Contacts of the helix formed by residues 70 - 91 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638 A 3.4 26.5 + - - +
648 T 4.1 2.1 + - - -
69I THR* 1.3 75.1 - - - +
71I PRO* 1.3 69.8 - - - +
72I ASN 3.0 0.2 - - - -
73I ARG* 2.9 31.8 + - - +
90K ILE* 5.5 1.0 - - - +
99K MET* 5.3 0.2 - - - +
111L PHE* 3.6 19.4 - - - -
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Residues in contact with PRO 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638 A 3.7 30.3 - - + +
648 T 3.6 25.8 - - - +
69I THR 4.4 0.2 - - - +
70I GLY* 1.3 83.9 - - - +
72I ASN* 1.3 65.5 + - - +
73I ARG 3.1 0.2 - - - -
74I ALA* 3.0 6.1 + - + +
75I ILE* 3.0 24.1 + - - +
71L PRO* 3.6 19.3 - - + +
74L ALA* 4.8 0.7 - - + -
75L ILE* 3.6 38.4 - - + +
107L TYR* 6.5 1.1 - - + -
111L PHE* 4.6 5.8 - - + -
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Residues in contact with ASN 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68I ILE* 3.5 16.4 - - + -
69I THR 3.3 14.0 + - - +
70I GLY 3.0 0.6 - - - -
71I PRO* 1.3 75.0 - - - +
73I ARG* 1.3 65.3 + - - +
75I ILE* 3.3 18.7 + - + +
76I TYR* 3.1 26.3 - - + -
72L ASN* 3.1 24.3 - - - +
75L ILE* 3.5 11.4 - - - +
111L PHE 3.2 25.9 + - - -
112L ASN* 4.6 11.1 + - - +
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Residues in contact with ARG 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638 A 2.9 38.5 + - - +
60I SER* 2.7 45.7 + - - +
63I LEU* 3.5 17.8 - - + +
64I THR* 3.0 32.3 + - - +
68I ILE* 2.8 54.1 + - + +
69I THR* 3.9 8.3 - - - +
70I GLY 2.9 13.4 + - - +
72I ASN* 1.3 76.2 - - - +
74I ALA* 1.3 59.2 + - - +
76I TYR 3.1 3.1 + - - -
77I GLN* 2.8 32.8 + - - +
89K ARG 4.6 0.6 + - - -
90K ILE* 3.7 26.8 + - - +
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Residues in contact with ALA 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2877 A 4.1 25.4 - - + +
628 T 4.3 5.3 - - - +
638 A 3.8 38.3 + - + +
70I GLY 3.7 1.2 + - - -
71I PRO* 3.0 11.5 + - + +
73I ARG* 1.3 79.7 - - - +
75I ILE* 1.3 61.2 + - - +
77I GLN* 3.6 9.2 - - - +
78I GLY* 2.9 21.0 + - - -
71L PRO* 4.8 4.3 - - + -
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Residues in contact with ILE 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71I PRO 3.0 14.0 + - - +
72I ASN* 3.4 23.8 - - + +
74I ALA* 1.3 78.7 - - - +
76I TYR* 1.3 69.4 + - + +
78I GLY* 3.3 0.7 + - - -
79I PHE* 3.2 16.8 + - - +
107I TYR* 3.5 30.9 - - + -
111I PHE* 4.8 11.0 - - + +
113I ALA* 4.2 20.0 - - + -
71L PRO* 3.5 28.0 - - + +
72L ASN* 3.5 35.0 - - - +
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Residues in contact with TYR 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59I VAL* 4.3 6.1 - - - +
63I LEU* 3.6 34.3 - - + -
68I ILE* 4.0 19.7 - - + +
72I ASN* 3.1 26.7 + - + -
73I ARG 3.1 2.7 + - - +
75I ILE* 1.3 80.6 - - + +
77I GLN* 1.3 60.6 + - - +
79I PHE* 3.2 7.5 + - - +
80I GLY* 2.9 25.6 + - - -
113I ALA* 4.0 8.8 - - + -
114I ASN* 2.9 38.1 + - - +
117I VAL* 3.7 28.6 - - + +
118I LEU* 3.6 29.8 - - + -
121I VAL* 4.4 8.4 - - + +
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Residues in contact with GLN 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628 T 3.2 33.0 + - + +
638 A 3.2 20.1 + - - +
55I VAL* 5.2 0.7 - - - +
56I ASN* 3.1 41.6 + - - +
59I VAL* 3.3 23.7 - - - +
60I SER* 3.4 12.1 - - - +
63I LEU* 4.0 4.2 - - + +
73I ARG 2.8 22.8 + - - +
74I ALA* 3.6 7.4 - - - +
76I TYR* 1.3 76.9 - - - +
78I GLY* 1.3 57.8 + - - +
80I GLY* 3.2 1.7 + - - -
81I LEU* 2.9 37.4 + - + +
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Residues in contact with GLY 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2877 A 5.6 1.3 - - - -
2887 T 3.7 30.2 + - - +
74I ALA 2.9 14.5 + - - -
75I ILE* 3.8 3.1 - - - -
77I GLN* 1.3 76.5 - - - +
79I PHE* 1.3 61.8 + - - +
81I LEU* 3.3 6.1 + - - +
82I LYS* 3.0 23.6 + - - +
107I TYR* 3.5 11.6 + - - -
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Residues in contact with PHE 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75I ILE 3.2 12.4 + - - +
76I TYR 3.4 7.6 - - - +
78I GLY* 1.3 76.3 - - - +
80I GLY* 1.3 64.0 + - - +
82I LYS* 3.1 5.4 + - - +
83I VAL* 3.1 29.6 + - + +
100I ILE* 5.0 0.9 - - + -
103I LEU* 3.6 31.2 - - + -
104I LYS* 3.8 28.5 - - + -
107I TYR* 3.5 27.1 + + + -
118I LEU* 3.3 49.1 - - + -
121I VAL* 3.8 17.0 - - + -
122I VAL* 3.6 24.7 - - + -
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Residues in contact with GLY 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I VAL* 4.1 6.1 - - - -
59I VAL* 4.7 2.0 - - - -
76I TYR 2.9 12.4 + - - -
77I GLN 3.2 2.9 + - - -
79I PHE* 1.3 75.8 - - - +
81I LEU* 1.3 62.1 - - - +
83I VAL* 3.1 3.4 + - - -
84I ALA* 3.1 18.9 + - - +
121I VAL* 3.6 14.6 - - - -
125I ILE* 3.2 29.6 - - - +
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Residues in contact with LEU 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2887 T 3.6 23.8 - - + +
2897 A 3.4 29.8 - - - +
618 A 4.9 7.2 - - + +
628 T 5.2 2.5 - - - +
52I PHE* 3.7 37.1 - - + +
55I VAL* 4.3 6.5 - - + -
56I ASN* 3.3 31.0 - - - +
77I GLN* 2.9 25.6 + - + +
78I GLY* 3.6 4.5 - - - +
79I PHE 3.3 0.2 - - - -
80I GLY* 1.3 75.4 - - - +
82I LYS* 1.3 56.7 + - - +
84I ALA* 3.3 6.7 + - - +
85I ARG* 2.9 27.9 + - - +
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Residues in contact with LYS 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2887 T 4.0 13.9 + - - +
2897 A 2.9 32.6 + - - +
528 T 5.6 1.6 - - - -
538 A 3.8 12.5 + - - -
78I GLY 3.0 12.6 + - - +
79I PHE* 3.1 10.7 + - - +
81I LEU* 1.3 74.0 - - - +
83I VAL* 1.3 65.8 + - - +
85I ARG* 3.2 10.3 + - + +
86I ALA* 3.1 24.5 + - + +
99I MET* 4.7 17.0 - - + -
103I LEU* 3.5 27.6 - - + +
106I TYR* 5.5 4.0 - - - -
107I TYR* 5.2 1.3 - - + -
106J TYR* 2.7 37.2 + - - -
111J PHE* 6.1 0.2 - - - -
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Residues in contact with VAL 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I PHE* 3.1 34.5 + - + +
80I GLY* 3.1 8.9 + - - +
82I LYS* 1.3 77.2 - - - +
84I ALA* 1.3 61.9 + - - +
86I ALA* 3.4 6.3 + - - +
87I LEU* 3.0 21.1 + - + +
96I LEU* 4.3 3.8 - - + +
99I MET* 6.3 0.4 - - - -
100I ILE* 4.3 19.3 - - + -
103I LEU* 3.6 19.3 - - + -
122I VAL* 4.5 8.7 - - + -
125I ILE* 3.7 27.4 - - + -
126I THR* 4.3 16.4 - - + -
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Residues in contact with ALA 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I LYS 5.5 1.1 - - - +
52I PHE* 3.6 20.2 - - + -
55I VAL* 4.0 20.9 - - + -
80I GLY 3.1 10.4 + - - +
81I LEU* 3.5 8.3 - - - +
82I LYS 3.2 0.2 - - - -
83I VAL* 1.3 79.0 - - - +
85I ARG* 1.3 64.3 + - - +
87I LEU* 3.1 11.4 + - + +
88I ASN* 2.9 27.0 + - - +
125I ILE* 4.5 7.4 - - + -
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Residues in contact with ARG 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2897 A 3.0 36.1 + - - +
2907 T 3.1 34.3 + - - +
528 T 3.8 34.8 + - - +
538 A 3.9 20.7 + - - -
52I PHE* 3.6 11.1 - - - -
81I LEU 2.9 14.2 + - - +
82I LYS* 3.2 15.7 + - + +
84I ALA* 1.3 76.9 - - - +
86I ALA* 1.3 64.8 + - - +
88I ASN* 3.1 5.6 + - - +
89I ARG* 3.0 51.7 + - - +
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Residues in contact with ALA 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528 T 5.4 3.4 - - - -
82I LYS* 3.1 12.6 + - - +
83I VAL* 3.7 8.3 - - - +
85I ARG* 1.3 76.3 - - - +
87I LEU* 1.3 58.1 + - - +
89I ARG* 4.5 2.9 - - - +
90I ILE* 2.7 51.7 + - + +
96I LEU* 3.9 10.1 - - + -
99I MET* 3.8 33.0 - - + -
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Residues in contact with LEU 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83I VAL* 3.0 14.7 + - + +
84I ALA* 3.1 12.8 + - + +
86I ALA* 1.3 76.4 - - - +
88I ASN* 1.3 65.3 + - - +
91I GLY* 2.7 31.6 + - - +
92I SER* 3.6 32.5 - - - +
96I LEU* 3.8 24.0 - - + +
125I ILE* 4.8 22.9 - - + +
126I THR* 6.1 2.5 - - + -
57n GLU* 5.8 3.8 - - - +
58n ASN* 6.2 0.2 - - - +
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Residues in contact with ASN 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2907 T 5.9 1.3 - - - +
7H SER* 3.8 18.0 + - - +
48I ASN* 4.9 5.6 + - - -
51I LYS* 3.9 30.1 + - - +
52I PHE* 3.3 34.9 - - + -
84I ALA* 2.9 12.6 + - - +
85I ARG* 3.1 7.4 + - - +
87I LEU* 1.3 86.9 - - - +
89I ARG* 1.3 63.2 + - + +
90I ILE 3.7 0.3 + - - -
91I GLY* 4.8 0.5 + - - -
57n GLU* 5.2 4.9 - - - +
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Residues in contact with ARG 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2907 T 3.8 18.8 + - - +
2917 A 4.3 14.5 + - - -
508 T 4.7 3.8 + - - -
518 A 3.6 25.9 + - - +
528 T 3.5 35.9 + - - +
60G SER* 4.7 2.4 + - - -
73G ARG* 4.6 3.6 + - - -
7H SER* 3.6 36.2 - - - +
8H ARG* 5.5 2.8 - - - +
85I ARG* 3.0 53.8 + - + +
86I ALA* 4.2 1.8 - - - +
88I ASN* 1.3 80.6 - - + +
90I ILE* 1.3 62.3 + - + +
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Residues in contact with ILE 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518 A 5.4 0.9 - - - +
528 T 4.4 11.4 - - - +
60G SER* 4.7 2.8 + - - -
64G THR* 2.6 36.1 + - - +
69G THR* 4.4 17.5 - - + -
70G GLY 5.5 0.7 - - - +
73G ARG* 3.7 19.8 + - - +
86I ALA* 2.7 27.2 + - + +
88I ASN 5.0 0.7 - - - -
89I ARG* 1.3 80.6 - - - +
91I GLY* 1.3 68.4 + - - +
95I ALA* 3.5 26.0 - - + +
96I LEU* 4.2 4.0 - - - +
99I MET* 3.7 30.7 - - + -
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Residues in contact with GLY 91 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G THR* 3.7 1.3 - - - +
86I ALA 3.6 0.2 + - - -
87I LEU* 2.7 31.0 + - - -
88I ASN 4.6 0.6 + - - -
90I ILE* 1.3 89.5 - - - +
92I SER* 1.3 68.0 + - - +
96I LEU* 3.6 10.4 - - - +
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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