Contacts of the helix formed by residues 70 - 91 (chain a) in PDB entry 3J9X
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 GLY 70 (chain a).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1718 A 3.4 26.2 + - - +
1728 T 4.1 2.5 + - - -
69a THR* 1.3 75.5 - - - +
71a PRO* 1.3 70.1 - - - +
72a ASN 3.0 0.2 - - - -
73a ARG* 2.9 32.1 + - - +
90c ILE* 5.5 0.8 - - - +
99c MET* 5.3 0.2 - - - +
111d PHE* 3.6 19.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 71 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1718 A 3.7 30.3 - - + +
1728 T 3.6 25.8 - - - +
69a THR 4.4 0.2 - - - +
70a GLY* 1.3 83.6 - - - +
72a ASN* 1.3 65.1 + - - +
73a ARG 3.1 0.2 - - - -
74a ALA* 3.0 6.3 + - + +
75a ILE* 3.0 24.3 + - - +
71d PRO* 3.6 19.6 - - + +
74d ALA 4.8 0.4 - - - -
75d ILE* 3.6 37.9 - - + +
107d TYR* 6.5 1.1 - - + -
111d PHE* 4.6 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 72 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68a ILE* 3.5 15.0 - - + -
69a THR 3.3 14.4 + - - +
70a GLY 3.0 1.0 - - - -
71a PRO* 1.3 75.0 - - - +
73a ARG* 1.3 65.3 + - - +
75a ILE* 3.3 18.8 + - + +
76a TYR* 3.1 26.2 - - + -
72d ASN* 3.1 23.9 - - - +
75d ILE* 3.5 11.4 - - - +
111d PHE 3.2 25.9 + - - -
112d ASN* 4.6 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1718 A 2.9 39.2 + - - +
60a SER* 2.7 45.5 + - - +
63a LEU* 3.5 17.7 - - + +
64a THR* 3.0 32.3 + - - +
68a ILE* 2.8 53.7 + - + +
69a THR* 3.9 8.3 - - - +
70a GLY 2.9 13.2 + - - +
72a ASN* 1.3 76.4 - - - +
74a ALA* 1.3 59.3 + - - +
76a TYR 3.1 3.1 + - - -
77a GLN* 2.8 32.4 + - - +
89c ARG 4.6 0.4 + - - -
90c ILE* 3.7 28.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
1797 A 4.1 25.3 - - + +
1708 T 4.3 5.6 - - - +
1718 A 3.8 38.2 + - + +
70a GLY 3.7 0.8 + - - -
71a PRO* 3.0 11.5 + - + +
73a ARG* 1.3 79.7 - - - +
75a ILE* 1.3 61.2 + - - +
77a GLN* 3.6 9.6 - - - +
78a GLY* 2.9 21.0 + - - -
71d PRO* 4.8 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71a PRO 3.0 14.4 + - - +
72a ASN* 3.4 24.0 - - + +
73a ARG 3.2 0.4 - - - -
74a ALA* 1.3 78.3 - - - +
76a TYR* 1.3 69.3 + - + +
78a GLY* 3.3 0.5 + - - -
79a PHE* 3.2 16.8 + - - +
107a TYR* 3.5 30.9 - - + -
111a PHE* 4.8 11.0 - - + +
113a ALA* 4.2 20.0 - - + -
71d PRO* 3.5 26.9 - - + +
72d ASN* 3.5 34.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 76 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59a VAL* 4.3 6.1 - - - +
63a LEU* 3.6 34.1 - - + -
68a ILE* 4.0 19.1 - - + +
72a ASN* 3.1 26.6 + - + -
73a ARG 3.1 2.3 + - - +
75a ILE* 1.3 80.8 - - + +
77a GLN* 1.3 60.4 + - - +
79a PHE* 3.2 7.7 + - - +
80a GLY* 2.9 25.8 + - - -
113a ALA* 4.0 9.2 - - + -
114a ASN* 2.9 37.7 + - - +
117a VAL* 3.7 29.1 - - + +
118a LEU* 3.6 30.3 - - + -
121a VAL* 4.4 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 77 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1708 T 3.2 33.4 + - + +
1718 A 3.2 19.9 + - - +
55a VAL* 4.8 0.7 - - - +
56a ASN* 3.1 41.6 + - - +
59a VAL* 3.3 23.4 - - - +
60a SER* 3.4 11.9 - - - +
63a LEU* 4.0 3.9 - - + +
73a ARG 2.8 22.4 + - - +
74a ALA* 3.6 7.4 - - - +
76a TYR* 1.3 77.4 - - - +
78a GLY* 1.3 57.2 + - - +
80a GLY* 3.2 1.6 + - - -
81a LEU* 2.9 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 78 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1797 A 5.6 1.1 - - - -
1807 T 3.7 31.1 + - - +
74a ALA 2.9 14.3 + - - -
75a ILE 3.8 3.1 - - - -
77a GLN* 1.3 77.4 - - - +
79a PHE* 1.3 62.4 + - - +
81a LEU* 3.3 5.7 + - - +
82a LYS* 3.0 22.9 + - - +
107a TYR* 3.5 11.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75a ILE 3.2 12.4 + - - +
76a TYR 3.4 7.4 - - - +
78a GLY* 1.3 75.7 - - - +
80a GLY* 1.3 64.0 + - - +
82a LYS* 3.2 5.5 + - - +
83a VAL* 3.1 29.3 + - + +
100a ILE* 5.0 1.1 - - + -
103a LEU* 3.6 31.2 - - + -
104a LYS* 3.8 27.8 - - + -
107a TYR* 3.5 26.5 + + + -
118a LEU* 3.3 49.8 - - + -
121a VAL* 3.8 17.0 - - + -
122a VAL* 3.6 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 80 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55a VAL* 4.1 6.1 - - - -
59a VAL* 4.7 2.2 - - - -
76a TYR 2.9 12.2 + - - -
77a GLN 3.2 3.1 + - - -
79a PHE* 1.3 75.8 - - - +
81a LEU* 1.3 61.5 - - - +
83a VAL* 3.1 3.4 + - - -
84a ALA* 3.1 18.9 + - - +
121a VAL* 3.6 14.6 - - - -
125a ILE* 3.2 30.0 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
1807 T 3.6 24.0 - - + +
1817 A 3.4 30.0 - - + +
1698 A 4.9 6.5 - - + +
1708 T 5.2 2.2 - - - +
52a PHE* 3.7 37.4 - - + +
55a VAL* 4.3 6.7 - - + -
56a ASN* 3.3 30.3 - - - +
77a GLN* 2.9 25.6 + - + +
78a GLY* 3.6 4.7 - - - +
79a PHE 3.3 0.2 - - - -
80a GLY* 1.3 75.6 - - - +
82a LYS* 1.3 57.5 + - - +
84a ALA* 3.3 6.7 + - - +
85a ARG* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 82 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1807 T 4.0 13.9 + - - +
1817 A 2.9 31.9 + - - +
1608 T 5.6 1.6 - - - -
1618 A 3.8 13.0 + - - -
78a GLY 3.0 12.7 + - - +
79a PHE* 3.2 10.7 + - - +
81a LEU* 1.3 74.2 - - - +
83a VAL* 1.3 66.0 + - - +
85a ARG* 3.2 10.2 + - + +
86a ALA* 3.1 24.6 + - + +
99a MET* 4.7 16.8 - - + -
103a LEU* 3.5 27.8 - - + +
106a TYR* 5.5 4.4 - - - -
107a TYR* 5.2 1.3 - - + -
106b TYR* 2.7 36.5 + - - -
111b PHE* 6.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79a PHE* 3.1 34.5 + - + +
80a GLY* 3.3 8.7 - - - +
82a LYS* 1.3 77.5 - - - +
84a ALA* 1.3 62.6 + - - +
86a ALA* 3.4 6.1 + - - +
87a LEU* 3.0 20.9 + - + +
96a LEU* 4.3 3.8 - - + +
99a MET* 6.3 0.2 - - - -
100a ILE* 4.3 19.5 - - + -
103a LEU* 3.6 19.1 - - + -
122a VAL* 4.5 8.5 - - + -
125a ILE* 3.7 26.7 - - + -
126a THR* 4.3 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51a LYS 5.5 0.9 - - - +
52a PHE* 3.6 21.1 - - + -
55a VAL* 4.0 20.4 - - + -
80a GLY 3.1 10.2 + - - +
81a LEU* 3.5 8.1 - - - +
82a LYS 3.2 0.2 - - - -
83a VAL* 1.3 79.0 - - - +
85a ARG* 1.3 63.8 + - - +
87a LEU* 3.1 11.7 + - + +
88a ASN* 2.9 27.4 + - - +
125a ILE* 4.5 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 85 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1817 A 3.0 36.1 + - - +
1827 T 3.1 34.3 + - - +
1608 T 3.8 34.8 + - - +
1618 A 3.9 20.9 + - - -
52a PHE* 3.6 10.9 - - - -
81a LEU 2.9 13.8 + - - +
82a LYS* 3.2 15.7 + - + +
84a ALA* 1.3 76.0 - - - +
86a ALA* 1.3 64.4 - - - +
88a ASN* 3.1 5.5 + - - +
89a ARG* 3.0 52.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1608 T 5.4 3.1 - - - -
82a LYS* 3.1 12.4 + - - +
83a VAL* 3.7 8.1 - - - +
85a ARG* 1.3 77.1 - - - +
87a LEU* 1.3 57.8 + - - +
89a ARG* 4.5 2.9 - - - +
90a ILE* 2.7 50.8 + - + +
96a LEU* 3.9 10.3 - - + -
99a MET* 3.8 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576 GLU* 5.8 3.4 - - - +
83a VAL* 3.0 14.1 + - + +
84a ALA* 3.1 13.0 + - + +
86a ALA* 1.3 76.5 - - - +
88a ASN* 1.3 65.0 + - - +
91a GLY* 2.7 31.6 + - - +
92a SER* 3.6 33.0 - - - +
96a LEU* 3.8 24.4 - - + +
125a ILE* 4.8 22.4 - - + +
126a THR* 6.1 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 88 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576 GLU* 5.2 4.7 - - - +
1827 T 5.9 1.1 - - - +
7Z SER* 3.8 17.9 + - - +
48a ASN* 4.9 5.4 + - - -
51a LYS* 3.9 30.2 + - - +
52a PHE* 3.3 34.3 - - + -
84a ALA* 2.9 11.9 + - - +
85a ARG* 3.1 7.6 + - - +
87a LEU* 1.3 86.8 - - - +
89a ARG* 1.3 63.9 + - + +
90a ILE 3.7 0.3 + - - -
91a GLY 4.8 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 89 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1827 T 3.8 19.1 + - - +
1837 A 4.3 14.5 + - - -
1588 T 4.7 4.4 + - - -
1598 A 3.6 25.7 + - - +
1608 T 3.5 35.9 + - - +
60Y SER* 4.7 2.4 + - - -
73Y ARG* 4.6 4.0 + - - -
7Z SER* 3.6 35.2 - - - +
8Z ARG* 5.5 3.0 - - - +
85a ARG* 3.0 54.1 + - + +
86a ALA* 4.2 1.6 - - - +
88a ASN* 1.3 80.7 - - + +
90a ILE* 1.3 62.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 90 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1598 A 5.4 0.7 - - - +
1608 T 4.4 11.7 - - - +
60Y SER* 4.7 3.0 + - - -
64Y THR* 2.6 36.9 + - - +
69Y THR* 4.4 17.9 - - + -
70Y GLY 5.5 0.7 - - - +
73Y ARG* 3.7 18.7 + - - +
86a ALA* 2.7 27.8 + - + +
88a ASN 5.0 0.7 - - - -
89a ARG* 1.3 80.2 - - - +
91a GLY* 1.3 68.7 + - - +
95a ALA* 3.5 26.2 - - + +
96a LEU* 4.2 3.6 - - - +
99a MET* 3.7 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 91 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64Y THR* 3.7 0.9 - - - +
86a ALA 3.6 0.2 + - - -
87a LEU* 2.7 30.8 + - - -
88a ASN 4.6 0.2 - - - -
90a ILE* 1.3 90.2 - - - +
92a SER* 1.3 67.5 + - - +
96a LEU* 3.6 10.4 - - - +
----------------------------------------------------------
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