Contacts of the helix formed by residues 66 - 88 (chain J) in PDB entry 1RQF
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 PRO 66 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H ARG* 3.2 36.6 - - - +
150H ARG* 3.7 26.2 - - - +
62J LEU 5.5 1.1 - - - +
63J GLU 4.9 2.2 - - - +
64J ASP 2.8 22.2 - - - +
65J ASN* 1.3 75.9 - - - +
67J ASN* 1.3 58.0 + - - +
69J SER* 2.6 21.3 - - - -
70J ASP* 2.2 33.4 + - - +
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Residues in contact with ASN 67 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A GLU* 3.4 26.4 + - - +
174A TYR* 3.4 49.9 + - - +
17H ARG* 2.9 27.8 + - - +
65J ASN* 3.7 1.8 - - - +
66J PRO* 1.3 76.6 - - - +
68J GLN* 1.3 58.2 + - - +
69J SER 2.7 13.4 + - - -
70J ASP* 2.7 21.9 + - - +
71J LEU* 3.1 19.5 + - - +
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Residues in contact with GLN 68 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A TYR* 5.7 0.2 + - - -
117A GLN* 4.5 8.1 + - - +
139A LYS* 5.9 0.3 + - - -
173A GLU 4.9 5.4 - - - +
174A TYR 4.0 13.8 - - - +
175A ARG 4.7 10.5 - - - +
176A PRO* 4.2 18.7 - - + +
177A LYS* 5.0 3.4 - - + +
45J HIS* 4.4 14.9 - - - -
61J GLU* 4.4 11.9 - - + +
65J ASN* 3.0 32.0 + - - +
67J ASN* 1.3 75.3 - - - +
69J SER* 1.3 61.7 + - - +
71J LEU* 3.7 26.2 + - - +
72J ILE* 3.6 21.7 + - - +
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Residues in contact with SER 69 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52J MET* 5.0 0.3 - - - +
61J GLU* 3.7 18.1 - - - +
62J LEU* 3.1 28.1 - - - +
65J ASN 3.1 17.8 + - - -
66J PRO* 2.6 19.1 - - - -
67J ASN 2.7 0.4 + - - -
68J GLN* 1.3 77.0 - - - +
70J ASP* 1.3 52.4 + - - -
72J ILE* 2.8 27.3 + - - +
73J GLU* 3.1 23.3 + - - +
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Residues in contact with ASP 70 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66J PRO* 2.2 46.7 + - - +
67J ASN* 2.7 12.9 + - - +
69J SER* 1.3 70.5 - - - +
71J LEU* 1.3 63.7 + - + +
73J GLU* 3.1 24.3 + - - +
74J GLN* 3.0 31.1 + - + +
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Residues in contact with LEU 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A TYR* 5.4 8.3 - - + +
102A GLN* 4.5 27.4 - - + +
117A GLN* 6.3 0.4 - - - +
118A PRO* 5.9 4.0 - - + -
174A TYR* 4.5 17.7 - - + +
44J PRO* 5.4 1.0 - - - +
45J HIS* 4.0 18.3 - - - +
67J ASN* 3.1 21.2 + - - +
68J GLN* 3.7 39.5 - - - +
69J SER 3.1 0.2 + - - -
70J ASP* 1.3 78.9 - - + +
72J ILE* 1.3 58.0 + - - +
74J GLN* 3.6 8.9 + - + +
75J ALA* 3.1 24.8 + - - +
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Residues in contact with ILE 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45J HIS* 4.2 14.4 - - + +
48J GLN* 2.8 63.7 - - + +
49J ALA* 4.1 2.2 - - + +
52J MET* 3.9 18.8 - - + -
61J GLU* 3.6 29.2 - - + +
68J GLN* 3.6 14.4 - - - +
69J SER* 2.8 9.2 + - - +
71J LEU* 1.3 75.8 - - - +
73J GLU* 1.3 61.5 + - - +
75J ALA* 3.1 6.8 + - - +
76J ALA* 2.9 27.4 + - - +
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Residues in contact with GLU 73 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J TRP* 5.0 3.0 + - - +
12J TRP* 6.0 2.1 - - - -
52J MET* 3.7 30.5 - - + +
62J LEU* 5.2 1.0 - - - +
69J SER* 3.1 27.0 + - - +
70J ASP* 3.1 28.9 + - - +
72J ILE* 1.3 77.6 - - - +
74J GLN* 1.3 66.8 + - - +
76J ALA* 3.3 4.2 + - - +
77J GLU* 3.1 21.5 + - - +
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Residues in contact with GLN 74 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70J ASP* 3.0 22.1 + - + +
71J LEU* 4.0 9.0 - - + +
73J GLU* 1.3 82.2 - - - +
75J ALA* 1.3 57.7 + - - +
77J GLU* 3.1 32.1 + - - +
78J MET* 3.0 27.0 + - - +
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Residues in contact with ALA 75 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43J VAL* 4.5 2.5 - - + +
44J PRO* 3.1 40.4 - - + +
45J HIS* 4.4 2.2 - - + -
49J ALA* 3.6 11.6 - - + +
71J LEU 3.1 15.5 + - - +
72J ILE* 3.1 12.5 + - - +
74J GLN* 1.3 74.8 - - - +
76J ALA* 1.3 60.1 + - - +
78J MET* 3.2 6.3 + - - +
79J LEU* 2.8 31.4 + - - +
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Residues in contact with ALA 76 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J TRP* 4.0 10.5 - - + -
49J ALA* 3.4 27.3 - - - +
52J MET* 3.9 19.3 - - + -
53J ILE* 3.5 12.7 - - + +
72J ILE 2.9 13.8 + - - +
73J GLU 3.6 8.3 - - - +
75J ALA* 1.3 75.6 - - - +
77J GLU* 1.3 53.9 + - - +
80J TYR* 2.8 37.2 + - - +
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Residues in contact with GLU 77 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J TRP* 4.3 11.0 - - + -
12J TRP* 6.1 1.4 - - - -
13J PHE* 3.5 31.5 - - + -
16J LEU* 6.0 1.6 - - - +
73J GLU 3.1 11.4 + - - +
74J GLN* 3.1 33.5 + - - +
75J ALA 3.1 0.2 - - - -
76J ALA* 1.3 78.6 - - - +
78J MET* 1.3 60.7 + - - +
80J TYR* 3.6 2.3 + - - +
81J GLY* 3.2 17.8 + - - -
158J TYR* 4.4 9.2 - - + -
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Residues in contact with MET 78 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLN 5.4 6.7 - - - +
108A TYR* 5.0 7.0 - - - +
42J GLN 4.1 12.1 - - - +
43J VAL* 3.7 24.9 - - + -
44J PRO* 4.6 8.1 - - - -
74J GLN 3.0 16.0 + - - +
75J ALA* 3.2 6.3 + - - +
77J GLU* 1.3 76.0 - - - +
79J LEU* 1.3 65.0 + - - +
81J GLY* 3.1 3.1 + - - -
82J LEU* 3.0 30.2 + - + +
128J PRO* 4.4 19.5 - - + -
158J TYR* 3.4 26.3 - - + +
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Residues in contact with LEU 79 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36J LEU* 5.5 1.8 - - + -
39J LEU* 4.1 23.6 - - + -
40J ASN* 4.4 8.7 - - - +
43J VAL* 3.9 27.3 - - + +
46J TYR 4.0 7.4 - - - +
49J ALA* 4.2 3.8 - - + -
50J LEU* 3.8 43.7 - - + +
53J ILE* 3.8 10.1 - - + -
75J ALA 2.8 17.0 + - - +
76J ALA 3.8 3.4 - - - +
78J MET* 1.3 77.6 - - - +
80J TYR* 1.3 62.1 + - - +
82J LEU* 3.4 2.5 + - + +
83J ILE* 3.1 44.2 + - + +
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Residues in contact with TYR 80 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J TRP* 3.6 24.2 - + + -
10J ILE* 3.7 20.5 - - + +
13J PHE* 3.6 36.8 - + + -
14J CYS* 3.5 13.9 - - - -
22J PHE* 4.2 14.8 - + - -
23J CYS 2.7 24.4 + - - -
24J GLU* 3.6 0.3 - - - -
25J VAL* 3.1 37.5 + - + +
30J ILE* 4.6 3.6 - - + -
53J ILE* 3.7 17.9 - - + +
76J ALA 2.8 22.4 + - - +
77J GLU 4.0 2.9 - - - +
79J LEU* 1.3 72.9 - - - +
81J GLY* 1.3 54.1 + - - +
83J ILE* 3.2 7.3 + - + +
84J HIS* 2.8 34.8 + + - +
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Residues in contact with GLY 81 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J PHE* 4.5 5.6 - - - -
77J GLU 3.2 6.5 + - - -
78J MET 3.1 4.7 + - - -
80J TYR* 1.3 79.8 - - - +
82J LEU* 1.3 61.0 + - - +
84J HIS* 3.0 9.4 + - - +
85J ALA 2.9 18.0 + - - -
158J TYR* 3.4 42.3 - - - -
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Residues in contact with LEU 82 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39J LEU* 3.7 24.0 - - + +
42J GLN* 3.8 31.9 - - + +
43J VAL* 3.6 29.4 - - + -
78J MET* 3.0 17.9 + - + +
79J LEU* 3.9 4.7 - - + +
81J GLY* 1.3 74.2 - - - +
83J ILE* 1.3 61.6 + - - +
85J ALA* 3.3 20.0 + - + +
86J ARG* 3.4 12.3 + - - +
126J ASP 5.6 0.9 - - - +
128J PRO* 3.8 28.5 - - + -
157J ALA* 5.0 5.8 - - + +
158J TYR* 4.0 12.3 - - + -
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Residues in contact with ILE 83 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25J VAL* 4.2 15.3 - - + -
29J TYR* 3.9 25.6 - - + -
30J ILE* 4.3 18.4 - - + -
36J LEU* 3.9 24.9 - - + -
39J LEU* 3.5 23.3 - - + -
50J LEU* 4.8 0.4 - - + -
53J ILE* 4.5 7.9 - - + -
79J LEU* 3.1 35.0 + - + +
80J TYR* 3.5 11.0 - - + +
82J LEU* 1.3 73.2 - - - +
84J HIS* 1.3 62.4 + - - +
86J ARG* 3.1 5.8 + - - +
87J TYR* 2.8 30.0 + - - +
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Residues in contact with HIS 84 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J PHE* 3.6 29.8 - + + -
23J CYS* 3.2 49.8 + - - +
25J VAL* 4.3 9.6 - - + -
80J TYR* 2.8 18.6 + - + +
81J GLY* 3.0 13.7 + - - +
83J ILE* 1.3 77.0 - - - +
85J ALA* 1.3 61.8 + - - +
87J TYR* 3.2 5.9 + + - +
88J ILE* 2.9 41.4 + - + +
97J MET* 4.4 4.2 - - + -
158J TYR 2.9 18.3 + - - +
159J PHE* 3.7 22.9 - + - -
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Residues in contact with ALA 85 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81J GLY 2.9 8.6 + - - +
82J LEU* 3.3 13.5 - - + +
83J ILE 3.1 0.2 - - - -
84J HIS* 1.3 78.6 - - - +
86J ARG* 1.3 63.4 + - + +
88J ILE* 3.6 15.6 - - - +
89J LEU* 3.6 13.8 - - - +
157J ALA 3.5 24.9 - - - +
158J TYR 3.5 11.2 + - - +
159J PHE* 4.4 3.2 - - - +
160J GLY* 4.8 5.3 - - - +
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Residues in contact with ARG 86 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B HIS* 4.2 6.8 + - - -
29J TYR* 3.5 13.7 - - - +
34J PHE 4.8 0.6 + - - -
35J ASN 2.9 30.5 + - - -
36J LEU 3.7 0.6 - - - -
37J THR* 2.8 38.9 + - - +
38J GLY* 4.2 5.3 - - - -
39J LEU* 4.0 28.8 - - + +
42J GLN* 5.2 2.6 - - - +
82J LEU 3.4 11.2 + - - +
83J ILE* 3.1 5.5 + - - +
85J ALA* 1.3 74.9 - - + +
87J TYR* 1.3 68.1 + - - +
89J LEU* 3.0 28.6 + - - +
90J THR* 3.7 6.8 - - + +
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Residues in contact with TYR 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J CYS* 4.0 15.3 - - - -
25J VAL* 3.6 30.7 - - + -
26J ASP* 3.3 16.2 + - - -
29J TYR* 3.7 51.3 + + + -
83J ILE 2.8 17.9 + - - +
84J HIS* 3.4 6.5 - - - +
86J ARG* 1.3 76.9 - - - +
88J ILE* 1.3 59.8 + - + +
89J LEU 2.9 4.5 + - - -
90J THR* 2.8 34.3 + - - -
92J ARG* 2.8 22.0 + - + -
93J GLY* 3.4 15.0 - - - -
96J GLN* 2.4 37.8 + - - -
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Residues in contact with ILE 88 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J CYS* 4.1 9.2 - - - -
84J HIS* 2.9 49.5 + - + +
85J ALA 3.6 10.1 - - - +
87J TYR* 1.3 71.5 - - + +
89J LEU* 1.3 58.3 + - + +
90J THR 3.5 0.4 - - - -
93J GLY* 4.0 7.9 - - - +
94J ILE* 3.2 20.1 - - - +
97J MET* 3.6 30.7 - - + -
159J PHE* 3.6 32.8 - - + +
163J PHE* 3.3 39.0 - - + -
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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