Contacts of the helix formed by residues 57 - 77 (chain A) in PDB entry 3CVW
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 GLY 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A VAL* 1.3 75.8 - - - +
58A ALA* 1.3 64.1 + - - -
59A ASN* 3.3 2.9 - - - -
60A ARG* 3.6 3.5 + - - +
61A TRP* 3.0 26.5 + - - -
214A GLU* 5.6 1.3 - - - -
393A GLN* 2.9 38.6 + - - -
394A LEU* 5.4 2.5 - - - -
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Residues in contact with ALA 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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57A GLY* 1.3 72.1 - - - -
59A ASN* 1.3 64.5 + - - +
61A TRP* 3.2 9.2 + - - +
62A ARG 3.0 18.5 + - - -
209A VAL* 4.0 11.3 - - + +
211A ARG* 3.5 25.1 - - - +
214A GLU* 3.8 25.0 + - + +
215A LEU* 3.4 24.3 - - + +
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Residues in contact with ASN 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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57A GLY* 3.3 1.3 - - - -
58A ALA* 1.3 78.0 - - - +
60A ARG* 1.3 55.6 + - - +
62A ARG* 3.3 18.1 + - - +
63A PHE 3.1 19.9 + - - -
214A GLU 4.4 5.0 + - - -
215A LEU* 3.6 9.6 - - - -
216A GLY 3.2 23.5 + - - -
218A ASN* 5.9 0.2 + - - -
358A ARG 3.2 16.6 + - - -
359A GLN 3.0 24.2 + - - +
360A GLU 4.7 4.0 - - - +
361A GLY* 3.9 12.9 - - - +
394A LEU* 4.7 8.8 + - - +
396A LEU* 3.3 22.5 - - + +
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Residues in contact with ARG 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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54A MET* 3.6 4.8 - - - -
55A GLN 2.8 25.8 + - - -
56A VAL* 3.5 28.2 - - + +
57A GLY 3.6 4.2 + - - +
58A ALA 3.3 0.2 - - - -
59A ASN* 1.3 75.1 - - - +
61A TRP* 1.3 60.4 + - - +
63A PHE* 3.2 2.1 + - - +
64A LEU* 3.0 27.5 + - - +
266A LYS* 3.8 10.1 - - - +
267A PHE* 3.6 17.2 - - + -
392A GLU 2.7 21.1 + - - -
393A GLN 3.3 14.5 + - - +
394A LEU 5.6 0.8 + - - +
395A LEU 2.9 30.5 + - - +
396A LEU* 3.7 24.8 - - + +
398A GLN* 3.6 18.7 - - - +
1422A FO1 2.9 21.8 + - + -
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Residues in contact with TRP 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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46A LEU* 4.8 11.4 - - + -
47A ASP 5.9 0.2 - - - -
50A ILE* 4.0 20.2 - - + -
51A LEU* 4.3 24.6 - - + +
56A VAL* 3.4 37.3 + - + +
57A GLY 3.0 23.4 + - - -
58A ALA* 3.2 10.6 + - - +
60A ARG* 1.3 79.0 - - - +
62A ARG* 1.3 55.4 + - - +
64A LEU* 3.5 24.3 + - + +
65A GLN* 3.0 28.1 + - - +
208A LEU* 3.4 53.7 + - + +
209A VAL* 3.8 18.3 - - + +
210A LYS 5.7 1.6 - - - -
1422A FO1 4.2 6.5 - + - -
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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 ALA 3.0 12.7 + - - +
59A ASN* 3.5 24.2 + - - +
60A ARG 3.2 0.2 - - - -
61A TRP* 1.3 73.8 - - - +
63A PHE* 1.3 64.5 + - - +
65A GLN* 3.3 5.7 + - - +
66A GLN* 3.0 39.6 + - - +
205A MET* 3.8 24.8 - - - +
209A VAL* 3.9 6.6 - - + +
215A LEU* 3.6 29.2 - - + +
216A GLY 2.7 34.9 + - - +
217A PRO 3.5 13.7 + - - -
218A ASN* 3.1 33.6 - - - +
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Residues in contact with PHE 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 ASN 3.1 13.4 + - - +
60A ARG* 3.2 10.1 + - - +
62A ARG* 1.3 77.2 - - - +
64A LEU* 1.3 52.2 + - - +
66A GLN* 3.3 7.5 + - - -
67A THR* 2.6 47.3 + - - -
220A PHE* 3.4 29.4 - - + -
222A GLY* 3.6 14.8 - - - -
223A GLY 4.4 2.0 - - - -
263A PRO* 3.9 23.6 - - + -
264A TYR* 3.5 36.6 - + - -
267A PHE* 3.4 35.4 - + + -
269A CYS* 4.4 6.1 - - - -
396A LEU* 3.8 20.0 - - + -
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Residues in contact with LEU 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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16A LEU* 4.2 10.8 - - + -
44A PHE* 4.1 26.7 - - + -
46A LEU* 6.0 1.6 - - + -
60A ARG 3.0 15.0 + - - +
61A TRP* 3.8 22.9 - - + +
62A ARG 3.3 0.2 - - - -
63A PHE* 1.3 74.9 - - - +
65A GLN* 1.3 60.3 + - - +
67A THR* 3.5 5.2 - - - -
68A LEU* 2.9 47.1 + - + +
208A LEU* 4.4 6.3 - - + -
267A PHE* 3.7 31.0 - - + -
1422A FO1 3.7 35.7 - - + +
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Residues in contact with GLN 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 TRP 3.0 18.6 + - - +
62A ARG* 3.5 9.4 - - - +
63A PHE 3.3 0.2 - - - -
64A LEU* 1.3 77.7 - - - +
66A GLN* 1.3 68.5 + - - +
68A LEU* 3.6 4.9 + - - +
69A GLU* 3.2 51.1 + - - +
202A CYS* 5.2 3.3 - - - +
203A PRO* 2.9 28.8 + - - +
204A THR* 3.9 9.7 - - - +
205A MET* 4.0 34.4 - - - +
208A LEU* 3.8 15.2 - - + +
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Residues in contact with GLN 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* 3.0 30.6 + - + +
63A PHE* 3.7 8.2 - - - +
65A GLN* 1.3 83.8 - - - +
67A THR* 1.3 60.4 + - - +
69A GLU* 3.8 9.3 - - - +
70A ASP* 3.1 28.2 + - - +
205A MET* 5.9 0.6 - - - -
218A ASN* 2.9 34.8 + - - +
220A PHE 4.3 0.5 - - - +
221A PRO* 3.5 10.2 - - + +
222A GLY 3.0 34.5 + - - +
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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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16A LEU* 3.8 34.1 - - + +
63A PHE* 2.6 35.2 + - - -
64A LEU* 3.2 10.4 + - + -
66A GLN* 1.3 76.0 - - - +
68A LEU* 1.3 59.1 + - - +
70A ASP* 3.3 2.6 + - - +
71A LEU* 2.8 28.6 + - - +
222A GLY 4.0 0.2 - - - -
223A GLY* 3.4 21.1 + - - +
224A GLU 5.5 0.2 + - - -
267A PHE* 5.1 0.7 - - - -
269A CYS* 3.5 26.0 - - - -
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Residues in contact with LEU 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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16A LEU* 4.3 13.0 - - + -
44A PHE* 3.6 45.5 - - + -
46A LEU* 5.7 1.1 - - + -
64A LEU* 2.9 39.2 + - + +
65A GLN* 4.1 3.6 - - - +
67A THR* 1.3 75.1 - - - +
69A GLU* 1.3 58.3 + - - +
71A LEU* 4.3 2.5 - - + -
72A ASP* 3.1 21.1 + - - +
82A LEU* 3.4 24.2 - - + +
84A VAL* 4.5 4.5 - - + -
202A CYS* 3.4 18.2 - - + -
203A PRO* 4.0 29.4 - - + -
208A LEU* 5.0 2.0 - - + -
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Residues in contact with GLU 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 GLN* 3.2 45.6 + - - +
66A GLN* 3.8 9.2 - - - +
67A THR 3.2 0.2 - - - -
68A LEU* 1.3 77.0 - - - +
70A ASP* 1.3 60.0 + - - +
72A ASP* 3.7 2.6 + - - +
73A ASN* 3.0 40.3 + - - +
202A CYS* 4.1 16.7 - - + +
204A THR* 6.2 0.2 - - - +
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Residues in contact with ASP 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 GLN 3.1 18.8 + - - +
67A THR 3.7 3.4 - - - +
69A GLU* 1.3 75.2 - - - +
71A LEU* 1.3 59.8 + - - +
73A ASN* 3.0 10.5 + - - +
74A GLN* 2.8 44.6 + - - +
222A GLY 4.7 1.6 - - - +
223A GLY* 4.0 7.6 - - - -
224A GLU* 2.8 33.3 + - - +
225A THR* 2.8 32.8 + - - -
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Residues in contact with LEU 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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12A PHE* 4.0 23.1 - - + -
16A LEU* 3.8 35.7 - - + +
17A ARG* 3.8 32.5 - - - +
18A LEU* 4.7 7.0 - - + +
67A THR* 2.8 21.5 + - + +
68A LEU* 4.0 6.5 - - + +
69A GLU 3.5 0.2 - - - -
70A ASP* 1.3 74.3 + - - +
72A ASP* 1.3 57.5 + - - +
74A GLN* 3.6 4.7 + - - +
75A LEU* 3.0 43.2 + - + +
82A LEU* 3.8 25.6 - - + -
224A GLU* 4.8 5.4 - - + +
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Residues in contact with ASP 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 LEU 3.1 19.3 + - - +
69A GLU 3.8 4.5 - - - +
71A LEU* 1.3 74.8 - - - +
73A ASN* 1.3 54.9 + - - +
75A LEU 3.3 1.2 + - - -
76A ARG* 2.8 53.3 + - - +
81A ARG* 3.5 15.2 + - - +
82A LEU* 2.7 43.7 + - + +
202A CYS* 3.7 21.1 + - - -
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Residues in contact with ASN 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 GLU* 3.0 26.3 + - - +
70A ASP* 3.0 15.1 + - - +
72A ASP* 1.3 76.6 - - - +
74A GLN* 1.3 66.8 + - - +
76A ARG* 2.7 45.2 + - - +
77A LYS* 3.5 29.7 + - - +
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Residues in contact with GLN 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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18A LEU* 3.5 34.4 - - + +
70A ASP* 2.8 35.0 + - - +
71A LEU* 3.9 6.7 - - - +
73A ASN* 1.3 80.3 - - - +
75A LEU* 1.3 63.2 + - - +
77A LYS* 3.5 42.2 + - - +
78A LEU* 3.7 6.1 + - - +
224A GLU* 4.3 14.1 - - + +
225A THR* 3.0 25.1 + - - +
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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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12A PHE* 4.2 4.9 - - + -
18A LEU* 3.7 23.3 - - + -
24A LEU* 4.8 4.7 - - + -
28A PHE* 4.0 27.4 - - + -
42A PRO* 3.9 32.8 - - + -
71A LEU* 3.0 29.3 + - + +
72A ASP 3.7 3.6 - - - +
74A GLN* 1.3 73.9 - - - +
76A ARG* 1.3 63.5 + - - +
78A LEU* 3.2 11.3 + - + +
80A SER* 3.1 26.5 + - - -
81A ARG* 3.9 17.0 - - - +
82A LEU* 4.0 20.6 - - + -
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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 ASP* 2.8 42.7 + - - +
73A ASN* 2.7 48.6 + - - +
74A GLN 3.3 0.4 - - - -
75A LEU* 1.3 78.2 - - - +
77A LYS* 1.3 60.9 + - + +
79A ASN* 3.2 16.6 + - - +
80A SER 3.4 14.9 + - - +
81A ARG* 4.8 3.1 - - + +
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Residues in contact with LYS 77 (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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73A ASN* 3.5 17.7 - - - +
74A GLN* 3.5 35.7 + - - +
75A LEU 3.2 0.4 - - - -
76A ARG* 1.3 77.1 - - + +
78A LEU* 1.3 63.5 + - + +
79A ASN* 3.2 3.6 + - - -
180A LYS* 3.7 22.0 - - - +
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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