Contacts of the helix formed by residues 55 - 77 (chain A) in PDB entry 1ES0
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 GLU 55 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 4.5 18.5 - - + +
54A PHE* 1.3 85.2 - - - +
56A PRO* 1.3 74.6 - - + +
57A GLN* 2.9 13.8 + - + +
58A GLY* 2.9 11.8 + - - +
208B GLU* 3.7 30.1 + - + +
209B ILE 5.1 0.6 + - - -
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Residues in contact with PRO 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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34A VAL* 4.0 25.9 - - + +
39A LYS* 3.8 26.5 - - + +
40A LYS* 4.1 6.5 - - - -
41A THR* 3.6 15.0 - - - +
53A LEU* 6.0 0.2 - - + -
54A PHE 3.1 11.1 - - - +
55A GLU* 1.3 89.3 - - - +
57A GLN* 1.3 64.3 + - - +
59A GLY* 2.8 16.5 + - - -
60A LEU* 3.1 15.8 + - + +
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Residues in contact with GLN 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLU* 4.2 11.4 - - + +
56A PRO* 1.3 80.3 - - - +
58A GLY* 1.3 63.1 + - - +
60A LEU* 3.3 21.1 + - - +
61A GLN* 3.0 27.3 + - - +
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Residues in contact with GLY 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TYR* 4.6 3.1 - - - -
54A PHE* 4.5 7.6 - - - -
55A GLU* 2.9 12.4 + - - +
56A PRO 2.8 1.0 + - - -
57A GLN* 1.3 78.6 - - - +
59A GLY* 1.3 61.4 + - - -
61A GLN* 2.9 29.1 + - - +
62A ASN* 3.1 10.5 + - - +
211B PRO* 4.6 14.1 - - - -
213B PHE* 4.8 3.3 - - - -
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Residues in contact with GLY 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TYR* 3.3 38.4 - - - -
34A VAL* 4.5 4.7 - - - -
36A LEU* 5.6 0.2 - - - -
54A PHE* 3.9 8.5 - - - -
56A PRO 2.8 13.2 + - - -
58A GLY* 1.3 71.6 - - - +
60A LEU* 1.3 62.0 + - - -
62A ASN 3.3 0.9 + - - -
63A ILE* 3.0 30.1 + - - +
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 4.2 11.4 - - + -
36A LEU* 3.8 36.6 - - + +
39A LYS* 4.4 34.3 - - + -
56A PRO* 3.1 13.7 + - + +
57A GLN* 3.6 22.4 - - - +
59A GLY* 1.3 76.1 - - - +
61A GLN* 1.3 62.7 + - - +
63A ILE* 3.4 6.0 + - + +
64A ALA* 3.0 23.9 + - - +
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Residues in contact with GLN 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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57A GLN* 3.0 17.2 + - + +
58A GLY* 2.9 12.3 + - - +
60A LEU* 1.3 76.2 - - - +
62A ASN* 1.3 59.2 + - - +
64A ALA* 3.0 8.7 + - - +
65A ALA* 2.8 30.2 + - + +
70B ARG* 4.0 13.5 + - - -
213B PHE* 3.6 34.2 - - + +
214B VAL 5.7 3.0 - - - +
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Residues in contact with ASN 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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9A GLY* 3.6 4.8 + - - -
11A THR* 3.2 17.5 - - - +
22A TYR* 3.1 26.7 + - + -
58A GLY 3.1 7.2 + - - -
59A GLY 3.8 6.3 - - - +
61A GLN* 1.3 79.9 - - - +
63A ILE* 1.3 58.3 + - - +
65A ALA* 3.2 2.3 + - - +
66A GLU* 2.7 34.0 + - - +
211B PRO* 4.5 4.0 - - - +
212B VAL 3.2 20.8 + - - -
213B PHE* 3.4 11.0 - - - +
214B VAL* 2.6 41.8 + - + +
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Residues in contact with ILE 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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11A THR* 3.4 15.3 - - + -
12A VAL 4.0 1.8 - - - +
13A TYR* 3.9 22.9 - - + -
20A GLY* 4.1 5.4 - - - -
21A GLN* 3.2 45.8 - - - +
22A TYR* 4.0 3.6 - - + -
36A LEU* 4.0 25.1 - - + -
59A GLY 3.0 21.6 + - - +
60A LEU* 3.5 8.7 - - + +
62A ASN* 1.3 74.5 - - - +
64A ALA* 1.3 59.9 - - - +
66A GLU* 3.0 5.2 + - - +
67A LYS* 2.8 26.3 + - - +
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Residues in contact with ALA 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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60A LEU 3.0 12.8 + - - +
61A GLN* 3.0 11.3 + - - +
63A ILE* 1.3 78.1 - - - +
65A ALA* 1.3 63.4 + - - +
67A LYS* 2.9 23.0 + - + +
68A HIS* 3.0 12.5 + - - +
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Residues in contact with ALA 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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61A GLN* 2.8 19.5 + - + +
62A ASN* 3.6 7.6 - - - +
64A ALA* 1.3 71.8 - - - +
66A GLU* 1.3 58.0 + - - +
68A HIS* 3.0 5.9 + - - +
69A ASN* 2.8 31.0 + - - -
214B VAL* 3.6 34.3 - - + +
216B LEU* 3.8 24.2 - - + +
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Residues in contact with GLU 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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11A THR* 3.3 33.0 - - + -
13A TYR* 3.9 14.4 - - + +
62A ASN 2.7 17.0 + - - +
63A ILE 3.4 4.7 - - - +
65A ALA* 1.3 70.8 - - - +
67A LYS* 1.3 66.7 + - - +
69A ASN* 3.0 27.6 + - - +
70A LEU* 2.9 25.5 + - - +
9B HIS* 2.4 38.3 + - - +
10B GLN* 3.2 17.2 + - - -
11B PHE* 3.7 11.5 - - - +
30B TYR* 4.7 0.5 - - - -
214B VAL* 3.2 12.9 - - + +
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Residues in contact with LYS 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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13A TYR* 3.6 46.8 - - + +
18A ASP* 3.6 17.7 + - - -
63A ILE 2.8 11.0 + - - +
64A ALA* 2.9 15.2 + - - +
66A GLU* 1.3 77.8 - - - +
68A HIS* 1.3 63.0 + - - +
70A LEU* 3.6 8.0 + - - +
71A GLY* 3.6 8.3 + - - -
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Residues in contact with HIS 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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64A ALA 3.0 10.4 + - - +
65A ALA 3.1 9.2 - - - +
67A LYS* 1.3 80.3 - - - +
69A ASN* 1.3 69.0 + - - +
71A GLY* 3.4 8.3 + - - -
72A ILE* 3.5 28.3 + - + +
216B LEU* 3.5 35.8 - - + +
217B GLU 3.2 23.3 + - - -
219B VAL* 3.8 22.8 - - + +
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Residues in contact with ASN 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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65A ALA 2.8 14.4 + - - +
66A GLU* 3.0 23.9 + - - +
68A HIS* 1.3 78.8 - - - +
70A LEU* 1.3 62.2 + - - +
72A ILE* 3.3 5.3 + - - +
73A LEU* 3.0 28.3 + - + +
9B HIS* 3.7 23.3 - - + +
30B TYR* 4.1 6.8 - - - -
37B TYR* 4.9 2.2 - - - +
61B TYR* 3.8 3.5 + - - -
214B VAL* 3.3 19.6 - - - +
215B LEU 3.7 9.6 + - - +
216B LEU* 4.0 0.6 - - - -
217B GLU* 3.1 34.6 + - + +
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Residues in contact with LEU 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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13A TYR* 3.6 28.5 - - + +
14A GLN* 3.6 17.5 - - - -
15A SER* 3.7 20.6 - - - +
66A GLU 2.9 17.4 + - - +
67A LYS 3.9 5.2 - - - +
68A HIS 3.3 0.4 - - - -
69A ASN* 1.3 76.6 - - - +
71A GLY* 1.3 55.3 + - - +
73A LEU* 4.9 0.4 - - - -
74A THR* 2.5 50.9 + - - +
7B PHE* 3.8 9.9 - - + +
8B VAL 3.6 32.1 - - - +
9B HIS* 3.6 12.9 - - + -
32B TYR* 4.4 4.5 - - + -
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Residues in contact with GLY 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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67A LYS 3.6 6.2 + - - -
68A HIS 3.4 6.3 + - - -
69A ASN 3.3 0.6 - - - -
70A LEU* 1.3 79.6 - - - +
72A ILE* 1.3 61.5 + - - +
74A THR* 3.7 5.5 - - - -
75A LYS* 3.2 36.1 + - - +
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Residues in contact with ILE 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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68A HIS* 3.5 43.5 + - + +
69A ASN 3.3 6.2 + - - +
70A LEU 3.3 0.2 - - - -
71A GLY* 1.3 72.6 - - - +
73A LEU* 1.3 63.6 + - + +
75A LYS* 3.2 12.6 + - - +
76A ARG* 2.9 39.8 + - - +
217B GLU* 3.5 38.6 - - + +
218B TYR 3.7 17.3 - - - +
219B VAL* 4.2 12.1 - - + -
220B THR* 5.0 8.3 - - - +
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Residues in contact with LEU 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 ASN* 3.0 17.6 + - + +
70A LEU 4.2 0.2 - - - +
72A ILE* 1.3 82.5 - - + +
74A THR* 1.3 67.8 + - - +
76A ARG* 3.1 31.6 + - + +
77A SER* 2.9 25.8 + - - -
9B HIS* 4.0 7.2 - - + +
32B TYR* 3.6 19.1 - - + -
37B TYR* 3.3 50.7 - - + +
53B LEU* 4.0 28.7 - - + -
217B GLU* 4.4 7.9 - - + +
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Residues in contact with THR 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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15A SER* 5.5 0.2 + - - -
70A LEU* 2.5 43.4 + - - +
71A GLY* 3.7 7.6 - - - -
73A LEU* 1.3 76.0 - - - +
75A LYS* 1.3 62.5 + - + +
77A SER* 2.7 20.6 + - - -
79A PHE* 3.0 38.8 + - + -
7B PHE* 3.8 29.1 - - + +
32B TYR* 3.6 13.2 - - - +
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Residues in contact with LYS 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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71A GLY* 3.2 21.2 - - - +
72A ILE* 3.2 9.8 + - - +
74A THR* 1.3 76.4 - - - +
76A ARG* 1.3 55.8 + - - +
78A ASN* 2.5 33.4 + - - +
79A PHE* 4.0 29.4 - - + -
219B VAL* 5.9 5.1 - - - +
220B THR 5.8 9.7 + - - -
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Residues in contact with ARG 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 ILE* 2.9 20.4 + - - +
73A LEU* 3.3 29.7 - - + +
75A LYS* 1.3 76.3 - - - +
77A SER* 1.3 58.4 + - - +
78A ASN* 3.4 8.8 + - - -
53B LEU* 2.4 53.7 + - + +
54B GLY* 4.4 0.4 - - - -
56B HIS* 5.6 4.2 - - - +
57B SER* 3.1 28.8 + - - +
217B GLU* 3.3 26.9 + - - +
218B TYR 5.2 1.0 + - - -
220B THR* 5.7 7.1 - - - -
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Residues in contact with SER 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU 2.9 9.0 + - - -
74A THR 2.7 15.1 + - - -
75A LYS 2.8 0.6 + - - -
76A ARG* 1.3 75.5 - - - +
78A ASN* 1.3 70.9 + - - +
80A THR* 2.9 37.3 + - - -
32B TYR* 3.1 30.4 + - - -
53B LEU* 4.5 12.3 - - - -
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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