Contacts of the helix formed by residues 81 - 104 (chain E) 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 LEU 81 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D PHE* 4.0 23.6 - - + -
19D GLY 5.6 2.7 - - - +
20D ARG* 6.5 0.7 - - - -
21D LEU* 3.9 30.7 - - + +
154D SER* 6.1 4.0 - - - +
30E ALA* 4.9 5.9 - - + +
80E GLY* 1.3 67.3 - - - -
82E ALA* 1.3 64.2 + - - +
83E PRO* 3.5 10.8 - - + -
84E ASP* 3.4 30.9 + - + +
85E ALA 3.4 0.3 + - - -
130E ARG* 4.1 4.5 - - - +
133E GLY 2.7 21.3 + - - +
134E VAL* 3.3 20.3 - - - +
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Residues in contact with ALA 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D THR* 5.0 4.9 - - + -
64E GLN* 3.8 34.1 - - - +
65E LYS 5.7 0.2 - - - +
78E LEU* 4.0 18.0 - - + +
80E GLY 3.2 5.3 + - - +
81E LEU* 1.3 68.6 - - - +
83E PRO* 1.4 69.4 - - + +
85E ALA* 2.9 20.1 + - - +
86E ARG* 3.1 10.7 + - - +
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Residues in contact with PRO 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D LEU* 5.2 12.6 - - + -
154D SER 3.2 26.7 - - - +
155D GLY* 3.9 15.5 - - - +
156D THR* 3.9 15.3 - - - +
81E LEU* 3.6 13.9 - - + -
82E ALA* 1.4 92.4 - - + +
84E ASP* 1.3 60.2 + - - +
86E ARG* 3.3 11.1 + - + +
87E VAL* 3.1 30.2 + - - +
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Residues in contact with ASP 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E LEU* 3.4 20.4 + - + +
82E ALA 3.1 0.8 - - - -
83E PRO* 1.3 79.6 - - - +
85E ALA* 1.3 63.3 + - - +
87E VAL* 3.6 9.7 + - - +
88E LEU* 3.1 29.6 + - - +
130E ARG* 2.6 46.1 + - - -
132E TYR* 3.4 16.6 - - + -
133E GLY* 2.9 15.6 + - - -
134E VAL* 3.8 16.2 - - + -
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Residues in contact with ALA 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E ILE* 4.4 5.4 - - + -
78E LEU* 3.7 40.8 - - + -
81E LEU 3.4 2.4 + - - -
82E ALA 2.9 13.6 + - - +
84E ASP* 1.3 77.4 - - - +
86E ARG* 1.3 57.3 + - - +
88E LEU* 3.9 1.0 - - - +
89E SER* 2.8 34.5 + - - -
134E VAL* 4.0 15.0 - - + +
136E LEU* 4.1 10.9 - - + +
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Residues in contact with ARG 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D GLN* 3.1 40.6 + - - +
118D ASP* 2.8 41.0 + - - -
65E LYS* 6.2 0.4 - - - +
68E ILE* 4.9 4.9 - - + +
82E ALA 3.1 10.2 + - - +
83E PRO* 3.5 12.8 - - + +
84E ASP 3.2 0.2 - - - -
85E ALA* 1.3 74.7 - - - +
87E VAL* 1.3 68.1 + - + +
89E SER* 3.1 7.5 + - - +
90E ASN* 2.9 49.1 + - - +
93E ARG* 5.0 9.7 - - - +
68L PHE 5.8 1.2 + - - -
69L ASP* 5.2 9.3 + - - -
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Residues in contact with VAL 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D LEU* 5.9 6.5 - - + -
83E PRO 3.1 15.2 + - - +
84E ASP* 3.8 13.0 - - - +
86E ARG* 1.3 78.8 - - + +
88E LEU* 1.3 61.1 + - - +
90E ASN* 3.3 5.9 - - - +
91E TYR* 3.2 20.8 + - - +
119E LYS* 5.0 8.2 - - - +
132E TYR* 4.1 27.8 - - + +
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Residues in contact with LEU 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E LEU* 5.3 1.1 - - - -
84E ASP 3.1 21.6 + - - +
85E ALA 4.1 1.8 - - - +
86E ARG 3.2 0.2 - - - -
87E VAL* 1.3 74.8 - - - +
89E SER* 1.3 64.6 + - - +
90E ASN 3.1 1.6 - - - -
91E TYR* 3.3 5.4 + - - +
92E LEU* 3.0 23.3 + - - +
116E LEU* 3.9 25.5 - - + +
119E LYS* 3.7 30.5 - - + -
120E ALA 5.3 0.2 - - - +
132E TYR* 4.0 33.4 - - + -
134E VAL* 3.8 21.5 - - + -
136E LEU* 3.9 18.4 - - + -
151E PHE* 4.0 16.2 - - + -
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Residues in contact with SER 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E ILE* 3.8 33.2 - - - +
70E CYS* 4.3 3.2 - - - -
76E LEU* 3.9 22.1 - - - +
85E ALA 2.8 27.4 + - - -
86E ARG* 3.1 11.4 + - - +
88E LEU* 1.3 73.1 - - - +
90E ASN* 1.3 59.9 + - - +
92E LEU* 3.6 7.2 - - - +
93E ARG* 2.9 37.9 + - - +
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Residues in contact with ASN 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E ARG* 2.9 51.1 + - - +
87E VAL* 3.3 7.9 - - - +
89E SER* 1.3 78.0 + - - +
91E TYR* 1.3 63.2 + - - +
93E ARG* 3.2 20.8 + - - +
94E GLN* 3.1 37.3 + - - +
65L TRP* 4.5 11.4 - - - -
69L ASP* 5.7 2.6 + - - -
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Residues in contact with TYR 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E VAL 3.2 10.3 + - - +
88E LEU 3.3 8.3 + - - +
90E ASN* 1.3 79.6 - - - +
92E LEU* 1.3 62.6 + - + +
94E GLN* 3.2 18.0 + - - +
95E GLN* 2.9 59.4 + - + +
115E LEU* 3.8 47.2 + - + +
116E LEU* 4.8 8.7 - - + -
119E LYS* 3.7 40.4 - - + +
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Residues in contact with LEU 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E CYS* 3.8 25.4 - - + -
74E MET* 4.5 15.9 - - - -
76E LEU* 4.1 13.0 - - + -
88E LEU 3.0 15.2 + - - +
89E SER* 3.6 5.6 - - - +
90E ASN 3.2 0.2 - - - -
91E TYR* 1.3 80.0 - - + +
93E ARG* 1.3 60.1 + - - +
95E GLN* 3.3 10.5 + - + +
96E CYS* 3.0 33.9 + - - +
107E LEU* 5.1 0.7 - - + -
112E ALA* 3.8 34.8 - - + +
115E LEU* 5.3 2.7 - - + -
116E LEU* 3.9 27.8 - - + -
138E ILE* 4.7 8.3 - - + -
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Residues in contact with ARG 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E ILE* 3.6 19.1 - - - +
69E LYS* 2.8 28.8 + - - +
70E CYS* 3.5 27.8 - - - +
86E ARG* 5.0 8.3 - - - +
89E SER* 2.9 20.8 + - - +
90E ASN* 3.2 23.2 + - - +
92E LEU* 1.3 75.9 - - - +
94E GLN* 1.3 55.3 - - - +
96E CYS* 3.4 2.9 + - - +
97E ASN* 3.0 28.2 + - - +
64L LYS* 5.3 1.4 + - - -
65L TRP* 3.7 20.9 - - + -
68L PHE* 3.4 62.1 + - + +
69L ASP* 4.8 3.8 + - - -
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Residues in contact with GLN 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E ASN* 3.1 25.7 + - - +
91E TYR* 3.2 23.0 + - - +
93E ARG* 1.3 75.1 - - - +
95E GLN* 1.3 66.5 + - - +
97E ASN* 3.2 6.9 + - - +
98E TYR* 2.8 31.4 + - - +
65L TRP* 4.0 18.0 - - + -
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Residues in contact with GLN 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E TYR* 2.9 63.2 + - + +
92E LEU* 3.3 8.5 + - + +
94E GLN* 1.3 78.8 + - - +
96E CYS* 1.3 64.1 + - - +
98E TYR* 4.0 14.2 - - - +
99E SER* 3.2 22.9 + - - -
107E LEU* 4.1 10.0 - - + +
111E ARG* 5.8 0.9 + - - -
115E LEU* 4.0 31.8 - - + +
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Residues in contact with CYS 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E CYS* 4.2 7.6 - - - +
71E ASP* 3.8 40.7 - - + +
73E HIS* 4.3 2.9 - - - -
74E MET* 4.0 25.4 - - - -
92E LEU* 3.0 21.1 + - - +
93E ARG 3.6 5.4 - - - +
95E GLN* 1.3 75.5 - - - +
97E ASN* 1.3 63.0 + - - +
99E SER* 3.5 4.3 + - - -
100E SER* 3.2 23.6 + - - -
105E ARG 4.6 0.3 - - - +
106E LYS* 5.8 0.2 - - - -
107E LEU* 4.2 23.6 + - - +
64L LYS* 5.0 0.7 - - - +
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Residues in contact with ASN 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E ARG 3.0 18.4 + - - +
94E GLN* 3.3 8.7 - - - +
96E CYS* 1.3 74.1 - - - +
98E TYR* 1.3 66.4 + - - +
100E SER* 3.1 6.1 + - - -
101E LEU* 2.9 36.8 + - - +
61L ASN* 3.0 39.7 - - - +
64L LYS* 2.9 30.4 - - - +
65L TRP* 3.1 19.2 + - + -
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Residues in contact with TYR 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E GLN 2.8 20.5 + - - +
95E GLN* 4.0 15.9 - - - +
97E ASN* 1.3 71.4 - - - +
99E SER* 1.3 63.0 + - - +
101E LEU* 4.6 7.0 - - - -
102E VAL* 2.9 57.6 + - + +
103E PHE* 4.1 20.9 - + - -
86M TYR* 6.1 0.5 - - - -
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Residues in contact with SER 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E GLN 3.2 16.0 + - - -
96E CYS 3.6 5.2 - - - -
97E ASN 3.2 0.6 - - - -
98E TYR* 1.3 83.6 - - - +
100E SER* 1.3 61.1 + - - +
103E PHE* 3.1 29.0 + - - +
105E ARG* 2.7 42.3 + - - +
107E LEU* 3.7 27.3 + - - +
111E ARG* 5.9 0.4 - - - -
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Residues in contact with SER 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E ASP* 4.4 8.8 + - - -
96E CYS 3.2 9.2 + - - -
97E ASN* 3.1 11.1 + - - -
99E SER* 1.3 75.7 - - - +
101E LEU* 1.3 64.9 + - - +
104E ASN* 2.7 36.2 + - - +
105E ARG 3.2 17.0 + - - +
106E LYS* 4.8 6.4 + - - +
57L LYS* 5.4 0.7 - - - -
64L LYS* 5.1 7.5 + - - -
85M GLU* 4.9 0.3 - - - +
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Residues in contact with LEU 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E ASN* 2.9 40.4 + - + +
98E TYR* 3.9 5.8 - - - +
100E SER* 1.3 78.0 - - - +
102E VAL* 1.3 65.6 + - + +
57L LYS* 3.2 54.8 + - + +
61L ASN* 3.7 31.0 - - + +
85M GLU* 3.8 4.3 - - - +
89M THR* 4.1 3.0 + - - -
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Residues in contact with VAL 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E TYR* 2.9 48.3 + - + +
101E LEU* 1.3 82.9 - - + +
103E PHE* 1.3 84.3 + - + +
104E ASN 3.6 0.2 - - - -
85M GLU* 3.1 7.7 - - - +
86M TYR* 3.1 39.8 + - + -
89M THR* 3.9 25.6 - - + +
93M GLN* 5.7 0.7 - - - +
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Residues in contact with PHE 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E TYR* 4.1 17.9 - + - -
99E SER* 3.1 22.5 + - - +
102E VAL* 1.3 92.6 - - + +
104E ASN* 1.3 69.3 + - - +
105E ARG* 3.9 22.0 - - + -
61M LEU* 3.6 34.3 - - + -
78M LEU* 5.8 0.9 - - + -
82M TYR* 3.1 41.5 - - + +
85M GLU* 3.9 4.0 - - - -
86M TYR* 3.7 34.8 - + + -
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Residues in contact with ASN 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E SER* 2.7 30.3 + - - +
102E VAL 3.6 1.2 - - - -
103E PHE* 1.3 79.6 - - - +
105E ARG* 1.3 56.0 + - - +
106E LYS 4.4 0.3 + - - -
81M SER* 4.6 14.2 + - - +
82M TYR* 3.7 10.9 - - + -
85M GLU* 3.9 27.9 + - + +
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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) + - + + + + + -
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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