Contacts of the helix formed by residues 50 - 71 (chain J) in PDB entry 3SDI
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 50 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J ALA* 1.3 76.7 - - - +
51J ASP* 1.3 65.7 + - - +
52J THR 3.0 3.9 + - - -
53J VAL* 3.5 5.2 + - - +
54J GLN* 3.3 23.4 + - - +
88K TYR* 3.9 9.2 - - - -
91K LYS* 3.3 3.4 - - - +
116K ASP 3.2 23.4 + - - -
117K GLY* 3.8 18.7 - - - +
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Residues in contact with ASP 51 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48J GLU* 3.9 18.8 - - + +
50J GLY* 1.3 76.5 - - - +
52J THR* 1.3 56.7 + - - +
54J GLN 3.9 0.4 - - - -
55J PHE* 2.9 34.5 + - - +
93J ARG* 3.1 25.4 + - - -
94J PRO 3.5 4.9 - - - +
95J TYR* 4.1 6.4 - - + -
96J GLN* 3.1 29.6 + - - +
97J VAL* 3.4 14.1 - - + +
88K TYR* 3.0 29.3 + - - -
91K LYS* 3.7 5.9 - - - +
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Residues in contact with THR 52 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J ARG* 6.1 0.7 - - - +
45J PHE* 3.4 29.1 - - + -
46J ALA* 3.8 6.8 + - - -
47J GLY 3.8 19.5 + - - +
48J GLU 3.4 12.8 + - - +
49J ALA* 3.5 17.0 - - - +
50J GLY 3.0 0.8 + - - -
51J ASP* 1.3 79.4 - - - +
53J VAL* 1.3 86.2 + - + +
55J PHE* 3.9 2.4 - - - +
56J ALA* 3.2 22.0 + - - +
97J VAL* 3.8 13.6 - - - +
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Residues in contact with VAL 53 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J ARG* 4.0 14.8 - - - +
45J PHE* 4.4 13.2 - - + -
49J ALA 5.3 1.8 - - - +
50J GLY 3.5 5.2 + - - +
52J THR* 1.3 90.8 - - + +
54J GLN* 1.3 70.5 + - + +
56J ALA* 3.0 7.9 + - - +
57J GLU* 2.9 49.6 + - - +
81K LYS* 6.1 1.1 - - - -
119K ARG* 5.6 12.1 - - + +
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Residues in contact with GLN 54 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50J GLY* 3.3 17.6 + - - +
51J ASP 3.9 1.8 - - - +
53J VAL* 1.3 80.8 - - + +
55J PHE* 1.3 60.7 + - - +
57J GLU* 3.7 7.3 + - - +
58J TYR* 3.1 24.8 + - - +
95J TYR* 4.7 5.4 + - + +
81K LYS* 5.8 0.6 - - - -
84K SER* 4.8 3.6 + - - +
85K ASN* 2.8 31.7 + - - +
88K TYR* 3.6 52.4 - - + +
117K GLY 5.5 4.3 - - - +
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Residues in contact with PHE 55 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43J MET* 4.6 2.2 - - + -
45J PHE* 6.1 0.2 - - + -
51J ASP 2.9 19.8 + - - +
52J THR 3.9 2.5 - - - +
54J GLN* 1.3 74.6 - - - +
56J ALA* 1.3 69.1 + - - +
58J TYR* 3.3 8.8 + + - +
59J ILE* 3.0 60.7 + - + +
83J VAL* 4.1 14.4 - - + -
86J GLU* 4.2 13.9 - - + -
87J LEU* 3.5 37.7 - - + -
95J TYR* 3.6 39.4 - + + -
97J VAL* 4.1 22.4 - - + -
99J VAL* 4.3 12.1 - - + -
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Residues in contact with ALA 56 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J ARG* 3.8 14.1 - - + +
37J LEU* 4.5 0.5 - - - +
43J MET* 3.7 18.3 - - + +
45J PHE* 3.4 39.3 - - + -
52J THR 3.2 8.7 + - - +
53J VAL* 3.0 8.6 + - - +
55J PHE* 1.3 80.4 - - - +
57J GLU* 1.3 59.3 + - + +
59J ILE* 3.4 3.1 + - - +
60J GLN* 3.0 27.2 + - - +
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Residues in contact with GLU 57 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C LEU* 3.5 21.0 - - + +
104C GLU* 3.8 8.0 - - - +
35J ARG* 2.6 38.4 + - + +
53J VAL* 2.9 32.2 + - - +
54J GLN* 4.2 7.4 + - - +
56J ALA* 1.3 72.2 - - - +
58J TYR* 1.3 57.1 + - - +
60J GLN* 3.1 12.6 + - - +
61J ALA* 2.7 36.9 + - - +
81K LYS* 2.8 37.0 + - - -
119K ARG* 5.1 1.6 + - - -
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Residues in contact with TYR 58 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C LEU* 4.1 11.1 - - + +
54J GLN 3.1 20.2 + - - +
55J PHE* 3.5 14.1 - + - +
57J GLU* 1.3 77.4 - - - +
59J ILE* 1.3 74.9 + - + +
61J ALA* 3.3 6.2 + - + +
62J ASN* 3.0 52.6 + - - +
82J PHE* 5.2 0.8 - + - -
86J GLU* 3.1 39.0 + - + -
95J TYR* 4.6 16.2 - + - +
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Residues in contact with ILE 59 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J LEU* 3.9 21.8 - - + -
43J MET* 3.9 7.2 - - + -
55J PHE* 3.0 57.5 + - + +
56J ALA 3.7 4.5 - - - +
58J TYR* 1.3 83.8 - - + +
60J GLN* 1.3 58.2 + - - +
62J ASN* 3.3 5.4 + - - +
63J ILE* 2.9 43.0 + - + +
82J PHE* 3.9 19.7 - - + -
83J VAL* 3.6 26.9 - - + -
86J GLU* 4.2 9.4 - - + -
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Residues in contact with GLN 60 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J ARG* 3.7 22.7 + - + +
36J GLN* 2.5 38.6 + - - +
37J LEU* 3.9 15.0 - - + +
56J ALA 3.0 15.5 + - - +
57J GLU* 3.1 14.8 + - - +
59J ILE* 1.3 73.6 - - - +
61J ALA* 1.3 65.8 + - - +
63J ILE* 3.2 3.4 + - - +
64J GLN* 2.9 53.8 + - + +
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Residues in contact with ALA 61 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C GLN* 3.8 30.1 - - + +
101C LEU* 4.0 24.9 - - + -
57J GLU 2.7 20.1 + - - +
58J TYR* 3.5 6.5 - - + +
60J GLN* 1.3 74.1 - - - +
62J ASN* 1.3 59.7 + - - +
64J GLN* 3.4 3.1 + - - +
65J LEU* 3.0 29.3 + - - +
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Residues in contact with ASN 62 (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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58J TYR* 3.0 49.8 + - - +
59J ILE 3.7 3.8 - - - +
61J ALA* 1.3 78.0 - - - +
63J ILE* 1.3 64.4 + - - +
65J LEU* 3.6 15.8 + - - +
66J TYR* 3.2 20.8 + - - +
82J PHE* 3.8 34.7 - - + -
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Residues in contact with ILE 63 (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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103B TYR* 5.7 0.4 - - + -
37J LEU* 3.8 29.2 - - + +
38J SER* 4.5 9.2 - - - -
59J ILE* 2.9 31.6 + - + +
60J GLN 4.0 1.1 - - - +
62J ASN* 1.3 75.1 - - - +
64J GLN* 1.3 60.8 + - - +
66J TYR* 3.2 5.8 + - + +
67J SER* 3.0 29.2 + - - +
74J LEU* 4.5 24.0 - - + +
79J VAL* 4.2 33.2 - - + -
82J PHE* 3.7 31.6 - - + -
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Residues in contact with GLN 64 (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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97C GLN* 3.1 34.7 + - - +
100C ARG* 4.1 17.9 + - - +
36J GLN 4.2 4.6 + - - -
37J LEU 4.1 11.7 + - - +
60J GLN* 2.9 50.0 + - - +
61J ALA* 3.8 0.7 - - - +
63J ILE* 1.3 76.8 - - - +
65J LEU* 1.3 62.1 + - - +
67J SER* 3.4 9.7 + - - -
68J ILE* 3.2 25.5 + - + +
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Residues in contact with LEU 65 (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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90C GLU* 4.8 1.3 - - - +
93C ARG* 3.8 43.5 - - + +
94C VAL* 4.0 21.8 - - + +
97C GLN* 3.9 12.1 - - + +
61J ALA 3.0 17.7 + - - +
62J ASN* 3.6 17.3 - - - +
64J GLN* 1.3 73.8 - - - +
66J TYR* 1.3 66.6 + - - +
68J ILE* 3.2 5.5 + - + +
69J ARG* 3.0 51.9 + - - +
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Residues in contact with TYR 66 (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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99B TYR* 2.6 32.3 + + - -
103B TYR* 3.7 26.7 - + - +
108B PRO* 4.5 2.8 - - - +
111B ILE* 3.3 19.3 - - + +
62J ASN 3.2 10.2 + - - +
63J ILE* 3.2 11.5 + - + +
65J LEU* 1.3 80.3 - - - +
67J SER* 1.3 66.0 + - - +
69J ARG* 3.4 22.5 + - - +
70J GLU* 3.1 41.3 + - + +
72J TYR* 4.5 13.5 - + + -
74J LEU* 3.5 44.9 - - + +
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Residues in contact with SER 67 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J LEU 5.4 0.3 + - - -
38J SER* 4.5 13.7 - - - -
39J PRO* 5.6 2.1 - - - +
63J ILE* 3.0 17.2 + - - +
64J GLN* 3.5 12.7 - - - -
65J LEU 3.2 0.2 - - - -
66J TYR* 1.3 75.9 - - - +
68J ILE* 1.3 59.1 - - - +
71J ASP* 2.8 30.3 + - - -
72J TYR 3.2 22.5 + - - -
73J GLU* 4.4 8.5 - - - +
74J LEU 5.2 0.9 + - - -
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Residues in contact with ILE 68 (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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69C LYS* 3.9 18.4 - - + +
70C ILE 3.7 14.6 - - - +
71C ASP* 3.4 46.2 - - - +
72C SER* 4.0 4.5 - - - +
93C ARG* 3.5 41.3 + - + +
97C GLN* 4.2 13.0 - - + +
64J GLN* 3.2 10.7 + - + +
65J LEU* 3.2 6.3 + - + +
67J SER* 1.3 78.2 - - - +
69J ARG* 1.3 68.0 + - - +
70J GLU 3.3 0.5 + - - -
71J ASP* 3.5 9.6 + - - +
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Residues in contact with ARG 69 (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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114B ARG* 3.5 30.3 + - - +
90C GLU* 3.1 40.1 + - - +
93C ARG* 3.6 26.0 + - - +
65J LEU* 3.0 45.0 + - + +
66J TYR* 3.8 30.6 - - - +
68J ILE* 1.3 79.0 - - - +
70J GLU* 1.3 76.5 + - - +
71J ASP 3.9 0.2 + - - -
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Residues in contact with GLU 70 (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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108B PRO* 6.0 0.9 - - + -
110B GLU* 5.2 1.7 - - - +
111B ILE* 3.4 36.0 - - + +
114B ARG* 2.6 35.3 + - - +
144B ARG* 2.8 35.9 + - - +
66J TYR* 3.1 38.4 + - + +
69J ARG* 1.3 97.5 + - - +
71J ASP* 1.3 68.4 + - - +
72J TYR* 4.1 9.2 - - + +
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Residues in contact with ASP 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ARG* 3.2 15.5 + - - +
69C LYS* 4.2 22.0 + - + +
67J SER 2.8 14.1 + - - -
68J ILE* 3.5 6.5 + - - +
69J ARG 3.5 3.0 - - - -
70J GLU* 1.3 79.0 - - - +
72J TYR* 1.3 56.5 + - - +
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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
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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) + - + + + + + -
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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