Contacts of the helix formed by residues 55 - 79 (chain B) in PDB entry 5AZS
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 ASN 55 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A GLN* 5.7 0.3 + - - -
51B ALA 2.8 24.4 + - - +
52B LEU 4.8 1.5 + - - +
53B ASP 5.3 0.7 - - - -
54B ASN* 1.3 75.0 - - - +
56B ARG* 1.3 76.6 + - - +
57B SER* 2.9 23.3 + - - -
58B LEU* 4.2 8.5 - - + +
59B ARG* 3.3 24.4 + - - +
152B LEU* 3.4 37.9 - - + +
231B LEU* 4.8 4.7 - - - +
232B LEU* 3.6 22.4 + - - +
233B LEU 3.9 2.3 + - - -
234B GLY* 4.6 4.3 - - - -
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Residues in contact with ARG 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PRO* 4.3 11.0 - - - +
352A ALA* 3.1 32.5 - - + +
355A GLU* 2.8 37.1 + - + +
356A GLY* 3.5 20.9 - - - +
359A GLN* 3.7 21.5 + - - +
54B ASN* 2.8 22.2 + - - +
55B ASN* 1.3 80.5 + - - +
57B SER* 1.3 57.8 + - - +
58B LEU 3.3 1.8 - - - -
59B ARG* 3.1 27.8 + - - +
60B GLN* 2.9 39.0 + - - +
234B GLY 2.6 30.7 + - - -
235B SER* 5.0 0.6 - - - +
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Residues in contact with SER 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASN* 2.9 18.3 + - - -
56B ARG* 1.3 72.8 - - - +
58B LEU* 1.3 61.0 + - - +
60B GLN* 3.5 11.7 + - - +
61B THR* 3.2 28.3 + - - +
148B ALA* 6.0 0.2 - - - -
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Residues in contact with LEU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 3.9 35.4 - - + +
55B ASN* 4.1 8.9 + - + +
56B ARG 3.3 0.4 - - - -
57B SER* 1.3 76.5 - - - +
59B ARG* 1.3 60.0 + - - +
61B THR* 2.7 28.2 + - - +
62B LEU* 2.9 41.6 + - + +
145B ALA 4.2 4.7 - - - +
148B ALA* 3.8 8.5 - - + +
149B ARG* 3.8 32.1 - - + +
152B LEU* 3.8 31.6 - - + -
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Residues in contact with ARG 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ASP 5.7 0.2 - - - -
352A ALA* 3.9 22.0 - - + +
355A GLU* 3.8 5.4 + - - -
53B ASP 3.0 27.1 + - - -
54B ASN* 3.6 19.9 + - - +
55B ASN 3.3 15.2 + - - +
56B ARG* 3.1 42.6 + - - +
58B LEU* 1.3 80.2 - - - +
60B GLN* 1.3 55.6 + - - +
62B LEU* 3.4 12.3 + - + +
63B LEU* 3.0 45.5 + - + +
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Residues in contact with GLN 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A SER* 3.9 16.9 + - - +
352A ALA* 3.6 19.1 - - + +
353A ALA* 3.5 36.1 + - - +
356A GLY* 5.6 1.4 - - - -
56B ARG* 2.9 25.7 + - - +
57B SER* 3.8 10.1 + - - +
59B ARG* 1.3 76.4 - - - +
61B THR* 1.3 56.9 + - + +
63B LEU* 3.4 8.4 + - - +
64B ASP* 3.0 30.8 + - - +
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Residues in contact with THR 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B SER 3.2 13.1 + - - +
58B LEU* 2.7 36.1 + - - +
60B GLN* 1.3 74.1 - - + +
62B LEU* 1.3 64.3 + - - +
64B ASP* 2.9 27.7 - - - +
65B ILE* 3.5 11.1 + - - +
141B SER 5.1 0.7 - - - +
144B ALA* 5.1 3.1 - - - +
145B ALA* 4.5 10.1 - - - +
148B ALA* 3.6 19.1 - - + +
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU 5.4 3.8 - - - +
58B LEU* 2.9 48.7 + - + +
59B ARG* 3.7 9.6 - - - +
61B THR* 1.3 76.8 + - - +
63B LEU* 1.3 58.6 + - + +
65B ILE* 3.2 36.0 - - + +
66B GLU* 3.5 6.1 + - - +
145B ALA* 4.2 17.9 - - + +
149B ARG* 6.5 0.2 - - + -
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ALA* 3.6 18.8 - - - +
348A ASP* 3.4 55.6 - - + +
349A SER* 3.5 10.3 - - - +
352A ALA* 4.5 0.9 - - + -
59B ARG* 3.0 39.1 + - + +
60B GLN 3.8 5.8 - - - +
61B THR 3.3 0.2 - - - -
62B LEU* 1.3 78.3 - - + +
64B ASP* 1.3 56.8 + - - +
65B ILE 3.3 0.4 - - - -
66B GLU* 3.2 18.5 - - + +
67B ALA* 3.2 18.2 + - - +
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Residues in contact with ASP 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A SER* 6.3 1.3 - - - -
60B GLN* 3.0 20.3 + - - +
61B THR* 2.9 27.2 - - - +
63B LEU* 1.3 74.1 - - - +
65B ILE* 1.3 59.8 + - - +
66B GLU 3.3 0.2 - - - -
67B ALA* 3.8 13.9 - - + +
68B ALA* 3.2 23.7 + - - +
141B SER* 4.1 11.1 + - - +
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Residues in contact with ILE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B THR 3.5 8.5 + - - +
62B LEU* 3.2 26.6 + - + +
64B ASP* 1.3 77.8 + - - +
66B GLU* 1.3 55.9 + - - +
68B ALA* 3.0 3.5 + - - +
69B ARG* 2.8 38.8 + - - +
138B TYR* 3.7 24.6 - - + +
141B SER* 3.8 22.9 - - - +
142B GLU* 4.0 22.7 - - + +
145B ALA* 3.5 24.5 - - + -
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Residues in contact with GLU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A SER* 4.8 8.2 - - - +
344A GLU* 5.0 9.8 - - + +
345A ALA* 3.7 16.9 - - + +
62B LEU 3.5 3.9 + - - +
63B LEU* 3.2 26.1 + - + +
65B ILE* 1.3 81.7 - - - +
67B ALA* 1.3 60.8 + - - +
69B ARG* 2.7 46.1 + - - +
70B ALA* 3.3 21.3 + - - +
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Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU* 3.6 24.1 - - + +
345A ALA* 3.8 8.7 - - + +
346A ARG* 5.4 5.6 - - + -
63B LEU 3.2 5.6 + - - +
64B ASP* 3.8 21.5 - - + +
66B GLU* 1.3 77.8 - - - +
68B ALA* 1.3 56.7 + - - +
70B ALA* 3.1 6.1 + - - +
71B GLN* 3.0 37.1 + - + +
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Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ASP 3.2 15.9 + - - +
65B ILE 3.0 5.0 + - - +
67B ALA* 1.3 79.5 - - - +
69B ARG* 1.3 59.5 + - - +
71B GLN* 3.5 12.7 + - - +
72B TYR* 3.2 16.6 + - - +
134B ALA 4.4 2.3 - - - +
137B GLN* 4.4 2.9 - - + +
138B TYR* 3.6 28.8 + - - +
141B SER* 3.6 21.3 - - - +
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Residues in contact with ARG 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ARG* 5.2 1.8 - - - +
341A SER* 6.2 1.4 - - - -
65B ILE* 2.8 19.9 + - - +
66B GLU* 2.7 50.2 + - - +
68B ALA* 1.3 70.2 - - - +
70B ALA* 1.3 67.3 + - - +
72B TYR* 3.2 10.5 + - + +
73B ARG* 3.0 63.4 + - + +
138B TYR* 3.5 41.3 + - + -
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ALA* 3.5 25.9 - - - +
341A SER* 4.4 7.6 - - - -
342A LEU* 3.7 19.1 - - + +
66B GLU 3.3 10.9 + - - +
67B ALA 3.1 9.9 + - - +
69B ARG* 1.3 79.2 - - - +
71B GLN* 1.3 58.8 + - - +
73B ARG* 3.0 12.1 + - - +
74B ILE* 2.9 33.6 + - - +
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Residues in contact with GLN 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU* 4.2 18.2 - - + +
346A ARG* 5.7 3.4 + - - +
67B ALA* 3.0 23.3 + - - +
68B ALA* 3.8 10.6 - - - +
69B ARG 3.3 0.4 - - - -
70B ALA* 1.3 74.8 - - - +
72B TYR* 1.3 62.0 + - - +
74B ILE* 3.5 15.7 + - + +
75B GLN* 3.4 21.3 + - - +
134B ALA* 4.2 7.5 - - + +
137B GLN* 5.8 4.3 + - - +
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Residues in contact with TYR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ALA 3.2 13.2 + - - +
69B ARG* 3.2 17.2 + - + +
71B GLN* 1.3 75.9 - - - +
73B ARG* 1.3 65.7 + - + +
75B GLN* 3.2 4.0 + - - +
76B ARG* 2.8 63.1 + - + +
131B THR* 3.6 26.7 - - + +
134B ALA* 3.7 19.9 - - + +
135B LEU* 3.5 52.3 - - + +
138B TYR* 4.6 5.8 - + + -
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Residues in contact with ARG 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A GLY 4.9 0.7 - - - +
334A GLY 4.1 6.5 - - - +
337A ARG* 3.1 37.5 - - - +
338A ALA* 4.0 13.2 - - + -
69B ARG* 3.0 58.6 + - - +
70B ALA* 3.0 10.2 + - - +
72B TYR* 1.3 84.5 - - + +
74B ILE* 1.3 56.3 + - - +
76B ARG* 3.6 41.4 + - - +
77B ALA* 2.9 28.1 + - - +
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Residues in contact with ILE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ARG* 4.0 24.0 + - + +
338A ALA* 3.6 19.5 - - + +
339A ASN* 3.5 25.1 - - - +
342A LEU* 4.9 11.0 - - + -
70B ALA 2.9 23.0 + - - +
71B GLN* 3.8 19.1 - - + +
72B TYR 3.2 0.2 - - - -
73B ARG* 1.3 75.7 - - - +
75B GLN* 1.3 62.4 + - + +
77B ALA* 3.6 7.7 - - - +
78B ASP* 3.5 17.3 + - - +
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Residues in contact with GLN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLN 3.4 9.1 + - - +
72B TYR 3.2 7.7 + - - +
74B ILE* 1.3 77.7 - - + +
76B ARG* 1.3 59.2 + - - +
77B ALA 3.2 0.4 - - - -
78B ASP* 3.1 36.4 + - - +
79B ARG* 3.7 2.4 + - - +
127B VAL* 3.9 8.7 - - - +
130B LEU* 3.2 52.9 - - + +
131B THR* 3.3 23.4 + - - +
134B ALA* 4.2 9.4 - - + -
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Residues in contact with ARG 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A GLY 4.7 12.5 + - - +
334A GLY* 5.5 3.0 + - - -
72B TYR* 2.8 49.4 + - + +
73B ARG* 3.6 41.7 + - - +
74B ILE 3.4 0.2 - - - -
75B GLN* 1.3 76.9 - - - +
77B ALA* 1.3 60.4 + - - +
79B ARG* 3.3 25.1 + - - +
80B VAL* 4.3 8.0 + - + +
131B THR* 3.8 19.5 + - + +
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Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A GLY* 3.5 43.4 + - - +
335A ARG* 3.9 30.7 + - + +
73B ARG 2.9 20.5 + - - +
74B ILE 3.6 8.3 - - - +
75B GLN 3.2 0.2 - - - -
76B ARG* 1.3 75.7 - - - +
78B ASP* 1.3 61.5 + - - +
79B ARG 3.4 0.3 + - - -
80B VAL 3.5 16.8 + - - +
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Residues in contact with ASP 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ARG* 5.3 14.4 + - - +
74B ILE 3.5 7.8 + - - +
75B GLN* 3.1 30.9 + - - +
77B ALA* 1.3 77.4 - - - +
79B ARG* 1.3 60.7 + - - +
80B VAL 3.4 4.2 + - - +
119B TYR* 4.4 8.8 - - - -
120B GLU* 5.2 8.7 + - - +
127B VAL* 4.0 22.1 - - + +
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Residues in contact with ARG 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLN 4.2 0.2 - - - +
76B ARG* 3.3 19.1 + - - +
77B ALA 3.2 1.0 - - - -
78B ASP* 1.3 78.3 - - - +
80B VAL* 1.3 63.4 + - + +
119B TYR* 3.1 22.1 + - - -
120B GLU 5.0 1.6 - - - +
122B ASP* 4.7 11.1 + - + +
127B VAL* 3.7 18.2 - - + +
128B LYS* 3.2 51.7 - - - +
131B THR* 3.6 37.1 - - - +
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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