Contacts of the helix formed by residues 45 - 70 (chain A) in PDB entry 4NTX
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 VAL 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A VAL* 1.3 68.7 + - - +
47A TRP* 3.1 7.0 + - - +
48A ALA* 3.4 12.2 + - + +
49A LEU* 3.3 19.2 + - - +
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Residues in contact with VAL 46 (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* 1.3 79.4 - - - +
47A TRP* 1.3 56.6 + - - +
49A LEU* 3.4 9.2 - - - +
50A CYS* 3.0 30.6 + - - +
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Residues in contact with TRP 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 3.1 3.7 - - - +
46A VAL* 1.3 75.6 - - - +
48A ALA* 1.3 81.9 + - + +
49A LEU 3.1 1.6 - - - -
50A CYS* 2.9 10.2 + - + +
51A PHE* 2.6 72.8 + + + +
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 3.4 13.2 + - + +
47A TRP* 1.3 96.9 - - + +
49A LEU* 1.3 60.0 + - - +
51A PHE* 3.9 3.1 - - + -
52A MET* 3.3 30.7 + - + +
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL 3.3 12.6 + - - +
46A VAL* 3.4 13.2 - - - +
47A TRP 3.1 0.2 - - - -
48A ALA* 1.3 78.5 - - - +
50A CYS* 1.3 57.8 + - - +
52A MET* 3.7 1.4 - - - +
53A GLY* 2.9 26.0 + - - -
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Residues in contact with CYS 50 (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 VAL* 3.0 14.7 + - - +
47A TRP* 2.9 13.3 + - + +
49A LEU* 1.3 75.4 - - - +
51A PHE* 1.3 58.6 + - - +
53A GLY* 3.6 2.1 - - - +
54A SER* 3.0 32.9 + - - -
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Residues in contact with PHE 51 (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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47A TRP* 2.6 59.1 + + + +
48A ALA* 4.2 2.7 - - - +
50A CYS* 1.3 73.6 - - - +
52A MET* 1.3 86.7 - - + +
53A GLY 3.2 0.2 - - - -
54A SER* 3.4 6.7 + - - -
55A LEU* 3.1 34.1 + - + +
442A ILE* 3.8 38.6 - - + +
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Residues in contact with MET 52 (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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48A ALA* 3.3 21.0 + - + +
49A LEU 3.7 1.6 - - - +
51A PHE* 1.3 91.2 - - + +
53A GLY* 1.3 59.3 + - - +
54A SER 3.4 0.2 - - - -
55A LEU* 3.6 35.0 - - + +
56A ALA* 3.2 24.3 + - - +
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Residues in contact with GLY 53 (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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49A LEU 2.9 18.1 + - - -
50A CYS* 3.2 4.5 + - - -
51A PHE 3.2 0.4 - - - -
52A MET* 1.3 79.8 - - - +
54A SER* 1.3 59.9 + - - +
55A LEU 3.3 0.2 - - - -
56A ALA* 3.9 5.2 + - - +
57A LEU* 3.7 24.3 + - - +
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Residues in contact with SER 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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50A CYS 3.0 17.4 + - - -
51A PHE* 3.8 5.8 - - - -
53A GLY* 1.3 75.2 - - - +
55A LEU* 1.3 60.0 + - - +
56A ALA 3.3 0.4 - - - -
57A LEU* 3.6 6.7 + - - +
58A LEU* 3.1 22.5 + - - +
441A PHE* 3.2 38.3 + - - +
442A ILE* 4.1 5.4 - - - -
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Residues in contact with LEU 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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51A PHE* 3.1 27.7 + - + +
52A MET* 3.7 36.1 - - + +
53A GLY 3.3 0.2 - - - -
54A SER* 1.3 76.7 - - - +
56A ALA* 1.3 59.0 + - - +
58A LEU* 3.3 23.9 + - + +
59A ALA* 3.0 28.0 + - + +
442A ILE* 4.1 12.5 - - + +
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Residues in contact with ALA 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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52A MET 3.2 18.3 + - - +
53A GLY* 4.1 7.9 - - - +
54A SER 3.3 0.2 - - - -
55A LEU* 1.3 76.6 - - - +
57A LEU* 1.3 63.6 + - + +
59A ALA* 3.2 16.8 + - - +
60A LEU* 3.2 20.2 + - + +
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Residues in contact with LEU 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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53A GLY 3.7 14.0 + - - +
54A SER* 3.6 5.8 + - - +
55A LEU 3.3 0.4 - - - -
56A ALA* 1.3 80.0 - - + +
58A LEU* 1.3 62.0 + - - +
60A LEU* 3.3 23.0 + - + +
61A VAL* 3.2 21.8 + - - +
441A PHE* 3.3 26.5 - - + -
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Residues in contact with LEU 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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54A SER 3.1 15.6 + - - +
55A LEU* 3.5 26.9 - - + +
56A ALA 3.2 0.2 - - - -
57A LEU* 1.3 75.6 - - - +
59A ALA* 1.3 60.4 + - - +
61A VAL* 3.4 2.7 + - + +
62A CYS* 2.9 39.4 + - - +
437A GLN* 3.1 45.1 - - + +
438A MET* 3.8 26.7 - - + +
441A PHE* 3.3 17.0 - - + -
442A ILE* 4.3 11.7 - - + -
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Residues in contact with ALA 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 LEU* 3.0 14.3 + - + +
56A ALA* 3.4 12.6 - - - +
58A LEU* 1.3 77.2 - - - +
60A LEU* 1.3 59.1 + - + +
62A CYS* 3.4 6.6 + - - +
63A THR* 2.8 36.0 + - + +
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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
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56A ALA* 3.2 13.8 + - + +
57A LEU* 3.6 29.2 - - + +
58A LEU 3.2 0.2 - - - -
59A ALA* 1.3 75.0 - - + +
61A VAL* 1.3 65.8 + - + +
63A THR* 3.0 18.2 + - - +
64A ASN* 3.1 14.4 + - - +
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Residues in contact with VAL 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 LEU 3.2 13.6 + - - +
58A LEU* 3.8 7.0 - - - +
60A LEU* 1.3 76.7 - - + +
62A CYS* 1.3 64.5 + - - +
64A ASN* 3.3 11.0 - - - +
65A ARG* 3.1 39.4 + - + +
437A GLN* 3.7 39.5 - - + +
441A PHE* 3.9 20.4 - - + -
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Residues in contact with CYS 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 LEU* 2.9 39.7 + - - +
59A ALA* 3.7 6.5 - - - +
60A LEU 3.2 0.2 - - - -
61A VAL* 1.3 76.6 - - - +
63A THR* 1.3 60.8 + - + +
65A ARG* 3.4 8.5 + - - +
66A ILE* 3.0 35.8 + - + +
434A ILE* 4.0 41.1 - - + +
437A GLN* 4.9 4.5 - - - -
438A MET* 5.8 1.3 - - - -
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Residues in contact with THR 63 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A ALA* 2.8 20.5 + - + +
60A LEU* 3.0 18.5 + - - +
62A CYS* 1.3 73.3 - - + +
64A ASN* 1.3 54.9 + - - +
66A ILE* 3.1 12.3 + - + +
67A GLN* 2.7 51.4 + - - +
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Residues in contact with ASN 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 3.1 13.7 + - - +
61A VAL* 3.3 13.5 - - - +
63A THR* 1.3 77.0 + - - +
65A ARG* 1.3 73.8 + - - +
67A GLN* 3.2 13.8 + - - +
68A TYR* 2.9 31.1 + - - +
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Residues in contact with ARG 65 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A VAL* 3.1 34.3 + - + +
62A CYS* 3.6 9.9 - - - +
63A THR 3.3 0.2 - - - -
64A ASN* 1.3 101.5 - - - +
66A ILE* 1.3 56.8 + - - +
68A TYR* 3.6 8.6 + - - +
69A TYR 3.1 20.3 + - - -
425A TYR* 3.6 29.7 - - - +
430A LEU* 3.4 17.7 - - + +
433A ASP* 3.5 24.9 + - + +
434A ILE* 5.0 5.8 - - + -
437A GLN* 4.9 9.9 + - + +
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Residues in contact with ILE 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 CYS* 3.0 25.3 + - + +
63A THR* 3.1 13.4 + - + +
65A ARG* 1.3 75.3 - - - +
67A GLN* 1.3 67.6 + - + +
69A TYR* 3.3 3.5 + - - +
70A PHE* 3.0 53.8 + - + -
430A LEU* 4.2 20.6 - - + -
434A ILE* 4.3 15.5 - - + -
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Residues in contact with GLN 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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63A THR* 2.7 36.0 + - - +
64A ASN* 3.7 12.3 + - - +
66A ILE* 1.3 74.1 - - + +
68A TYR* 1.3 62.6 + - - +
70A PHE* 3.3 15.4 + - - +
71A LEU* 3.3 19.3 + - - +
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Residues in contact with TYR 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 ASN* 2.9 18.9 + - - +
65A ARG* 3.7 11.0 - - - +
67A GLN* 1.3 76.2 - - - +
69A TYR* 1.3 64.6 + - - +
71A LEU* 2.9 38.0 + - + +
73A PRO* 3.4 38.4 - - + +
424A ALA* 4.5 8.5 + - - +
425A TYR* 3.5 44.6 - + + -
504A NA 4.1 19.9 - - - -
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Residues in contact with TYR 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 ARG 3.1 11.6 + - - +
66A ILE 3.3 7.6 + - - +
68A TYR* 1.3 79.4 - - - +
70A PHE* 1.3 93.8 + + - +
72A TYR* 3.0 45.6 + + - -
73A PRO* 4.3 2.1 - - - +
425A TYR* 3.2 38.1 - - + -
426A GLU* 3.9 5.8 - - - -
427A VAL* 3.4 38.7 - - + +
430A LEU* 4.0 25.1 - - + -
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Residues in contact with PHE 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 ILE* 3.0 45.9 + - + +
67A GLN* 3.3 8.5 + - - +
68A TYR 3.1 1.2 - - - -
69A TYR* 1.3 98.8 - + - +
71A LEU* 1.3 62.6 + - - +
72A TYR* 3.2 36.0 - + - -
430A LEU* 5.7 2.5 - - + -
19B ALA* 4.2 9.4 + - - +
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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
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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