Contacts of the helix formed by residues 48 - 71 (chain H) 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 THR 48 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H GLY* 1.3 67.5 - - - -
49H ALA* 1.3 68.0 + - - +
50H ALA* 4.5 1.3 - - + +
51H ASP* 3.0 42.9 + - - +
52H THR* 3.1 14.3 + - - +
96H GLY* 3.0 16.8 + - - -
91I ARG* 4.0 13.2 + - - +
114I ASP* 5.8 2.2 - - - +
116I ILE* 4.0 17.5 - - + -
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Residues in contact with ALA 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H SER* 6.0 2.0 - - - +
47H GLY 3.0 9.0 + - - +
48H THR* 1.3 71.7 - - - +
50H ALA* 1.3 63.9 + - - +
52H THR* 3.1 22.1 + - - -
53H GLU* 3.2 12.7 + - - +
114I ASP* 5.3 2.4 + - - +
118I CYS* 3.5 25.6 - - + -
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Residues in contact with ALA 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H THR* 3.4 1.0 - - - +
49H ALA* 1.3 78.8 - - - +
51H ASP* 1.3 56.7 + - - +
53H GLU* 3.7 4.2 + - - +
54H ALA* 3.0 30.7 + - - +
88I TYR* 3.8 7.3 - - + -
114I ASP* 4.6 1.9 + - - +
116I ILE* 3.7 40.6 - - + +
117I GLY 4.5 0.4 - - - -
118I CYS* 3.6 31.7 - - + +
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Residues in contact with ASP 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H THR* 3.0 19.9 + - - +
50H ALA* 1.3 77.3 - - - +
52H THR* 1.3 59.9 + - - +
54H ALA* 3.3 1.4 + - - +
55H VAL* 2.9 33.4 + - - +
95H ILE* 3.4 20.1 - - + +
96H GLY 2.8 29.6 + - - +
97H ALA* 4.5 1.8 - - - -
88I TYR* 3.0 19.0 + - - -
91I ARG* 2.8 42.5 + - - -
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Residues in contact with THR 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H HIS* 4.9 9.1 + - - -
45H GLY* 4.0 20.3 + - - -
46H ALA 3.7 25.4 - - - +
48H THR 3.1 10.9 + - - +
49H ALA* 3.1 14.4 + - - -
51H ASP* 1.3 75.5 - - - +
53H GLU* 1.3 61.0 + - - +
55H VAL* 3.5 8.0 - - - +
56H THR* 3.0 32.9 + - - -
96H GLY 4.3 0.2 - - - +
97H ALA* 3.8 18.8 - - + -
99H LEU* 3.9 12.7 - - + +
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Residues in contact with GLU 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H HIS* 3.8 34.7 + - - +
49H ALA 3.2 12.4 + - - +
50H ALA* 4.0 4.5 - - - +
52H THR* 1.3 81.4 + - - +
54H ALA* 1.3 58.0 + - - +
56H THR* 3.5 6.3 + - - +
57H GLN* 3.0 66.8 + - - +
118I CYS* 6.4 2.0 - - - -
119I ILE* 5.9 5.3 - - + +
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Residues in contact with ALA 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H ALA 3.0 19.7 + - - +
51H ASP 3.3 1.5 + - - +
53H GLU* 1.3 74.3 - - - +
55H VAL* 1.3 61.5 + - - +
56H THR 3.0 1.8 - - - -
57H GLN* 3.2 4.3 + - - +
58H LEU* 2.8 33.3 + - - +
88I TYR* 3.5 39.9 - - + +
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Residues in contact with VAL 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H ASP 2.9 16.5 + - - +
52H THR* 3.5 11.2 - - - +
54H ALA* 1.3 77.7 - - - +
56H THR* 1.3 61.6 + - - +
58H LEU* 4.6 4.3 - - - -
59H ILE* 3.3 28.3 + - + +
83H LEU* 3.5 15.0 - - + +
86H HIS* 3.5 33.7 - - + +
87H LEU* 4.0 15.9 - - + -
95H ILE* 4.8 4.7 - - + -
97H ALA* 4.1 11.2 - - + -
99H LEU* 3.9 26.5 - - + -
88I TYR* 5.3 0.4 + - - +
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Residues in contact with THR 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H HIS* 3.6 31.7 - - + -
36H ARG 3.9 14.7 - - - +
37H ILE* 4.4 10.1 - - + +
43H CYS* 3.2 26.3 - - - -
52H THR 3.0 21.4 + - - -
53H GLU* 3.5 8.7 - - - +
54H ALA 3.0 0.4 - - - -
55H VAL* 1.3 80.2 - - - +
57H GLN* 1.3 65.9 + - + +
59H ILE* 4.2 0.2 - - - -
60H GLY* 2.9 26.5 + - - -
83H LEU* 5.2 2.5 - - - +
99H LEU* 4.5 3.6 - - - +
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Residues in contact with GLN 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LYS* 5.4 9.7 + - - +
102A ARG* 6.2 0.9 - - - -
104A GLY* 5.0 10.5 + - - -
36H ARG 6.0 0.4 - - - +
53H GLU* 3.0 48.2 + - - +
54H ALA* 4.0 4.2 - - - +
56H THR* 1.3 77.0 - - + +
58H LEU* 1.3 65.2 + - - +
60H GLY* 3.7 1.1 - - - -
61H SER* 2.9 26.6 + - - -
81I GLN* 4.5 17.0 + - - +
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Residues in contact with LEU 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ARG* 4.0 32.5 - - - +
54H ALA 2.8 22.3 + - - +
55H VAL* 4.2 4.0 - - - +
57H GLN* 1.3 75.8 - - - +
59H ILE* 1.3 71.1 + - + +
61H SER* 3.1 5.5 + - - -
62H ASN* 3.0 34.1 + - - +
86H HIS* 3.6 35.4 - - + +
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Residues in contact with ILE 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H ILE* 4.4 10.3 - - + -
55H VAL* 3.3 21.4 + - + +
56H THR 4.5 0.7 - - - +
58H LEU* 1.3 98.3 - - + +
60H GLY* 1.3 58.0 + - - +
62H ASN* 3.3 9.9 + - - +
63H ILE* 2.9 41.5 + - + +
79H ALA* 4.2 12.3 - - + +
82H MET* 3.8 24.7 - - + +
83H LEU* 3.7 30.5 - - + +
86H HIS* 4.4 21.3 - - + +
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Residues in contact with GLY 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LYS* 6.3 0.4 - - - -
36H ARG 5.3 1.1 - - - -
37H ILE* 3.3 31.6 - - - +
56H THR 2.9 21.3 + - - -
57H GLN* 3.7 1.1 - - - -
58H LEU 3.2 0.2 - - - -
59H ILE* 1.3 75.7 - - - +
61H SER* 1.3 56.7 + - - +
63H ILE* 3.4 2.3 + - - +
64H GLU* 3.0 28.6 + - - +
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Residues in contact with SER 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A HIS* 2.7 33.0 - - - +
101A LYS* 5.6 7.9 - - - +
102A ARG* 3.0 33.7 + - - +
57H GLN 2.9 18.3 + - - -
58H LEU* 3.3 5.4 - - - -
60H GLY* 1.3 76.5 - - - +
62H ASN* 1.3 61.0 + - - +
64H GLU* 3.3 6.3 + - - +
65H LEU* 3.2 23.9 + - - +
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Residues in contact with ASN 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ARG* 3.0 21.0 + - - +
58H LEU* 3.0 36.4 + - - +
59H ILE* 3.9 9.7 - - - +
61H SER* 1.3 75.7 - - - +
63H ILE* 1.3 57.3 + - - +
65H LEU* 3.5 11.3 + - - +
66H HIS* 2.9 28.6 + - - +
82H MET* 3.4 26.4 - - + +
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Residues in contact with ILE 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H ILE* 4.3 9.2 - - + +
38H SER* 4.0 17.7 - - - -
41H ILE* 5.2 0.7 - - + -
59H ILE* 2.9 27.5 + - + +
60H GLY* 3.7 6.3 - - - +
62H ASN* 1.3 74.5 - - - +
64H GLU* 1.3 66.3 + - - +
66H HIS* 3.3 11.9 + - + +
67H SER* 2.9 23.4 + - - -
74H PRO* 3.7 29.7 - - + +
75H ARG 4.3 5.4 - - - +
78H SER* 3.9 28.9 - - - -
79H ALA* 4.0 10.1 - - + +
82H MET* 3.9 15.7 - - - -
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Residues in contact with GLU 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PRO* 4.9 3.8 - - - +
97A HIS* 3.1 27.5 + - - +
101A LYS* 4.5 6.1 + - - -
106A TYR* 2.5 32.8 + - - -
60H GLY 3.0 14.2 + - - +
61H SER* 3.4 10.5 - - - +
63H ILE* 1.3 77.0 - - - +
65H LEU* 1.3 62.6 + - - +
67H SER* 3.0 8.4 + - - -
68H LEU* 2.9 40.4 + - + +
74H PRO* 6.1 0.4 - - - -
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Residues in contact with LEU 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ARG* 3.6 39.0 - - + +
94A LYS* 4.1 28.5 - - + +
97A HIS* 3.7 21.8 - - + +
102A ARG* 4.1 19.5 - - - +
61H SER 3.2 14.6 + - - +
62H ASN* 3.7 13.7 - - - +
63H ILE 3.3 0.2 - - - -
64H GLU* 1.3 74.3 - - - +
66H HIS* 1.3 56.2 + - - +
68H LEU* 3.4 9.7 + - + +
69H TYR* 2.9 32.0 + - - +
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Residues in contact with HIS 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G PHE* 3.5 16.2 - + - -
103G TYR* 3.5 49.6 - + + -
105G TYR* 2.8 42.1 + + - -
62H ASN 2.9 17.8 + - - +
63H ILE* 3.3 14.6 + - + +
65H LEU* 1.3 74.1 - - - +
67H SER* 1.3 58.9 + - - +
69H TYR* 3.3 6.5 + + + +
70H THR* 2.9 47.7 + - + +
74H PRO* 5.9 4.0 - - - +
78H SER* 4.7 6.3 + - - -
82H MET* 5.4 0.7 - - + -
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Residues in contact with SER 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H ILE 2.9 18.0 + - - -
64H GLU* 3.0 7.8 + - - -
66H HIS* 1.3 74.3 + - - +
68H LEU* 1.3 65.6 + - - +
70H THR* 3.9 1.8 - - - -
71H SER* 2.9 26.3 + - - -
72H ARG 2.7 31.1 + - - -
73H GLU* 4.3 1.2 + - - -
74H PRO* 3.7 24.9 - - - +
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Residues in contact with LEU 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU* 4.7 25.6 - - + +
70A LEU 4.8 3.4 - - - +
93A ARG* 3.5 61.1 + - + +
97A HIS* 5.6 2.2 - - + -
114G LYS* 4.6 1.4 + - - -
64H GLU* 2.9 37.3 + - + +
65H LEU* 3.6 9.2 - - + +
67H SER* 1.3 82.7 - - - +
69H TYR* 1.3 60.8 + - - +
70H THR 3.5 0.2 + - - -
71H SER* 3.7 10.2 + - - -
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Residues in contact with TYR 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ASP* 3.7 35.9 - - + -
93A ARG* 4.8 2.0 - - - +
111G VAL* 4.3 18.4 - - + +
114G LYS* 3.0 45.7 + - + +
115G ARG* 3.6 37.1 + - + -
118G ASN* 3.6 12.3 + - - -
65H LEU 2.9 18.9 + - - +
66H HIS* 3.6 7.6 - + + +
68H LEU* 1.3 79.1 - - - +
70H THR* 1.3 69.0 + - + +
71H SER* 4.5 2.8 + - - -
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Residues in contact with THR 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G PHE* 4.4 1.8 - - + -
105G TYR* 4.2 9.7 + - - +
110G ASP* 4.0 2.0 - - - +
111G VAL* 3.7 36.5 - - + +
66H HIS* 2.9 52.5 + - + +
67H SER* 3.7 2.6 + - - -
69H TYR* 1.3 82.6 - - + +
71H SER* 1.3 72.5 + - - +
72H ARG* 3.1 40.2 + - - +
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Residues in contact with SER 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110G ASP* 5.3 2.7 - - - -
67H SER 2.9 10.2 + - - -
68H LEU 3.7 9.2 + - - -
69H TYR 3.5 3.6 + - - -
70H THR* 1.3 81.9 - - - +
72H ARG* 1.3 63.4 + - - +
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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) + - + + + + + -
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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