Contacts of the helix formed by residues 53 - 76 (chain A) in PDB entry 3PJA
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 ASP 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A GLN* 1.3 75.7 - - - +
54A ILE* 1.3 64.3 + - - +
55A PRO* 3.7 15.3 - - - +
56A LYS* 3.2 42.7 + - + +
57A ARG* 3.6 27.7 + - - +
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Residues in contact with ILE 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A VAL* 3.5 30.5 - - + -
52A GLN* 3.9 19.5 + - + +
53A ASP* 1.3 70.3 - - - +
55A PRO* 1.3 69.4 - - + +
57A ARG* 2.6 34.7 + - + +
58A CYS* 2.9 32.9 + - - -
108A LEU* 3.9 26.5 - - + +
154A LEU* 6.3 0.2 - - + -
166A ARG* 3.6 32.1 - - - +
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Residues in contact with PRO 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ASP* 3.7 13.7 - - - +
54A ILE* 1.3 96.5 - - + +
56A LYS* 1.3 55.4 + - - +
58A CYS* 3.8 7.2 - - + +
59A LEU* 3.0 42.6 + - + +
109A GLU* 6.3 0.2 - - + -
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Residues in contact with LYS 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ASP* 3.2 33.0 + - + +
54A ILE 3.1 0.8 - - - -
55A PRO* 1.3 74.5 - - - +
57A ARG* 1.3 70.5 + - - +
59A LEU* 3.4 10.1 + - - +
60A LYS* 3.0 25.3 + - + +
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Residues in contact with ARG 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 2.9 49.3 + - + +
42A LEU* 4.2 9.9 - - + +
44A GLY* 3.8 23.2 + - - -
45A VAL* 3.9 22.8 - - - +
52A GLN* 4.5 10.7 + - - +
53A ASP* 3.6 27.3 + - - +
54A ILE* 2.6 22.2 + - + +
56A LYS* 1.3 79.6 - - - +
58A CYS* 1.3 56.7 + - - +
60A LYS* 3.3 7.2 + - - +
61A ALA* 3.0 27.4 + - - +
108A LEU* 6.0 1.1 - - + -
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Residues in contact with CYS 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LEU* 4.5 3.1 - - - -
54A ILE* 2.9 22.0 + - - +
55A PRO* 3.8 9.6 - - + +
57A ARG* 1.3 74.3 - - - +
59A LEU* 1.3 60.9 + - + +
61A ALA* 3.4 9.0 + - - +
62A ARG* 3.0 31.7 + - - +
105A VAL* 4.1 9.6 - - + +
108A LEU* 3.4 41.3 - - - -
109A GLU* 3.8 31.6 - - + +
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Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A PRO* 3.0 33.8 + - + +
56A LYS* 3.7 9.2 - - - +
58A CYS* 1.3 76.6 - - + +
60A LYS* 1.3 62.0 + - - +
62A ARG* 3.1 14.7 + - + +
63A GLU* 3.0 24.2 + - - +
109A GLU* 4.8 10.3 - - - +
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Residues in contact with LYS 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 3.2 29.2 - - + -
56A LYS* 3.0 19.7 + - + +
57A ARG* 3.3 4.5 + - - +
59A LEU* 1.3 73.6 - - - +
61A ALA* 1.3 64.5 + - - +
63A GLU* 3.0 50.3 + - - +
64A HIS* 3.1 44.2 + - - -
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ILE* 4.3 12.1 - - + -
41A LEU* 3.9 11.3 - - + +
42A LEU* 3.6 33.0 - - + -
57A ARG 3.0 6.4 + - - +
58A CYS 3.5 9.4 - - - +
59A LEU 3.3 0.2 - - - -
60A LYS* 1.3 75.8 - - - +
62A ARG* 1.3 62.6 + - - +
64A HIS* 2.9 16.0 + - - +
65A PHE* 3.0 18.6 + - + -
105A VAL* 3.7 12.8 - - + -
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Residues in contact with ARG 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A CYS 3.0 13.5 + - - +
59A LEU* 3.1 19.5 + - + +
61A ALA* 1.3 75.7 - - - +
63A GLU* 1.3 60.1 + - - +
65A PHE* 3.4 26.0 + - + +
66A GLY* 3.8 2.8 + - - -
69A LYS* 5.3 2.3 + - - -
105A VAL* 4.0 11.4 - - + +
106A VAL* 4.2 18.4 - - - +
109A GLU* 3.1 39.7 + - - -
122A ILE* 4.3 27.6 - - + +
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU 3.0 10.0 + - - +
60A LYS* 3.0 53.2 + - + +
62A ARG* 1.3 77.4 - - - +
64A HIS* 1.3 59.4 + - - +
66A GLY* 3.0 20.0 + - - -
67A THR* 4.1 3.8 + - - +
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Residues in contact with HIS 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A THR* 4.1 9.1 - - + +
37A GLU* 3.1 36.6 + - + +
38A ILE* 3.5 18.8 - - + -
41A LEU* 3.7 14.4 - - + +
60A LYS* 3.1 44.8 + - - +
61A ALA* 2.9 9.9 + - - +
63A GLU* 1.3 71.8 - - - +
65A PHE* 1.3 59.2 + - - +
66A GLY 2.9 10.2 + - - -
67A THR* 2.7 38.4 + - + -
68A VAL* 3.1 8.3 + - - +
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Residues in contact with PHE 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ILE* 3.7 26.9 - - + -
61A ALA 3.0 29.5 + - - -
62A ARG* 3.4 17.3 - - + +
63A GLU 3.2 0.4 - - - -
64A HIS* 1.3 75.4 - - - +
66A GLY* 1.3 56.0 + - - +
68A VAL* 3.3 17.5 - - + +
69A LYS* 3.0 35.9 + - - +
98A LEU* 4.4 10.1 - - + -
101A LEU* 3.9 9.0 - - + -
102A ALA* 3.6 31.9 - - + -
105A VAL* 4.4 13.5 - - + -
122A ILE* 3.9 27.2 - - + +
123A LEU* 3.5 34.1 - - + -
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Residues in contact with GLY 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ARG 3.8 2.6 + - - -
63A GLU* 3.0 12.5 + - - -
64A HIS 2.9 2.2 + - - -
65A PHE* 1.3 74.2 - - - +
67A THR* 1.3 64.8 + - - +
68A VAL 3.0 1.1 - - - -
69A LYS* 3.0 23.3 + - - +
70A THR* 3.1 20.5 + - - +
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Residues in contact with THR 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A THR* 3.8 18.6 + - - +
63A GLU 4.1 3.5 + - - +
64A HIS* 2.7 28.4 + - + +
66A GLY* 1.3 72.1 - - - +
68A VAL* 1.3 62.7 + - - +
70A THR* 2.9 23.4 + - - +
71A HIS* 3.0 26.4 + - - -
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Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 4.1 17.0 - - + -
34A THR* 3.4 27.4 - - + -
38A ILE* 4.0 10.3 - - + -
64A HIS 3.1 8.4 + - - +
65A PHE* 3.3 27.6 - - + +
66A GLY 3.0 0.6 - - - -
67A THR* 1.3 74.7 - - - +
69A LYS* 1.3 67.6 + - - +
71A HIS* 3.0 4.0 + - - +
72A LEU* 3.0 39.7 + - + +
98A LEU* 4.2 19.3 - - + -
123A LEU* 4.1 7.4 - - + +
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Residues in contact with LYS 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ARG 5.3 1.8 + - - -
65A PHE* 3.0 25.2 + - - +
66A GLY* 3.0 13.2 + - - +
68A VAL* 1.3 74.9 - - - +
70A THR* 1.3 60.7 + - + +
72A LEU* 3.3 3.1 + - - +
73A THR* 3.0 31.8 + - + +
121A GLU 3.5 15.9 - - - -
122A ILE* 2.6 30.5 + - - +
123A LEU 3.1 23.3 - - - +
124A GLY* 3.7 10.4 - - - +
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Residues in contact with THR 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A GLY 3.1 14.8 + - - +
67A THR* 2.9 19.1 + - - +
69A LYS* 1.3 77.7 - - + +
71A HIS* 1.3 74.5 + - - +
73A THR* 2.8 20.8 + - - -
74A SER* 3.0 14.4 + - - -
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Residues in contact with HIS 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 3.3 19.6 - - + +
30A SER* 2.7 36.6 + - - -
31A LEU* 3.5 26.7 - - + -
34A THR* 4.1 16.1 + - - -
67A THR* 3.0 27.8 + - - +
68A VAL 3.6 0.2 - - - +
70A THR* 1.3 86.3 + - - +
72A LEU* 1.3 57.5 + - - +
74A SER* 3.5 7.5 - - - -
75A LEU 3.0 19.8 + - - -
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 3.4 29.2 - - + -
68A VAL* 3.0 20.2 + - + +
69A LYS 3.7 7.0 - - - +
70A THR 3.1 0.2 - - - -
71A HIS* 1.3 74.7 - - - +
73A THR* 1.3 62.1 + - - +
74A SER 2.9 4.7 - - - -
75A LEU* 3.1 20.1 + - + +
76A LYS* 3.0 30.4 + - + +
95A LEU* 5.8 5.6 - - + -
98A LEU* 5.2 5.2 - - + -
123A LEU* 3.1 38.1 - - + +
124A GLY 4.7 2.2 - - - +
125A ILE* 3.5 28.3 - - + -
133A PHE* 4.9 9.3 - - + -
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Residues in contact with THR 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LYS 3.0 16.8 + - - +
70A THR* 2.8 20.6 + - - -
72A LEU* 1.3 75.3 - - - +
74A SER* 1.3 59.4 + - - +
76A LYS* 3.1 37.7 - - - +
77A THR* 3.6 19.8 - - - +
124A GLY 4.4 5.6 - - - +
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Residues in contact with SER 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 4.2 6.4 - - - +
70A THR 3.0 12.3 + - - -
71A HIS* 3.5 14.8 - - - -
72A LEU 2.9 0.4 - - - -
73A THR* 1.3 76.0 - - - +
75A LEU* 1.3 63.9 + - - +
76A LYS 3.1 1.3 - - - -
77A THR* 2.8 26.6 + - - -
78A LYS* 3.4 25.7 + - - +
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 4.0 33.9 - - + +
27A VAL* 3.5 36.5 - - + +
28A VAL* 4.5 4.7 - - + -
31A LEU* 5.0 2.0 - - + -
71A HIS 3.0 9.1 + - - +
72A LEU* 3.1 22.4 + - + +
74A SER* 1.3 75.6 - - - +
76A LYS* 1.3 58.1 + - - +
77A THR 2.9 6.5 + - - -
78A LYS* 2.9 17.8 + - + +
79A PHE* 3.5 14.9 - - + -
91A TRP* 3.9 18.2 - - + -
133A PHE* 3.7 34.1 - - + -
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Residues in contact with LYS 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU* 3.0 14.6 + - + +
73A THR* 3.1 47.3 - - - +
74A SER 3.1 0.6 - - - -
75A LEU* 1.3 75.2 - - - +
77A THR* 1.3 60.2 + - + +
78A LYS 3.4 0.4 - - - -
79A PHE* 3.3 26.2 - - - +
81A ALA* 5.2 4.7 + - - +
124A GLY 3.8 6.9 + - - +
125A ILE* 5.6 1.1 - - + -
126A GLU* 3.0 40.4 + - - +
132A GLY* 5.5 2.0 - - - -
133A PHE* 3.9 28.0 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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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