Contacts of the helix formed by residues 51 - 58 (chain A) in PDB entry 1C3Q
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 51 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ALA* 3.4 20.6 - - + +
47A TYR 4.4 1.9 + - - -
48A ALA* 2.9 11.9 + - + +
49A LYS 3.2 0.4 - - - -
50A GLU* 1.3 81.8 - - - +
52A VAL* 1.3 69.8 + - - +
53A ALA 3.1 2.9 - - - -
54A ASP* 3.0 11.4 + - - +
55A MET* 2.9 21.9 + - + +
68C THR 5.5 0.3 - - - -
69C LEU* 3.3 20.6 + - - +
101C THR* 2.8 35.0 + - - +
103C PHE* 3.9 12.6 - - + -
104C ARG* 2.6 45.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A HIS* 3.7 8.7 - - + -
23A ILE* 4.1 10.5 - - + -
46A ALA* 3.6 18.2 - - + +
47A TYR* 3.5 24.5 - - - +
48A ALA 3.0 20.6 + - - +
49A LYS* 4.0 11.7 - - - +
51A GLU* 1.3 76.6 - - - +
53A ALA* 1.3 58.6 + - - +
55A MET* 4.6 0.2 - - - -
56A ALA* 3.0 30.8 + - - +
76A ALA* 3.6 20.2 - - + +
79A ILE* 3.7 18.4 - - + -
80A ALA* 3.8 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LYS 5.2 2.4 + - - +
51A GLU 3.1 1.0 - - - -
52A VAL* 1.3 81.2 - - - +
54A ASP* 1.3 67.5 + - - +
56A ALA 3.5 0.2 + - - -
57A LYS* 3.2 15.6 + - - +
79A ILE* 4.2 18.2 - - + -
83A SER* 2.8 39.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLU 4.6 7.7 - - - +
51A GLU* 3.0 10.8 + - - +
53A ALA* 1.3 82.2 - - - +
55A MET* 1.3 60.7 + - - +
57A LYS* 3.3 41.5 + - - +
58A ILE* 3.8 13.2 - - - +
100C ALA 4.9 1.5 - - - +
101C THR* 3.8 18.7 - - + +
102C PRO* 3.2 28.3 - - + +
103C PHE 5.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 5.1 3.8 - - + +
21A HIS* 3.7 29.2 - - + +
44A VAL* 3.7 33.9 - - + -
46A ALA* 4.0 9.0 - - + -
51A GLU* 2.9 16.6 + - - +
54A ASP* 1.3 76.0 - - - +
56A ALA* 1.3 66.3 + - - +
58A ILE* 3.2 38.8 + - - +
59A ALA* 3.4 8.7 + - - +
97C GLY* 6.1 0.2 - - - -
100C ALA* 4.2 13.2 - - + -
101C THR* 3.9 17.2 - - + +
104C ARG* 3.6 31.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A HIS* 3.4 15.0 + - + +
52A VAL 3.0 19.7 + - - +
53A ALA 3.9 3.1 - - - +
55A MET* 1.3 78.7 - - - +
57A LYS* 1.3 62.6 + - - +
59A ALA* 3.1 18.9 + - - +
62A LEU* 4.4 5.4 - - + -
80A ALA* 3.6 26.7 - - + +
83A SER* 4.3 3.8 - - - +
84A ALA* 4.3 8.7 - - + +
89A VAL* 3.6 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ALA 3.2 12.5 + - - +
54A ASP* 3.3 43.6 + - - +
56A ALA* 1.3 78.4 - - - +
58A ILE* 1.3 66.3 + - + +
59A ALA 4.7 0.3 - - - +
83A SER* 3.9 6.7 + - - +
87A HIS* 3.7 52.8 - - + +
89A VAL* 4.3 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 4.0 21.3 - - + +
54A ASP 3.8 12.8 - - - +
55A MET* 3.2 31.9 - - - +
57A LYS* 1.3 89.5 - - + +
59A ALA* 1.3 62.2 + - - +
60A GLY 4.2 0.2 + - - -
100C ALA* 4.1 26.7 - - + +
----------------------------------------------------------
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