +
71A GLU* 3.1 49.6 + - - +
201A ZN 3.9 1.4 - - - -
78B HIS* 3.8 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLN* 3.0 22.9 + - - +
65A PHE* 3.6 7.0 - - + +
67A GLN* 1.3 77.1 + - - +
69A CYS* 1.3 62.2 + - - +
71A GLU* 3.7 10.5 + - - +
72A GLN* 3.1 24.8 + - - +
60D TYR* 2.9 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A TYR* 3.6 39.9 - - + -
65A PHE* 3.0 51.0 + - - +
66A PHE 3.3 9.4 - - - +
67A GLN 3.1 0.2 - - - -
68A ASP* 1.3 75.8 - - - +
70A TYR* 1.3 60.6 + - - +
72A GLN* 3.3 3.6 + - - +
73A VAL* 2.9 31.9 + - - +
161A ARG* 4.0 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A TYR* 3.4 38.5 - + + +
47A TYR* 3.5 19.5 - - + +
48A GLN* 3.5 39.3 + - + +
51A HIS* 4.0 12.2 - + + -
52A PHE* 5.7 0.2 - - - -
66A PHE 2.9 25.6 + - - -
67A GLN* 3.4 30.8 + - + +
69A CYS* 1.3 73.5 - - - +
71A GLU* 1.3 72.2 + - + +
73A VAL* 3.6 6.0 - - - -
74A GLN* 2.7 35.7 + - - +
78B HIS* 3.2 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLN* 3.1 49.3 + - - +
68A ASP* 4.0 9.9 - - - +
70A TYR* 1.3 90.7 + - + +
72A GLN* 1.3 63.7 + - - +
74A GLN* 3.5 8.2 + - - +
75A ASP* 3.3 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASP 3.1 19.3 + - - +
69A CYS 3.7 3.8 - - - +
71A GLU* 1.3 75.5 - - - +
73A VAL* 1.3 62.1 + - - +
75A ASP* 3.1 22.7 + - + +
76A HIS* 3.3 17.4 + - + +
157A LYS* 3.7 30.4 + - + +
160A GLU* 5.0 7.2 + - - +
161A ARG* 3.1 42.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 3.1 43.1 - - + +
43A LEU* 4.2 5.8 - - + -
44A TYR* 3.8 12.6 - - + +
47A TYR* 4.0 15.7 - - + -
69A CYS 2.9 21.0 + - - +
70A TYR* 3.6 7.0 - - - +
72A GLN* 1.3 73.2 - - - +
74A GLN* 1.3 64.8 + - - +
76A HIS* 2.9 11.0 + - - +
77A VAL* 2.9 20.1 + - + +
161A ARG* 3.7 30.5 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
44A TYR* 3.9 15.3 - - + -
70A TYR* 2.7 20.6 + - + +
71A GLU* 3.8 9.0 - - - +
72A GLN 3.4 0.2 - - - -
73A VAL* 1.3 72.5 - - - +
75A ASP* 1.3 57.9 + - - +
77A VAL* 3.4 7.9 + - - +
78A HIS* 3.0 24.4 + - - +
44B TYR* 2.6 42.6 + - - -
48B GLN* 3.1 16.2 + - - +
70B TYR* 4.0 15.3 + - - -
74B GLN* 3.7 17.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLU 3.3 11.5 + - - +
72A GLN* 3.1 16.9 + - + +
73A VAL 3.1 0.8 - - - -
74A GLN* 1.3 75.1 - - - +
76A HIS* 1.3 67.7 + - + +
78A HIS* 3.4 12.1 + - - +
79A ALA* 3.2 24.0 + - - +
157A LYS* 4.6 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 3.7 41.1 - + + -
72A GLN* 3.7 17.7 + - + -
73A VAL* 2.9 11.3 + - - +
75A ASP* 1.3 76.2 + - - +
77A VAL* 1.3 64.4 + - - +
79A ALA* 3.4 2.9 + - - +
80A LEU* 3.0 31.4 + - - +
154A ILE* 3.7 29.2 - - + +
157A LYS* 3.8 34.0 - - + +
158A THR* 4.0 3.6 + - - -
161A ARG* 2.9 32.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
37A LEU* 3.7 16.7 - - + +
40A PHE* 3.9 25.1 - - + +
41A GLN* 3.4 39.5 - - + +
44A TYR* 4.8 2.2 - - + -
73A VAL* 2.9 17.7 + - + +
74A GLN* 3.4 14.6 - - - +
76A HIS* 1.3 75.3 - - - +
78A HIS* 1.3 57.1 + - - +
80A LEU* 5.0 0.4 - - - -
81A GLY 2.9 26.9 + - - -
44B TYR* 4.4 0.7 - - - +
48B GLN* 3.3 28.7 - - - +
52B PHE* 3.6 3.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLN* 3.0 24.6 + - - +
75A ASP* 3.7 13.4 + - - +
77A VAL* 1.3 77.7 - - - +
79A ALA* 1.3 62.8 + - - +
82A GLU* 2.9 27.9 + - - +
48B GLN* 5.0 0.2 - - - +
51B HIS* 3.3 4.6 + + - -
52B PHE* 3.4 19.0 - + - -
67B GLN* 3.9 19.8 + - - -
70B TYR* 4.2 8.3 + - - +
202B ZN 2.0 37.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASP* 3.2 16.2 + - - +
76A HIS* 3.8 5.8 - - - +
77A VAL 3.4 0.4 - - - -
78A HIS* 1.3 79.2 - - - +
80A LEU* 1.3 58.4 + - - +
82A GLU* 4.0 3.2 - - - +
83A ARG* 3.0 29.8 + - - +
150A LEU* 4.2 27.3 - - + +
154A ILE* 4.8 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A MET* 3.6 19.6 - - + +
36A LEU* 3.8 29.2 - - + -
37A LEU* 4.1 15.9 - - + +
40A PHE* 3.8 26.5 - - + -
76A HIS 3.0 16.8 + - - +
77A VAL* 4.1 2.0 - - - +
79A ALA* 1.3 75.0 - - - +
81A GLY* 1.3 61.2 + - - +
84A LEU* 2.8 34.4 + - - +
150A LEU* 4.1 13.5 - - + -
151A TYR* 3.7 26.5 - - + -
154A ILE* 3.8 19.5 - - + -
----------------------------------------------------------
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