Contacts of the helix formed by residues 52 - 68 (chain A) in PDB entry 4WNP
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 ASN 52 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 3.1 41.3 + - - +
27A PHE* 4.1 18.2 - - + -
49A ASN* 3.0 7.3 + - - +
51A LYS* 1.3 90.7 - - - +
53A LEU* 1.3 64.6 + - - +
54A ALA 3.2 2.8 + - - -
55A LYS* 3.3 5.3 + - + -
56A SER* 2.9 20.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ILE* 3.5 34.8 - - + -
49A ASN 3.8 7.0 - - - -
50A LYS* 3.5 26.2 + - + +
51A LYS 3.7 0.4 - - - -
52A ASN* 1.3 74.1 - - - +
54A ALA* 1.3 60.0 + - - +
56A SER* 3.4 1.2 + - - -
57A GLN* 2.9 43.9 + - - +
86A ASN* 4.9 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASN 3.3 0.4 - - - -
53A LEU* 1.3 82.2 - - - +
55A LYS* 1.3 59.8 + - - +
57A GLN* 3.7 6.2 - - - +
58A THR* 2.9 31.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 3.2 36.5 - - + -
52A ASN* 3.3 7.6 + - + +
54A ALA* 1.3 77.5 - - - +
56A SER* 1.3 60.2 + - - +
58A THR* 3.3 6.6 + - - -
59A LEU* 2.9 62.4 + - + +
168A PHE* 3.9 16.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 2.4 41.4 + - - -
48A ILE* 3.4 9.3 - - - -
49A ASN 2.9 29.1 + - - -
52A ASN 2.9 18.0 + - - -
53A LEU 3.7 2.5 - - - -
55A LYS* 1.3 75.3 - - - +
57A GLN* 1.3 66.6 + - - +
59A LEU* 3.3 1.8 + - - +
60A LEU* 3.0 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ILE* 4.1 22.7 - - + +
53A LEU* 2.9 31.3 + - - +
54A ALA* 3.7 6.0 - - - +
56A SER* 1.3 75.9 - - - +
58A THR* 1.3 63.3 + - - +
60A LEU* 3.6 1.7 + - - +
61A GLY* 3.1 20.8 + - - -
83A GLU* 5.2 1.5 - - - +
84A MET 3.7 8.7 + - - -
85A ALA 2.7 34.6 + - - +
86A ASN* 3.9 5.8 - - - +
87A SER 4.0 3.4 - - - +
88A VAL* 4.0 17.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ALA 2.9 18.9 + - - -
55A LYS* 3.6 7.8 - - - -
56A SER 3.2 0.2 - - - -
57A GLN* 1.3 77.5 - - - +
59A LEU* 1.3 65.5 + - + +
61A GLY* 3.4 2.1 + - - -
62A LYS* 3.0 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 3.6 37.0 - - + +
55A LYS* 2.9 47.9 + - + +
56A SER* 3.9 3.6 - - - +
58A THR* 1.3 76.3 - - + +
60A LEU* 1.3 64.6 + - + +
62A LYS* 3.4 14.3 + - + +
63A GLU* 2.9 29.3 + - - +
167A GLY* 3.3 33.0 - - - +
168A PHE* 4.1 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE 4.3 3.6 - - - +
28A ALA* 4.3 5.2 - - + -
46A LYS* 3.7 38.8 - - + -
47A CYS* 3.5 9.6 - - - +
48A ILE* 3.5 42.6 - - + +
56A SER* 3.0 21.9 + - - +
57A GLN 4.1 1.3 - - - +
59A LEU* 1.3 75.7 - - + +
61A GLY* 1.3 65.5 + - - +
63A GLU* 3.3 7.7 + - - +
64A ILE* 3.0 28.7 + - - +
88A VAL* 3.9 18.6 - - + +
90A LEU* 3.9 18.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLN 3.1 14.1 + - - -
58A THR 3.8 3.1 - - - -
59A LEU 3.3 0.2 - - - -
60A LEU* 1.3 78.5 - - - +
62A LYS* 1.3 60.2 + - - +
64A ILE* 3.3 6.9 + - - +
65A LYS* 3.2 20.1 + - - +
83A GLU* 3.8 29.9 - - - +
88A VAL* 4.5 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A THR* 3.0 37.1 + - + +
59A LEU* 3.7 11.3 - - + +
61A GLY* 1.3 72.8 - - - +
63A GLU* 1.3 65.0 + - - +
65A LYS* 3.2 10.5 + - + +
66A ILE* 3.1 28.4 + - + +
137A ARG* 5.5 6.1 - - - +
166A PHE 4.9 1.3 - - - +
167A GLY 3.9 19.7 + - - +
168A PHE* 5.6 1.2 + - - +
169A ALA 4.6 14.0 + - - +
170A ARG* 6.3 0.6 - - - +
180A TPO 5.5 3.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LYS* 2.5 34.3 + - - +
59A LEU 2.9 16.9 + - - +
60A LEU* 3.3 8.9 + - - +
62A LYS* 1.3 73.2 - - - +
64A ILE* 1.3 62.1 + - - +
66A ILE* 3.4 1.5 + - - +
67A LEU* 2.8 55.5 + - + +
90A LEU* 3.9 12.6 - - + +
92A MET* 5.3 2.9 - - - +
165A ASP* 3.2 12.8 + - - +
166A PHE* 2.8 39.8 + - + +
167A GLY* 4.0 9.6 + - - +
303A 3RJ 5.9 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU 3.0 14.6 + - - +
61A GLY* 3.4 7.0 - - - +
62A LYS 3.3 0.2 - - - -
63A GLU* 1.3 76.3 - - - +
65A LYS* 1.3 62.4 + - - +
68A LYS* 3.0 50.4 + - + +
78A LEU* 4.1 8.2 - - + +
81A PHE* 3.9 42.2 - - + -
83A GLU* 3.7 21.5 - - + +
88A VAL* 3.6 30.3 - - + -
89A TYR 4.5 0.2 - - - +
90A LEU* 3.6 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLY 3.2 10.1 + - - +
62A LYS* 3.2 13.4 + - + +
64A ILE* 1.3 80.6 - - - +
66A ILE* 1.3 68.7 + - + +
68A LYS* 3.7 19.0 - - - +
69A GLU* 3.8 13.0 - - - +
171A TYR* 5.2 4.8 + - + -
173B GLN* 6.2 0.4 - - - +
175B ASN* 3.8 25.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS* 3.1 17.0 + - + +
63A GLU 4.0 2.5 - - - +
65A LYS* 1.3 79.1 - - + +
67A LEU* 1.3 57.9 + - - +
69A GLU* 2.9 28.2 + - - +
70A LEU* 3.5 28.9 + - + +
134A ILE* 4.2 14.3 - - + +
166A PHE* 3.8 27.1 - - + +
169A ALA* 4.4 29.4 - - + +
170A ARG* 4.8 2.0 - - - -
171A TYR* 3.8 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLU* 2.8 48.4 + - + +
66A ILE* 1.3 68.9 - - - +
68A LYS* 1.3 65.2 + - - +
69A GLU 3.0 3.3 + - - -
70A LEU* 3.2 24.0 + - + +
71A LYS* 5.2 2.6 - - - +
75A ILE* 3.9 21.3 - - + -
76A VAL 4.1 6.1 - - - +
78A LEU* 3.9 26.7 + - + +
90A LEU* 4.5 3.6 - - + -
92A MET* 3.6 35.0 - - + -
166A PHE* 3.8 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE* 3.0 44.6 + - + +
65A LYS* 3.7 13.0 - - - +
66A ILE 3.2 0.2 - - - -
67A LEU* 1.3 76.4 - - - +
69A GLU* 1.3 69.4 + - - +
70A LEU 3.8 0.3 + - - -
71A LYS* 4.9 13.3 - - - +
78A LEU* 4.2 6.5 - - + +
81A PHE* 3.9 30.7 - - + -
----------------------------------------------------------
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