Contacts of the helix formed by residues 58 - 67 (chain A) in PDB entry 1M3V
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 CYS 58 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A CYS* 3.9 1.1 - - - -
38A CYS* 3.9 0.2 - - - -
42A LEU* 3.7 22.6 - - + +
45A ILE* 3.9 19.3 - - + -
48A SER 5.1 3.4 - - - -
49A SER* 5.8 0.2 - - - -
50A TYR* 3.6 3.9 - - - -
57A LEU* 1.3 76.5 - - - +
59A ARG* 1.3 60.4 + - - +
60A ASN* 3.4 13.9 - - - -
61A ASP* 2.9 28.7 + - - +
62A TYR* 2.9 27.0 + - - +
124A ZN 2.3 35.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 4.2 11.2 - - + +
48A SER* 4.6 9.5 - - - -
50A TYR* 3.3 35.5 + - + -
58A CYS* 1.3 75.5 - - - +
60A ASN* 1.3 62.8 + - - +
62A TYR* 3.3 4.6 + - - +
63A ILE* 3.1 38.7 + - + +
78A MET* 4.9 2.6 - - - +
80A SER 3.8 9.0 + - - -
81A GLY* 3.6 13.9 - - - -
83A ASP* 2.8 31.6 + - + +
85A MET* 6.0 2.9 - - + -
86A VAL* 3.8 20.8 - - + +
87A VAL* 3.3 23.8 - - - +
96A GLU* 4.6 10.3 + - - -
97A PHE 2.9 27.9 + - - -
98A GLY* 4.1 8.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A CYS* 3.5 23.6 - - - -
45A ILE* 5.6 0.2 - - - +
58A CYS* 3.4 8.1 - - - -
59A ARG* 1.3 76.5 - - - +
61A ASP* 1.3 65.1 + - - +
63A ILE* 3.2 10.5 + - - +
64A ARG* 3.0 65.4 + - - +
85A MET* 6.1 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A CYS* 3.2 2.3 - - - +
36A SER* 3.1 21.7 + - - -
37A SER* 2.7 42.3 + - - -
38A CYS* 3.6 2.6 - - - -
57A LEU* 3.5 11.8 - - + +
58A CYS* 2.9 23.8 + - - +
60A ASN* 1.3 76.9 - - - +
62A TYR* 1.3 58.6 + - - +
64A ARG* 3.2 8.0 + - - +
65A LEU* 2.9 32.6 + - - +
124A ZN 2.0 31.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TYR* 3.5 53.6 - + + -
52A LYS* 2.7 50.7 + - + +
57A LEU* 4.4 6.3 - - + -
58A CYS 2.9 19.7 + - - +
59A ARG* 3.4 5.8 - - - +
60A ASN 3.2 0.2 - - - -
61A ASP* 1.3 76.9 - - - +
63A ILE* 1.3 60.8 + - + +
65A LEU 3.2 0.2 + - - -
66A PHE* 2.7 58.5 + + + +
67A GLY 3.2 2.9 + - - -
97A PHE* 3.4 37.7 - + - -
99A ASP* 4.0 13.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG* 3.1 27.7 + - + +
60A ASN* 3.2 10.5 + - - +
62A TYR* 1.3 79.5 - - + +
64A ARG* 1.3 60.6 + - + +
67A GLY* 3.1 24.7 + - - +
96A GLU 5.2 1.8 - - - +
97A PHE* 3.7 39.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER* 5.3 11.0 - - - +
38A CYS* 5.1 6.9 - - - +
60A ASN* 3.0 48.1 + - - +
61A ASP* 3.5 13.2 - - - +
62A TYR 3.1 0.2 - - - -
63A ILE* 1.3 81.6 - - + +
65A LEU* 1.3 66.1 + - + +
67A GLY 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A SER* 5.3 1.8 - - - -
37A SER* 4.1 17.0 - - - +
55A MET* 4.3 11.9 - - + -
57A LEU* 3.9 20.0 - - + -
61A ASP 2.9 15.5 + - - +
64A ARG* 1.3 85.1 - - + +
66A PHE* 1.3 98.1 + - + +
67A GLY 3.5 1.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
52A LYS* 3.5 27.1 - - + -
53A SER* 3.2 28.0 - - - -
55A MET* 4.0 13.9 - - + -
57A LEU* 3.6 19.7 - - + -
62A TYR* 2.7 45.3 + + + +
65A LEU* 1.3 94.1 - - + +
67A GLY* 1.3 58.4 + - - +
68A ASN* 2.9 10.8 + - - +
97A PHE* 3.2 17.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A TYR 3.2 2.6 + - - -
63A ILE* 3.1 38.1 + - - +
65A LEU 3.5 2.4 + - - -
66A PHE* 1.3 73.0 - - - +
68A ASN* 1.3 64.5 + - - -
69A SER* 3.5 3.5 + - - -
97A PHE* 3.9 7.9 - - - -
----------------------------------------------------------
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