Contacts of the helix formed by residues 50 - 64 (chain A) in PDB entry 4NWO
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 50 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PRO* 2.9 15.6 + - + +
49A ASP* 1.3 76.6 - - - +
51A GLN* 1.3 65.4 + - - +
52A ASP* 3.3 2.9 - - + +
53A VAL* 3.0 25.0 + - + +
54A ILE* 3.0 23.8 + - - +
81A ARG* 4.1 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLU* 1.3 71.2 - - - +
52A ASP* 1.3 63.2 + - - +
54A ILE* 3.3 5.8 + - - +
55A GLU* 3.0 54.4 + - - +
83A VAL* 3.9 28.4 - - + +
86A GLU* 3.7 35.7 + - - +
87A ALA* 3.9 11.7 - - + +
90A ALA* 4.6 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLU* 3.3 2.8 - - + +
51A GLN* 1.3 77.3 - - - +
53A VAL* 1.3 64.0 - - + +
55A GLU* 3.8 10.0 - - - +
56A THR* 3.0 30.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ILE* 3.8 33.0 - - + -
48A PRO* 4.5 13.7 - - + +
50A GLU* 3.0 24.9 + - + +
52A ASP* 1.3 77.6 - - + +
54A ILE* 1.3 59.9 + - - +
56A THR* 3.4 6.4 + - - -
57A THR* 2.8 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 5.4 2.0 - - + -
11A VAL* 3.7 31.2 - - + -
47A ILE* 3.6 25.4 - - + -
48A PRO 4.1 5.2 - - - +
50A GLU 3.0 18.1 + - - +
51A GLN* 3.3 2.9 + - - +
53A VAL* 1.3 77.2 - - - +
55A GLU* 1.3 57.6 + - - +
57A THR* 3.1 2.4 + - - -
58A LEU* 2.9 44.1 + - + +
72A THR* 5.8 0.9 - - + -
83A VAL* 4.0 24.5 - - + -
84A THR* 4.0 18.6 - - + +
87A ALA* 3.6 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLN* 3.0 49.5 + - - +
52A ASP* 3.8 8.4 - - - +
54A ILE* 1.3 76.8 - - - +
56A THR* 1.3 63.0 + - - +
58A LEU* 3.3 2.2 + - - +
59A ILE* 3.0 34.4 + - + +
87A ALA* 3.7 22.9 - - + +
90A ALA* 3.4 18.0 - - - +
91A VAL* 3.8 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASP* 3.0 17.6 + - - +
53A VAL* 3.7 6.5 - - - -
55A GLU* 1.3 77.8 - - - +
57A THR* 1.3 58.3 + - - +
59A ILE* 3.8 8.7 - - - +
60A LYS* 2.9 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 4.1 31.9 - - + -
45A GLN* 4.1 23.8 + - + +
47A ILE* 3.7 22.9 - - + +
53A VAL* 2.8 25.5 + - - +
54A ILE 3.1 4.9 + - - -
56A THR* 1.3 75.7 - - - +
58A LEU* 1.3 65.1 - - + +
60A LYS* 3.3 6.0 + - - +
61A MET* 3.0 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 4.4 6.7 - - + -
54A ILE* 2.9 38.0 + - + +
55A GLU 3.8 3.8 - - - +
57A THR* 1.3 72.3 - - - +
59A ILE* 1.3 57.4 + - - +
61A MET* 3.3 4.7 + - - +
62A ALA* 3.0 31.9 + - - +
70A ILE* 3.6 30.8 - - + +
72A THR* 3.9 13.7 - - + -
87A ALA 4.4 2.7 - - - +
88A THR* 4.1 22.9 - - - +
91A VAL* 4.0 27.4 - - + -
124A ARG* 5.4 1.1 - - - -
129A ILE* 3.8 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLU* 3.0 27.6 + - + +
56A THR* 3.8 7.2 - - - +
58A LEU* 1.3 75.1 - - - +
60A LYS* 1.3 58.7 + - - +
63A ASP* 3.0 37.0 + - + +
91A VAL* 3.7 16.8 - - + -
124A ARG* 3.5 48.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A THR* 2.9 23.4 + - + +
57A THR* 3.3 7.2 + - - +
59A ILE* 1.3 76.9 - - - +
61A MET* 1.3 59.9 + - + +
64A GLU* 3.2 17.8 + - + +
65A GLN* 3.0 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLY* 4.0 18.8 - - - -
8A ILE 4.1 1.6 - - - +
9A VAL* 3.6 33.0 - - + -
43A ILE* 3.6 28.9 - - + +
45A GLN* 4.0 28.5 - - + +
57A THR* 3.0 23.8 + - + +
58A LEU* 3.3 1.3 + - - +
60A LYS* 1.3 81.0 - - + +
62A ALA* 1.3 58.6 + - - +
65A GLN* 3.6 18.6 - - - +
66A ASP 3.2 7.8 + - - -
67A CYS* 2.9 31.4 + - - +
70A ILE* 3.7 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU 3.0 16.5 + - - +
61A MET* 1.3 79.4 - - - +
63A ASP* 1.3 71.2 + - - +
66A ASP* 3.6 10.3 - - - -
67A CYS 4.1 1.6 - - - +
70A ILE* 3.8 9.2 - - + -
124A ARG* 4.2 15.2 - - + +
127A SER* 3.5 34.1 + - - +
129A ILE* 5.2 1.1 - - + -
201A CA 3.5 18.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 3.0 17.8 + - + +
62A ALA* 1.3 84.2 - - - +
64A GLU* 1.3 64.3 + - + +
66A ASP* 4.3 5.5 + - - +
124A ARG* 2.9 50.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE 3.9 0.4 + - - -
60A LYS* 3.2 20.5 + - + +
63A ASP* 1.3 81.1 - - + +
65A GLN* 1.3 65.8 + - + +
66A ASP* 3.7 2.3 + - - +
----------------------------------------------------------
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