Contacts of the helix formed by residues 73 - 87 (chain A) in PDB entry 3LM0
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 73 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LYS 4.7 0.2 - - - +
66A LYS 2.5 21.0 + - - +
68A ARG* 3.9 41.5 - - - +
69A ARG* 5.4 1.1 - - - -
71A GLN* 3.3 32.5 - - - -
72A ASP* 1.3 72.0 - - - +
74A ARG* 1.3 63.6 + - - +
75A ALA* 3.3 3.4 - - - -
76A GLU* 3.2 18.5 + - + +
77A ILE* 3.1 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 3.7 26.3 + - - +
19A ASN 2.5 32.7 + - - +
20A LEU* 3.5 4.8 - - - +
21A TYR* 3.4 48.2 + - + +
22A PHE* 6.0 0.4 - - + -
66A LYS* 3.9 11.3 + - + -
72A ASP* 3.3 15.9 + - - +
73A CYS* 1.3 76.1 - - - +
75A ALA* 1.3 52.6 + - - +
77A ILE* 3.1 13.8 + - - +
78A LEU* 2.8 42.7 + - + +
101A GLU* 2.9 27.6 + - - -
106A ILE* 3.8 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASP 5.2 2.9 + - - +
73A CYS* 3.3 0.8 - - - -
74A ARG* 1.3 78.9 - - - +
76A GLU* 1.3 57.8 + - + +
78A LEU* 3.2 18.0 + - + +
79A HIS* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ARG* 5.4 5.6 - - - +
73A CYS* 3.2 24.2 + - + +
75A ALA* 1.3 78.8 - - + +
77A ILE* 1.3 63.0 + - + +
79A HIS* 3.2 11.6 + - - +
80A GLU* 3.1 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 3.9 32.3 - - + +
65A LYS 3.7 24.5 - - - +
66A LYS* 4.0 23.6 - - + -
68A ARG* 4.2 12.3 - - - +
73A CYS 3.1 15.1 + - - +
74A ARG* 3.1 7.5 + - - +
76A GLU* 1.3 72.8 - - - +
78A LEU* 1.3 64.2 + - - +
80A GLU* 3.2 9.1 + - + +
81A ILE* 3.0 29.9 + - + +
106A ILE* 3.7 33.2 - - + -
108A LEU* 5.3 0.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
21A TYR* 4.7 20.0 - - + -
22A PHE* 3.7 34.1 - - + -
74A ARG* 2.8 34.9 + - + +
75A ALA* 3.2 17.0 + - + +
77A ILE* 1.3 71.6 - - - +
79A HIS* 1.3 63.1 + - - +
81A ILE* 3.5 7.6 + - + +
82A ALA* 3.0 24.0 + - - +
106A ILE* 5.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ALA 2.9 13.5 + - - +
76A GLU* 3.2 13.9 + - - +
78A LEU* 1.3 77.0 - - - +
80A GLU* 1.3 65.0 + - + +
82A ALA* 3.3 10.1 + - + +
83A VAL* 3.1 42.9 + - + +
180A PHE 5.3 1.1 - - - -
181A GLY 5.9 2.5 - - - -
183A SER* 3.6 27.5 + - - -
184A ARG* 4.9 5.8 - - - -
185A LYS* 5.6 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A CL 4.0 8.7 - - - +
62A LYS* 3.5 25.8 + - - -
64A LEU* 4.2 13.5 - - + +
76A GLU 3.1 12.4 + - - +
77A ILE* 3.2 10.1 + - + +
79A HIS* 1.3 81.0 - - + +
81A ILE* 1.3 62.7 + - - +
83A VAL* 3.1 8.0 + - - +
84A LEU* 3.0 31.5 + - + +
108A LEU* 4.6 13.2 - - + +
180A PHE* 3.5 33.3 + - + +
181A GLY* 3.7 21.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 3.7 37.0 - - + -
77A ILE* 3.0 27.7 + - + +
78A LEU* 3.7 10.1 - - + +
80A GLU* 1.3 75.0 - - - +
82A ALA* 1.3 63.4 + - - +
84A LEU* 3.2 5.5 + - - +
85A GLU* 2.9 26.2 + - + +
96A LEU* 3.7 22.9 - - + +
99A VAL* 4.1 9.9 - - + -
106A ILE* 4.2 0.4 - - + -
108A LEU* 3.9 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU 3.0 14.4 + - - +
79A HIS* 3.4 13.2 - - - +
81A ILE* 1.3 76.6 - - - +
83A VAL* 1.3 58.5 + - + +
85A GLU* 3.3 7.2 + - - +
86A LEU* 2.9 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A HIS* 3.1 42.5 + - + +
80A GLU* 3.1 10.1 + - - +
82A ALA* 1.3 74.1 - - + +
84A LEU* 1.3 65.1 + - - +
86A LEU* 3.4 10.9 + - + +
87A ALA* 3.2 21.3 + - - +
149A LEU* 5.1 0.2 - - + -
154A ILE* 3.9 28.2 - - + +
180A PHE* 3.6 33.7 - - + -
183A SER* 3.9 12.6 - - - +
185A LYS* 6.3 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLU* 3.0 26.4 + - + +
81A ILE* 3.7 6.5 - - - +
83A VAL* 1.3 77.1 - - - +
85A GLU* 1.3 62.7 + - - +
87A ALA* 3.3 7.4 + - - +
88A LYS* 3.2 19.1 + - - +
93A VAL* 4.4 2.5 - - + -
94A ILE* 3.8 36.2 - - + +
95A ASN* 6.2 0.2 - - - -
96A LEU* 4.3 25.4 + - + +
108A LEU* 4.3 18.6 - - + -
110A LEU* 3.9 23.3 - - + -
179A ASP 6.0 0.2 - - - +
180A PHE* 3.8 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 2.9 19.8 + - + +
82A ALA* 3.6 7.6 - - - +
84A LEU* 1.3 75.5 - - - +
86A LEU* 1.3 65.9 + - - +
88A LYS* 2.8 63.3 + - + +
96A LEU* 4.4 21.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ALA 2.9 16.8 + - - +
83A VAL* 3.6 9.6 - - + +
84A LEU 3.3 0.2 - - - -
85A GLU* 1.3 78.6 - - - +
87A ALA* 1.3 55.6 + - - +
88A LYS* 3.4 3.2 + - - +
89A SER* 4.9 1.2 + - - -
148A TYR* 3.0 15.3 + - + +
152A ASN* 4.0 27.4 - - + +
154A ILE* 3.4 35.0 - - + -
185A LYS* 5.6 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A VAL* 3.2 16.7 + - + +
84A LEU 3.3 4.2 + - - +
85A GLU 3.1 0.8 - - - -
86A LEU* 1.3 74.6 - - - +
88A LYS* 1.3 63.8 + - - +
89A SER 3.2 3.1 - - - -
90A CYS* 3.1 19.9 + - - +
93A VAL* 4.0 33.3 - - + +
94A ILE 5.6 0.6 - - - +
95A ASN* 5.2 0.2 - - - +
148A TYR* 3.6 22.2 - - + -
149A LEU* 4.3 11.7 - - + -
154A ILE* 5.4 1.3 - - + -
180A PHE* 5.6 0.2 - - + -
----------------------------------------------------------
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