Contacts of the helix formed by residues 70 - 91 (chain J) 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 J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2987 T 3.5 24.2 + - - +
2997 A 4.4 2.0 + - - -
111G PHE* 3.5 19.6 - - - -
90H ILE* 5.6 0.6 - - - +
99H MET* 5.3 0.6 - - - +
69J THR* 1.3 76.8 - - - +
71J PRO* 1.3 66.7 - - - +
73J ARG* 2.9 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 71 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2987 T 3.6 22.9 - - + +
2997 A 3.9 33.2 - - - +
71G PRO* 3.6 19.4 - - + +
74G ALA* 4.8 3.1 - - + -
75G ILE* 3.5 37.0 - - + +
107G TYR* 6.5 0.9 - - + -
111G PHE* 4.6 7.2 - - + -
70J GLY* 1.3 82.2 - - - +
72J ASN* 1.3 65.3 + - - +
73J ARG 3.1 0.9 - - - -
74J ALA* 3.1 4.5 + - - +
75J ILE* 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 72 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G ASN* 3.1 24.4 - - - +
75G ILE* 3.5 11.6 - - - +
111G PHE* 3.3 24.9 + - - +
112G ASN* 4.8 8.1 + - - +
68J ILE* 3.5 16.2 - - + -
69J THR* 3.3 14.8 + - - +
70J GLY 3.0 0.8 - - - -
71J PRO* 1.3 75.2 - - - +
73J ARG* 1.3 64.4 + - - +
75J ILE* 3.3 19.0 + - + +
76J TYR* 3.0 25.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2987 T 3.0 35.6 + - - +
89H ARG 4.6 0.8 + - - -
90H ILE* 3.7 27.0 + - - +
60J SER* 2.7 45.9 + - - +
63J LEU* 3.5 16.4 - - + +
64J THR* 2.9 32.3 + - - +
68J ILE* 2.8 56.9 + - + +
69J THR* 3.8 8.1 - - - +
70J GLY 2.9 15.9 + - - +
72J ASN* 1.3 77.0 - - - +
74J ALA* 1.3 58.9 + - - +
76J TYR* 3.0 5.4 + - - -
77J GLN* 2.8 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2977 A 4.1 17.5 - - + +
2987 T 3.0 40.9 + - + +
518 A 4.7 5.6 - - + -
528 T 4.4 5.9 - - - +
71G PRO* 4.8 3.6 - - + -
70J GLY 3.6 0.6 + - - -
71J PRO 3.1 8.4 + - - +
73J ARG* 1.3 77.6 - - - +
75J ILE* 1.3 64.3 + - - +
77J GLN* 3.6 9.7 - - - +
78J GLY* 2.9 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G PRO* 3.6 27.3 - - + +
72G ASN* 3.5 36.3 - - - +
71J PRO 3.0 14.4 + - - +
72J ASN* 3.4 22.2 - - + +
73J ARG 3.2 0.4 - - - -
74J ALA* 1.3 76.5 - - - +
76J TYR* 1.3 67.4 + - + +
78J GLY* 3.4 0.7 + - - -
79J PHE* 3.1 21.3 + - - +
107J TYR* 3.5 31.1 - - + -
111J PHE* 4.6 11.4 - - + +
112J ASN 5.9 0.4 - - - +
113J ALA* 4.1 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 76 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59J VAL* 4.4 2.1 - - - +
63J LEU* 3.6 28.3 - - + -
68J ILE* 4.0 17.8 - - + +
72J ASN* 3.0 27.8 - - + -
73J ARG 3.0 5.6 + - - +
75J ILE* 1.3 81.3 - - + +
77J GLN* 1.3 61.3 + - - +
79J PHE* 3.3 6.3 + - - +
80J GLY* 2.8 26.5 + - - -
112J ASN 5.0 0.5 + - - -
113J ALA* 3.9 9.0 - - + -
114J ASN* 2.9 38.5 + - - +
117J VAL* 3.7 30.4 - - + +
118J LEU* 3.7 30.7 - - + -
121J VAL* 4.2 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 77 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2977 A 3.4 33.0 + - + +
2987 T 3.1 21.7 + - - +
55J VAL* 5.4 0.7 - - - +
56J ASN* 3.4 24.1 + - - +
59J VAL* 3.3 21.0 - - - +
60J SER* 3.5 26.3 - - - +
63J LEU* 4.0 1.9 - - + +
73J ARG 2.8 22.4 + - - +
74J ALA* 3.6 9.4 - - - +
76J TYR* 1.3 77.8 - - - +
78J GLY* 1.3 56.5 + - - +
80J GLY* 3.3 0.7 + - - -
81J LEU* 2.9 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 78 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2977 A 5.4 1.2 + - - -
528 T 5.1 3.6 - - - -
538 A 4.1 24.8 - - - +
74J ALA 2.9 16.2 + - - -
75J ILE 3.8 1.8 - - - -
77J GLN* 1.3 75.4 - - - +
79J PHE* 1.3 62.0 + - - +
81J LEU* 3.8 5.0 - - - +
82J LYS* 3.0 24.9 + - - +
107J TYR* 3.5 13.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75J ILE 3.1 13.4 + - - +
76J TYR 3.5 8.3 - - - +
78J GLY* 1.3 75.7 - - - +
80J GLY* 1.3 63.2 + - - +
82J LYS* 3.1 5.7 + - - +
83J VAL* 2.9 32.8 + - + +
100J ILE* 5.1 1.6 - - + -
103J LEU* 3.7 24.2 - - + -
104J LYS* 3.8 22.9 - - + -
107J TYR* 3.5 34.1 + + + -
118J LEU* 3.3 54.1 - - + -
121J VAL* 3.8 17.3 - - + -
122J VAL* 3.7 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 80 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55J VAL* 4.5 6.5 - - - -
59J VAL* 5.0 2.0 - - - -
76J TYR 2.8 17.0 + - - -
77J GLN 3.8 1.1 - - - -
79J PHE* 1.3 73.2 - - - +
81J LEU* 1.3 61.9 + - - +
83J VAL* 3.1 2.3 + - - -
84J ALA* 3.0 20.3 + - - +
121J VAL* 3.5 26.7 - - - -
125J ILE* 3.1 17.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2967 T 5.5 1.3 - - - +
2977 A 5.6 3.8 - - - +
538 A 4.1 19.5 - - + +
548 T 3.4 36.5 - - - +
52J PHE* 3.5 42.4 - - + +
55J VAL* 4.5 6.7 - - + +
56J ASN* 3.4 31.9 - - - +
77J GLN* 2.9 29.0 + - + +
78J GLY* 3.8 4.0 - - - +
80J GLY* 1.3 75.1 - - - +
82J LYS* 1.3 57.3 + - - +
84J ALA* 3.2 3.8 + - - -
85J ARG 2.9 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 82 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2877 A 4.9 0.2 + - - -
2887 T 3.2 13.9 + - - -
538 A 3.7 25.8 + - - +
548 T 3.3 28.9 + - - +
106I TYR* 2.8 34.2 + - - -
78J GLY 3.0 16.9 + - - +
79J PHE* 3.1 5.4 + - - +
81J LEU* 1.3 74.9 - - - +
83J VAL* 1.3 65.0 + - - +
85J ARG* 3.3 10.8 + - - +
86J ALA* 3.1 21.8 + - - +
99J MET* 5.9 2.2 - - - -
103J LEU* 3.5 35.3 - - + +
106J TYR* 5.0 6.3 - - + -
107J TYR* 4.6 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79J PHE* 2.9 43.3 + - + +
80J GLY* 3.3 8.3 - - - +
82J LYS* 1.3 76.5 - - - +
84J ALA* 1.3 62.0 + - - +
86J ALA* 3.3 8.1 + - - +
87J LEU* 3.0 20.9 + - + +
96J LEU* 4.5 2.5 - - + +
99J MET* 6.5 0.2 - - - -
100J ILE* 4.3 26.5 - - + -
103J LEU* 3.7 18.8 - - + -
122J VAL* 4.6 7.9 - - + -
125J ILE* 3.9 25.8 - - + -
126J THR* 4.5 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51J LYS 5.7 0.4 - - - +
52J PHE* 3.6 20.2 - - + -
55J VAL* 4.2 20.4 - - + -
80J GLY 3.0 11.7 + - - +
81J LEU* 3.2 8.9 + - - +
83J VAL* 1.3 74.3 - - - +
85J ARG* 1.3 66.1 + - - +
87J LEU* 3.1 12.2 + - + +
88J ASN* 3.0 25.4 + - - +
125J ILE* 4.4 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 85 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2877 A 3.8 36.3 + - - -
2887 T 2.9 33.1 + - - +
548 T 3.0 36.3 + - - +
558 A 3.4 29.4 + - - +
52J PHE* 3.5 11.1 - - - -
81J LEU 2.9 12.9 + - - +
82J LYS* 3.3 21.0 - - - +
83J VAL 3.2 0.2 - - - -
84J ALA* 1.3 75.6 - - - +
86J ALA* 1.3 64.7 + - - +
88J ASN* 3.0 6.4 + - - +
89J ARG* 3.0 45.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2877 A 5.6 2.7 - - - -
82J LYS 3.1 9.3 + - - +
83J VAL* 3.6 10.3 - - - +
85J ARG* 1.3 77.6 - - - +
87J LEU* 1.3 58.3 + - - +
89J ARG* 4.5 3.1 - - - +
90J ILE* 2.7 47.6 + - + +
96J LEU* 3.8 16.6 - - + -
99J MET* 3.8 28.0 - - + -
100J ILE* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83J VAL* 3.0 14.0 + - + +
84J ALA* 3.1 13.0 + - + +
86J ALA* 1.3 75.2 - - - +
88J ASN* 1.3 64.5 + - - +
91J GLY* 2.7 30.6 + - - +
92J SER* 3.6 28.9 - - - +
96J LEU* 3.6 24.8 - - + +
125J ILE* 4.5 25.6 - - + +
126J THR* 6.0 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 88 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558 A 5.4 1.5 + - - +
48J ASN* 4.9 5.6 + - - +
51J LYS* 3.8 32.1 + - - +
52J PHE* 3.4 33.7 - - - -
84J ALA* 3.0 12.9 + - - +
85J ARG* 3.0 7.8 + - - +
87J LEU* 1.3 85.6 - - - +
89J ARG* 1.3 65.0 + - + +
90J ILE 4.8 0.2 - - - -
91J GLY* 4.5 1.4 + - - -
7K SER* 4.6 12.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 89 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2857 A 4.6 10.1 + - - -
2867 T 3.6 28.9 + - - +
2877 A 3.3 32.0 + - - +
558 A 4.1 17.3 + - - +
568 T 4.3 15.6 + - - -
85J ARG* 3.0 45.0 + - - +
86J ALA* 4.3 2.2 - - - +
88J ASN* 1.3 80.9 - - + +
90J ILE* 1.3 62.1 + - + +
7K SER* 4.1 32.3 - - - +
8K ARG* 6.2 0.2 - - - +
60L SER* 4.5 5.7 + - - -
73L ARG* 4.6 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 90 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2867 T 5.6 0.2 - - - +
2877 A 4.5 11.4 - - - +
86J ALA* 2.7 28.4 + - + +
88J ASN 4.8 0.9 - - - -
89J ARG* 1.3 78.0 - - - +
91J GLY* 1.3 67.8 + - - +
95J ALA* 3.6 25.6 - - + +
96J LEU* 4.0 5.2 - - + +
99J MET* 3.8 38.8 - - + -
60L SER* 4.9 1.9 + - - -
61L ALA* 5.8 0.7 - - - -
64L THR* 2.6 36.9 + - + +
69L THR* 4.4 10.3 - - + -
70L GLY 5.6 0.4 - - - +
73L ARG* 3.7 19.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 91 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86J ALA 3.6 0.6 + - - -
87J LEU* 2.7 31.7 + - - -
88J ASN 4.5 0.6 - - - -
90J ILE* 1.3 89.7 - - - +
92J SER* 1.3 67.6 + - - +
96J LEU* 3.4 9.8 - - - +
64L THR* 3.6 2.0 - - - +
----------------------------------------------------------
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