Contacts of the helix formed by residues 66 - 81 (chain A) in PDB entry 1X49
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 66 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLU* 4.9 14.5 + - - +
47A PHE* 3.4 46.6 - - + -
49A PHE* 3.7 27.4 - - + -
65A SER* 1.3 76.3 + - - +
67A GLN* 1.3 57.3 + - - +
69A ALA* 3.3 2.8 + - - +
70A ARG* 2.9 46.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A THR 4.7 1.4 + - - -
13A PRO* 4.0 14.5 - - - +
14A GLY* 4.0 22.1 - - - +
17A MET* 4.6 9.4 - - + +
65A SER* 2.9 7.3 + - - -
66A LYS* 1.3 75.1 - - - +
68A GLU* 1.3 68.7 + - - +
69A ALA 2.9 0.5 + - - -
70A ARG* 3.0 7.9 + - - +
71A ASN* 2.9 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ARG* 4.3 8.3 + - - -
62A LYS 5.3 0.2 - - - +
63A GLY* 4.0 4.7 - - - -
64A ARG* 3.5 31.6 + - - +
65A SER* 2.9 22.2 + - - +
67A GLN* 1.3 78.2 - - - +
69A ALA* 1.3 59.8 + - - +
71A ASN* 3.9 5.4 - - - +
72A ALA* 3.2 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PHE 2.9 29.8 - - - +
49A PHE* 3.4 25.1 - - + +
61A ALA 4.3 3.5 - - - +
62A LYS 4.3 2.5 - - - -
63A GLY* 3.7 11.1 - - - +
65A SER 2.8 11.5 + - - +
66A LYS* 3.5 4.3 - - - +
68A GLU* 1.3 74.5 - - - +
70A ARG* 1.3 67.5 + - - +
72A ALA* 3.0 4.9 + - - +
73A ALA* 2.9 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A MET* 3.6 30.2 - - + +
33A TYR* 3.6 46.7 + - + +
35A GLU* 4.6 8.3 + - - +
49A PHE* 3.3 50.2 - - + +
66A LYS* 2.9 32.1 + - - +
67A GLN* 3.7 4.0 - - - +
69A ALA* 1.3 72.7 - - - +
71A ASN* 1.3 62.8 + - - +
73A ALA* 3.4 3.6 + - - +
74A ALA* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A THR 4.3 4.9 + - - -
14A GLY* 3.6 28.3 - - - +
15A PHE* 3.7 8.7 - - - +
16A TYR* 3.4 28.1 + - - +
17A MET* 3.7 15.3 - - - -
67A GLN* 2.9 21.2 + - + +
68A GLU* 3.9 6.3 - - - +
70A ARG* 1.3 75.5 - - - +
72A ALA* 1.3 62.7 + - - +
74A ALA* 3.3 5.5 + - - +
75A LYS 3.2 15.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ALA* 3.7 16.4 - - + -
62A LYS 3.9 12.1 - - - +
68A GLU* 3.2 13.4 + - + +
69A ALA 3.0 8.8 + - - +
71A ASN* 1.3 76.8 - - - +
73A ALA* 1.3 58.0 + - - +
75A LYS* 2.7 38.1 + - + +
76A LEU* 3.5 6.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
33A TYR* 6.2 0.2 - - + -
49A PHE* 3.1 36.6 - - + +
50A GLN* 3.8 13.0 - - - +
51A VAL* 4.5 5.5 + - + +
58A PHE* 5.3 2.6 - - - +
59A PRO 4.5 4.8 - - - +
60A GLU* 4.6 0.9 - - - -
61A ALA* 3.4 13.7 - - + +
69A ALA 2.9 15.9 + - - +
70A ARG* 3.7 5.6 - - - +
72A ALA* 1.3 73.3 - - - +
74A ALA* 1.3 61.5 + - - +
76A LEU* 3.4 7.7 + - - +
77A ALA* 3.4 16.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
16A TYR* 3.8 15.0 - - + -
17A MET* 4.0 9.4 - - + +
20A LEU* 3.4 30.3 - - + -
51A VAL* 4.4 3.6 - - + +
70A ARG 3.1 12.2 + - - +
71A ASN 3.4 11.0 - - - +
72A ALA 3.0 0.6 - - - -
73A ALA* 1.3 75.6 - - - +
75A LYS* 1.3 59.7 + - - +
77A ALA* 3.0 3.8 + - - -
78A VAL* 2.7 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR* 3.4 50.6 - - + +
71A ASN 3.2 5.6 + - - +
72A ALA* 2.7 26.6 + - - +
74A ALA* 1.3 70.0 - - - +
76A LEU* 1.3 66.1 + - + +
78A VAL 4.1 0.3 - - - -
79A ASP* 2.5 47.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
59A PRO* 2.9 47.3 - - + +
60A GLU 3.5 10.1 - - - +
61A ALA* 4.1 12.1 - - + -
72A ALA 4.1 9.0 - - - +
73A ALA 3.8 4.0 - - - +
74A ALA 3.2 0.8 - - - -
75A LYS* 1.3 88.6 - - + +
77A ALA* 1.3 62.4 + - - +
79A ASP* 3.6 6.0 - - - +
80A ILE* 3.1 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 4.4 5.2 - - + -
51A VAL* 4.7 5.8 - - + -
53A ILE* 4.4 11.0 - - + -
58A PHE* 3.2 38.5 - - + -
73A ALA 3.4 8.8 + - - +
74A ALA* 3.0 12.0 + - - +
76A LEU* 1.3 75.7 - - - +
78A VAL* 1.3 57.0 + - - +
79A ASP 3.0 1.1 - - - -
80A ILE* 2.7 26.0 + - - +
81A LEU* 3.0 15.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR* 4.1 25.4 - - + +
19A LYS* 4.1 32.1 - - + +
20A LEU* 3.6 30.1 - - + +
74A ALA 2.7 25.7 + - - +
77A ALA* 1.3 71.8 - - - +
79A ASP* 1.3 61.2 + - - +
80A ILE 3.3 0.3 + - - -
81A LEU* 3.5 13.0 + - + +
82A ASP* 3.3 23.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR* 3.9 21.0 + - - -
75A LYS* 2.5 40.9 + - - +
76A LEU* 3.6 9.2 - - - +
77A ALA 3.0 0.2 + - - -
78A VAL* 1.3 76.4 - - - +
80A ILE* 1.3 63.0 + - + +
82A ASP* 4.0 11.7 - - - +
83A ASN* 4.2 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LYS* 4.7 13.0 - - - +
58A PHE* 3.6 30.3 - - + -
59A PRO* 4.3 14.4 - - + -
76A LEU* 3.1 19.7 - - + +
77A ALA 2.7 12.2 + - - +
79A ASP* 1.3 72.0 - - + +
81A LEU* 1.3 58.5 + - + +
83A ASN* 2.6 31.3 + - + +
84A GLU* 2.7 14.5 + - - +
85A ASN 4.9 14.1 - - - +
86A LYS* 5.4 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 3.9 27.8 - - + -
23A TYR* 4.1 44.4 - - + +
53A ILE* 4.0 11.4 - - + -
58A PHE* 3.7 27.4 - - + -
77A ALA 3.0 9.6 + - - +
78A VAL* 3.8 14.6 - - + +
80A ILE* 1.3 76.4 - - + +
82A ASP* 1.3 56.1 + - - +
83A ASN 2.6 3.5 + - - -
84A GLU* 2.5 51.0 + - - +
----------------------------------------------------------
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