Contacts of the helix formed by residues 71 - 83 (chain A) in PDB entry 1C72
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 GLN 71 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PHE* 5.6 2.2 - - + +
58A ASN* 4.1 12.7 + - - +
60A PRO 3.8 6.3 + - - -
70A THR* 1.3 86.0 - - - +
72A SER* 1.3 61.1 + - - +
74A ALA* 3.0 8.9 + - + +
75A ILE* 2.9 29.8 + - - +
220A EPY 3.1 40.5 + - - -
98B VAL* 3.7 18.8 - - + +
101B ASN* 3.4 34.3 + - + +
102B HIS* 3.6 24.0 + - + +
105B ASP* 3.2 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.3 21.4 - - - +
16A ILE* 4.1 23.2 - - - +
60A PRO* 4.3 6.1 - - - -
71A GLN* 1.3 71.8 - - - +
73A ASN* 1.3 72.6 + - - +
75A ILE* 3.3 5.3 + - - +
76A LEU* 3.0 32.0 + - - +
104A MET* 5.4 4.7 - - - -
158A LEU* 5.8 1.4 - - - +
220A EPY 2.7 32.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLN 3.3 0.4 - - - -
72A SER* 1.3 87.3 + - - +
74A ALA* 1.3 57.8 + - - +
76A LEU* 3.3 6.7 + - - +
77A ARG* 3.0 34.1 + - - +
100A GLU* 3.4 44.2 + - - +
101A ASN* 5.6 3.2 + - - -
104A MET* 4.8 17.9 - - - +
154A PHE* 4.7 1.3 - - - -
158A LEU* 3.6 27.9 - - - +
220A EPY 4.1 1.2 + - - -
101B ASN* 3.3 29.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 4.8 5.9 - - + +
70A THR 3.7 13.0 - - - +
71A GLN* 3.0 13.1 + - + +
73A ASN* 1.3 75.7 - - - +
75A ILE* 1.3 65.1 + - - +
77A ARG* 3.5 4.2 + - - +
78A TYR* 3.2 22.3 + - - +
81A ARG* 5.0 0.7 + - - -
97B ASP* 3.6 45.7 - - + +
98B VAL* 3.8 10.3 - - + +
101B ASN* 4.3 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 4.9 0.2 - - + -
16A ILE* 3.7 32.3 - - + -
60A PRO* 3.4 39.5 - - + +
61A TYR* 4.0 11.2 - - - -
62A LEU* 4.0 23.1 - - + -
69A LEU* 4.2 17.7 - - + -
70A THR* 3.9 10.5 - - - +
71A GLN 2.9 24.3 + - - +
72A SER* 3.3 6.0 + - - +
74A ALA* 1.3 76.7 - - - +
76A LEU* 1.3 61.8 + - - +
78A TYR* 3.2 16.4 + - - +
79A ILE* 3.3 15.2 + - + +
----------------------------------------------------------
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 LEU 5.9 0.4 - - - +
15A ALA* 3.9 13.5 - - + +
16A ILE* 3.7 33.9 - - + -
19A LEU* 3.4 32.3 - - + +
72A SER* 3.0 24.7 + - - +
73A ASN* 3.6 8.3 - - - +
75A ILE* 1.3 73.8 - - - +
77A ARG* 1.3 59.0 + - - +
79A ILE* 3.5 1.3 + - - -
80A ALA* 3.0 29.9 + - - +
154A PHE* 3.8 20.8 - - + +
157A PHE* 5.4 1.3 - - + -
158A LEU* 3.6 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN 3.0 22.4 + - - +
74A ALA* 3.7 3.6 - - - +
76A LEU* 1.3 75.6 - - - +
78A TYR* 1.3 58.4 + - - +
80A ALA* 3.6 6.5 - - - +
81A ARG* 3.0 39.9 + - - +
86A CYS* 4.2 8.6 - - - +
93A LYS* 6.0 1.6 - - - +
96A VAL* 4.4 5.1 - - - +
97A ASP* 2.8 32.9 + - - +
100A GLU* 2.8 39.6 + - - +
154A PHE* 4.0 25.0 - - + -
77B ARG* 3.9 29.7 - - - +
97B ASP* 3.4 33.4 - - - +
100B GLU* 4.8 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 4.2 20.0 - - + -
64A ASP* 3.1 29.0 + - + -
67A VAL* 3.8 23.6 - - + +
69A LEU* 3.8 20.9 - - + -
74A ALA 3.2 9.7 + - - +
75A ILE 3.2 9.9 + - - +
77A ARG* 1.3 78.3 - - - +
79A ILE* 1.3 71.1 + - + +
81A ARG* 3.5 16.6 + - - +
82A LYS* 3.4 44.8 + - + +
90B GLU* 3.2 28.5 - - - -
94B GLN* 3.5 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 4.2 16.8 - - + -
19A LEU* 3.7 31.6 - - + -
20A LEU* 3.8 30.1 - - + -
23A THR* 4.0 12.3 - - + +
25A THR* 4.5 4.9 - - + +
62A LEU* 4.6 9.6 - - + -
75A ILE* 3.3 15.4 + - + +
76A LEU 4.0 0.2 - - - +
78A TYR* 1.3 84.9 - - + +
80A ALA* 1.3 63.7 + - - +
82A LYS* 3.2 10.4 + - - +
83A HIS* 3.0 46.0 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
19A LEU* 4.6 0.6 - - - +
76A LEU 3.0 18.6 + - - +
77A ARG 3.6 4.9 - - - +
79A ILE* 1.3 78.6 - - - +
81A ARG* 1.3 57.9 + - - +
83A HIS 3.1 1.9 + - - -
84A ASN 2.8 25.5 + - - -
85A MET* 2.9 36.5 + - + +
86A CYS* 3.7 17.5 - - - -
154A PHE* 3.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 6.1 0.2 - - - +
74A ALA 5.0 1.2 + - - -
77A ARG* 3.0 28.1 + - - +
78A TYR* 3.8 18.7 - - - +
79A ILE 3.3 0.2 - - - -
80A ALA* 1.3 76.2 - - - +
82A LYS* 1.3 62.5 + - - +
83A HIS 3.1 1.4 + - - -
84A ASN* 3.5 10.2 + - - +
86A CYS* 4.0 16.5 - - - -
90B GLU* 3.2 36.5 + - + +
93B LYS* 3.8 31.4 - - - +
94B GLN* 3.9 26.5 - - - +
97B ASP* 2.9 29.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
64A ASP* 3.1 25.2 + - - +
78A TYR* 3.4 37.3 + - + +
79A ILE* 3.2 12.4 + - - +
81A ARG* 1.3 78.5 - - - +
83A HIS* 1.3 80.4 + - + +
84A ASN 3.7 0.2 - - - -
90B GLU* 5.0 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A THR* 3.5 40.7 + - + -
25A THR* 3.6 21.1 + - - -
79A ILE* 3.0 29.2 + - + +
80A ALA 3.1 3.3 + - - +
82A LYS* 1.3 100.4 + - + +
84A ASN* 1.3 69.0 + - - +
85A MET* 3.1 18.6 + - + +
----------------------------------------------------------
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