Contacts of the helix formed by residues 60 - 80 (chain A) in PDB entry 181L
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 LYS 60 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ARG* 5.4 6.1 - - - +
13A LEU* 3.8 30.2 - - + +
15A LEU* 3.7 21.3 - - + +
59A THR* 1.3 73.2 - - - +
61A ASP* 1.3 61.9 + - - +
63A ALA* 3.1 4.0 + - - +
64A GLU* 2.8 54.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A THR* 3.3 9.4 + - - +
60A LYS* 1.3 80.8 - - - +
62A GLU* 1.4 54.4 + - + +
64A GLU* 3.2 13.5 + - - +
65A LYS* 2.8 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 3.3 25.1 - - + +
52A ARG* 2.8 42.0 + - - -
58A ILE* 3.2 16.2 - - + +
59A THR* 2.9 38.1 + - - +
61A ASP* 1.4 74.3 - - + +
63A ALA* 1.3 66.6 + - - +
65A LYS* 3.2 7.0 + - - +
66A LEU* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.6 30.3 - - + -
15A LEU* 4.0 2.5 - - + -
28A GLY* 4.1 8.3 - - - -
29A ILE* 4.4 6.8 + - + +
58A ILE* 3.7 18.1 - - + +
59A THR 2.9 13.1 + - - +
60A LYS 3.2 9.6 - - - +
62A GLU* 1.3 76.8 - - - +
64A GLU* 1.3 57.5 + - + +
66A LEU* 3.2 6.9 + - - +
67A PHE* 2.9 28.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
8A ARG* 6.0 1.4 - - - -
13A LEU* 5.7 1.3 - - + +
29A ILE* 4.4 13.0 - - + -
60A LYS* 2.8 48.2 + - + +
61A ASP* 3.6 13.5 - - - +
63A ALA* 1.3 74.1 - - + +
65A LYS* 1.3 61.6 + - - +
67A PHE* 3.3 10.6 + - + +
68A ASN* 2.8 40.2 + - - +
----------------------------------------------------------
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 ASP 2.8 17.1 + - - +
62A GLU* 3.6 8.7 - - - +
63A ALA 3.2 0.2 - - - -
64A GLU* 1.3 78.6 - - - +
66A LEU* 1.4 63.4 + - + +
68A ASN* 3.1 11.7 + - + +
69A GLN* 3.0 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 4.2 19.1 - - + +
28A GLY* 5.7 1.1 - - - -
29A ILE 6.3 0.7 - - - +
31A HIS* 4.0 42.0 - - + +
46A LEU* 4.8 2.9 - - + -
49A ALA* 4.2 19.7 - - + +
50A ILE* 4.0 27.4 - - + -
58A ILE* 4.4 9.0 - - + -
62A GLU 3.0 17.3 + - - +
63A ALA* 3.2 6.5 + - - +
65A LYS* 1.4 76.7 - - + +
67A PHE* 1.3 58.1 + - - +
69A GLN* 3.1 22.6 + - - +
70A ASP* 2.8 33.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 3.6 53.4 - + + -
7A LEU* 3.7 20.6 - - + -
8A ARG* 4.1 5.8 - - + -
29A ILE* 3.5 50.5 - - + +
63A ALA 2.9 14.3 + - - +
64A GLU* 3.4 14.1 - - + +
66A LEU* 1.3 76.5 - - - +
68A ASN* 1.4 63.2 + - - +
70A ASP* 3.1 5.5 + - - -
71A VAL* 3.0 37.0 + - + +
104A PHE* 4.0 16.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 3.3 30.5 - - - -
64A GLU* 2.8 30.2 + - - +
65A LYS* 3.6 10.8 - - + +
67A PHE* 1.4 74.4 - - - +
69A GLN* 1.3 63.7 + - + +
71A VAL* 3.5 1.6 + - - +
72A ASP* 3.2 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A HIS* 5.9 1.2 - - - -
49A ALA 5.5 3.0 + - - -
65A LYS* 3.0 41.6 + - + +
66A LEU* 3.4 26.3 - - - +
68A ASN* 1.3 80.2 - - + +
70A ASP* 1.3 62.1 + - - +
72A ASP* 3.4 5.7 + - - +
73A ALA* 2.9 30.0 + - - +
76A ARG* 4.5 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE 5.2 0.3 - - - +
30A GLY 4.8 0.3 - - - +
31A HIS* 2.7 48.7 + - - +
66A LEU 2.8 20.1 + - - +
67A PHE* 3.1 3.3 + - - +
69A GLN* 1.3 79.5 + - - +
71A VAL* 1.3 60.3 + - - +
73A ALA* 3.8 5.1 - - - +
74A ALA* 3.0 28.2 + - - +
104A PHE* 3.5 27.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 4.4 19.7 - - + -
4A PHE* 3.8 39.9 - - + -
7A LEU* 4.1 15.7 - - + -
67A PHE* 3.0 39.4 + - + +
68A ASN 4.1 0.7 - - - +
69A GLN 3.3 0.2 - - - -
70A ASP* 1.3 75.0 - - - +
72A ASP* 1.3 65.7 + - - +
74A ALA* 3.0 8.6 + - - +
75A VAL* 3.0 31.3 + - + +
100A ILE* 4.6 3.6 - - + -
104A PHE* 4.3 2.9 - - + -
170A HED 5.6 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 5.8 0.2 - - - -
68A ASN 3.2 17.0 + - - +
69A GLN* 3.5 6.7 - - - +
71A VAL* 1.3 79.6 - - - +
73A ALA* 1.3 63.5 + - - +
75A VAL* 3.2 8.3 + - - +
76A ARG* 2.9 56.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLN 2.9 17.6 + - - +
70A ASP* 3.8 8.5 - - - +
72A ASP* 1.3 75.6 - - - +
74A ALA* 1.3 58.3 + - - +
76A ARG* 3.4 19.6 + - - +
77A GLY* 2.8 26.7 + - - -
80A ARG* 4.9 4.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
70A ASP 3.0 15.9 + - - +
71A VAL* 3.0 10.1 + - - +
73A ALA* 1.3 78.1 - - - +
75A VAL* 1.3 63.1 + - - +
77A GLY* 3.2 2.4 + - - -
78A ILE* 3.0 27.1 + - - +
100A ILE* 4.2 17.9 - - + +
103A VAL* 4.3 21.9 - - + +
104A PHE* 4.5 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 3.0 20.3 + - + +
72A ASP* 3.7 8.7 - - - +
74A ALA* 1.3 75.0 - - - +
76A ARG* 1.3 61.6 + - + +
78A ILE* 3.0 12.7 + - - +
79A LEU* 2.8 46.0 + - + +
88A TYR* 4.3 15.5 - - + +
100A ILE* 3.6 31.9 - - + -
170A HED 4.3 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLN* 4.5 1.8 + - - +
72A ASP* 2.9 52.7 + - - +
73A ALA* 3.4 23.5 - - - +
75A VAL* 1.3 80.1 - - + +
77A GLY* 1.3 63.3 + - - +
79A LEU* 3.1 11.3 + - + +
80A ARG* 2.9 50.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ALA 2.8 16.8 + - - -
74A ALA* 3.7 2.5 - - - -
76A ARG* 1.3 75.5 - - - +
78A ILE* 1.3 63.7 + - - +
80A ARG* 3.3 18.6 + - - +
81A ASN* 3.2 16.3 + - - +
103A VAL* 5.8 1.1 - - - -
108A GLU* 2.8 28.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA 3.0 16.2 + - - +
75A VAL* 3.0 9.0 + - - +
77A GLY* 1.3 75.6 - - - +
79A LEU* 1.3 67.3 + - + +
80A ARG 3.1 1.0 + - - -
81A ASN* 3.1 10.0 + - - +
84A LEU* 4.2 18.4 - - + -
85A LYS 3.6 14.1 + - - +
88A TYR* 3.5 54.7 - - + -
99A ALA 4.2 2.9 - - - +
100A ILE* 4.0 26.9 - - + -
103A VAL* 3.7 30.3 - - + +
400A BNZ 4.2 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL* 2.8 36.7 + - + +
76A ARG* 3.1 11.2 + - + +
78A ILE* 1.3 79.6 - - + +
80A ARG* 1.3 58.3 + - + +
85A LYS* 3.1 42.6 - - + +
88A TYR* 3.9 30.1 - - + -
89A ASP* 4.5 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ALA* 4.9 4.2 + - - +
76A ARG* 2.9 34.4 + - + +
77A GLY* 3.8 24.7 + - - +
79A LEU* 1.3 77.8 - - + +
81A ASN* 1.3 61.2 + - - +
82A ALA 3.6 2.6 + - - -
108A GLU* 5.0 8.5 + - - +
----------------------------------------------------------
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