Contacts of the helix formed by residues 46 - 68 (chain A) in PDB entry 1ATH
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 ARG 46 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ARG* 1.3 58.3 + - - +
48A VAL* 4.1 18.3 - - - +
49A TRP* 2.8 61.0 + - + +
50A GLU* 3.1 18.1 + - - +
416A PRO 4.1 17.6 + - - -
417A LEU* 5.9 2.8 - - - +
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Residues in contact with ARG 47 (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 ARG* 1.3 73.2 - - - +
48A VAL* 1.3 64.6 + - + +
50A GLU* 3.1 16.4 + - - +
51A LEU* 3.0 23.4 + - - +
114A LYS* 3.9 17.8 - - - +
118A GLN* 4.1 12.7 + - - +
121A PHE* 3.1 39.9 - - - -
122A PHE* 3.5 48.8 - - + -
125A LYS* 5.7 4.3 - - + -
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Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ARG* 3.2 18.6 + - + +
47A ARG* 1.3 75.5 - - + +
49A TRP* 1.3 57.6 + - - +
51A LEU* 3.5 5.0 + - - +
52A SER* 2.9 28.9 + - - -
122A PHE 4.5 2.0 - - - +
125A LYS* 3.9 15.3 - - + +
126A LEU* 3.7 41.2 - - + +
129A ARG* 5.3 7.6 - - - +
417A LEU* 3.8 43.1 - - + +
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Residues in contact with TRP 49 (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 ARG* 2.8 47.2 + - + +
48A VAL* 1.3 71.5 - - - +
50A GLU* 1.3 66.2 + - + +
52A SER* 2.7 21.9 + - - -
53A LYS* 3.2 52.3 + - + +
305A GLN* 5.7 3.8 - - - -
416A PRO 5.8 1.6 - - - -
417A LEU 4.8 8.3 - - - -
418A ASN* 4.5 18.9 - - + +
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Residues in contact with GLU 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 ARG 3.1 10.1 + - - +
47A ARG* 3.1 24.4 + - - +
49A TRP* 1.3 76.5 - - + +
51A LEU* 1.3 66.2 + - - +
53A LYS* 3.0 21.7 + - - +
54A ALA* 3.1 12.1 + - - +
111A ILE* 4.1 31.0 - - + +
112A SER* 4.4 12.3 + - - +
114A LYS* 5.0 6.1 - - - -
122A PHE* 4.5 7.7 - - + -
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Residues in contact with LEU 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 ARG 3.0 14.9 + - - +
48A VAL* 4.1 3.8 - - - +
50A GLU* 1.3 74.9 - - - +
52A SER* 1.3 56.4 + - - +
54A ALA* 3.0 3.6 + - + +
55A ASN* 2.9 51.4 + - - +
108A PHE* 3.9 11.4 - - + -
111A ILE* 3.8 27.5 - - + +
119A ILE* 4.8 3.6 - - + -
122A PHE* 3.8 13.2 - - + +
123A PHE* 3.5 51.8 - - + +
126A LEU* 4.0 16.6 - - + -
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Residues in contact with SER 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 VAL* 2.9 17.7 + - - -
49A TRP* 2.7 33.4 + - - -
51A LEU* 1.3 72.8 - - - +
53A LYS* 1.3 56.1 + - - +
55A ASN* 3.4 10.8 + - - +
56A SER* 2.9 34.4 + - - -
126A LEU* 5.5 2.2 - - - +
417A LEU 3.5 10.9 + - - -
418A ASN* 3.2 25.3 + - - +
419A THR* 4.5 9.8 - - - +
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Residues in contact with LYS 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 TRP* 3.2 65.0 + - + +
50A GLU* 3.0 13.7 + - - +
52A SER* 1.3 82.9 + - - +
54A ALA* 1.3 62.1 + - - +
56A SER* 3.1 8.7 + - - -
57A ARG* 3.1 41.3 + - - +
110A THR* 6.5 0.7 - - + -
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Residues in contact with ALA 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 GLU 3.1 7.1 + - - +
51A LEU* 3.0 18.4 + - + +
53A LYS* 1.3 75.7 - - - +
55A ASN* 1.3 64.6 + - - +
57A ARG* 2.9 25.6 + - - +
58A PHE* 3.1 10.9 + - - +
106A PHE 4.7 1.8 - - - -
107A LYS* 3.9 30.7 - - - +
108A PHE* 4.4 3.8 - - + -
110A THR* 4.9 4.5 - - - -
111A ILE* 4.4 16.2 - - + -
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Residues in contact with ASN 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 LEU* 2.9 47.3 + - - +
52A SER* 3.6 9.3 - - - +
54A ALA* 1.3 77.0 - - - +
56A SER* 1.3 56.1 + - - +
58A PHE* 3.6 4.1 + - - +
59A ALA* 3.0 28.4 + - - +
80A PRO* 5.1 1.7 - - - +
81A LEU* 4.1 16.0 - - + +
84A SER* 4.0 20.9 + - - +
106A PHE 5.3 0.7 - - - -
108A PHE* 3.5 18.4 - - - -
123A PHE* 4.0 3.9 - - - -
126A LEU* 3.9 15.9 - - - +
419A THR* 4.3 8.2 - - + +
420A ILE* 6.4 0.2 - - - -
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Residues in contact with SER 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 SER 2.9 19.2 + - - -
53A LYS* 3.1 8.3 + - - -
55A ASN* 1.3 75.1 - - - +
57A ARG* 1.3 62.9 + - - +
59A ALA* 3.2 8.1 + - - +
60A THR* 2.8 28.9 + - - -
301A PRO* 4.4 13.2 - - - -
304A LEU* 6.3 0.2 - - - -
418A ASN 4.6 7.3 + - - -
419A THR* 5.9 0.2 - - - +
420A ILE* 4.0 26.4 + - - +
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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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53A LYS* 3.1 28.8 + - - +
54A ALA* 2.9 8.5 + - - +
56A SER* 1.3 71.1 - - - +
58A PHE* 1.3 69.0 + - - +
60A THR* 3.2 2.9 + - - -
61A THR* 3.0 27.1 + - - +
107A LYS* 4.3 24.0 - - + +
110A THR* 3.4 33.5 - - - +
301A PRO* 3.9 21.0 - - + +
302A GLU* 3.0 28.9 + - - +
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Residues in contact with PHE 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 ALA 3.1 6.3 + - - +
55A ASN* 3.9 6.5 - - - +
57A ARG* 1.3 79.1 - - - +
59A ALA* 1.3 69.0 + - - +
61A THR* 3.1 2.8 + - - -
62A PHE* 2.8 62.7 + + + +
80A PRO* 5.0 6.1 - - + -
83A ILE* 3.8 26.7 - - + -
84A SER* 3.6 17.9 - - - +
105A VAL* 3.3 28.0 - - + -
106A PHE* 3.6 50.0 - + - +
107A LYS* 4.5 9.0 - - + +
335A LEU* 4.2 1.6 - - + -
338A MET* 4.1 15.7 - - + -
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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 ASN 3.0 21.0 + - - +
56A SER* 3.2 9.4 + - - +
58A PHE* 1.3 78.0 - - - +
60A THR* 1.3 61.9 + - - +
62A PHE* 3.6 2.1 + - - +
63A TYR* 3.0 24.9 + - - +
80A PRO* 3.6 30.7 - - + +
420A ILE* 4.4 9.2 - - + -
423A MET* 3.6 19.9 - - + +
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Residues in contact with THR 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 SER 2.8 15.8 + - - -
57A ARG 3.7 4.9 - - - -
59A ALA* 1.3 75.2 - - - +
61A THR* 1.3 53.9 + - - +
63A TYR* 2.9 10.1 + - - +
64A GLN* 2.8 41.5 + - - +
299A LEU* 2.9 48.2 - - + +
300A THR 4.4 0.2 - - - -
301A PRO* 3.5 27.8 - - + +
304A LEU* 4.8 8.6 - - + +
420A ILE* 5.4 1.8 - - - +
423A MET* 5.1 3.4 - - - -
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Residues in contact with THR 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 ARG* 3.0 16.6 + - - +
58A PHE* 3.1 4.0 + - - -
60A THR* 1.3 77.2 - - - +
62A PHE* 1.3 56.7 + - - +
64A GLN* 3.3 14.1 + - - +
65A HIS* 2.9 31.9 + - + +
107A LYS* 3.8 27.0 + - - +
338A MET* 4.2 14.6 - - + -
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Residues in contact with PHE 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 PHE* 2.8 50.2 + + + +
59A ALA* 4.1 3.8 - - - +
61A THR* 1.3 73.1 - - - +
63A TYR* 1.3 56.7 + - - +
65A HIS* 3.6 3.1 + - - +
66A LEU* 3.0 37.7 + - + +
78A LEU* 4.0 22.4 - - + -
80A PRO* 5.7 1.3 - - + -
83A ILE* 3.9 19.5 - - + -
329A PHE* 4.7 4.5 - + - -
331A LEU* 4.1 22.2 - - + -
334A GLN* 3.5 35.8 + - + -
335A LEU* 3.8 22.4 - - + -
338A MET* 3.7 20.1 - - - +
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Residues in contact with TYR 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 ALA 3.0 14.1 + - - +
60A THR* 2.9 9.6 + - - +
62A PHE* 1.3 78.3 - - - +
64A GLN* 1.3 60.5 + - + +
66A LEU* 3.0 7.7 + - + +
67A ALA* 2.7 43.6 + - + +
76A ILE* 3.7 26.8 - - + +
78A LEU* 4.3 17.2 - - + +
296A GLU* 2.7 39.3 + - + -
299A LEU* 4.6 16.4 - - + -
409A LEU* 3.5 12.4 - - + +
423A MET* 3.7 25.1 - - + -
424A GLY* 4.4 11.2 - - - -
425A ARG* 3.1 26.2 + - - +
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Residues in contact with GLN 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 THR* 2.8 25.4 + - + +
61A THR* 3.7 16.4 + - - +
63A TYR* 1.3 79.8 - - + +
65A HIS* 1.3 57.0 + - - +
67A ALA* 3.4 3.9 + - - +
68A ASP* 2.8 31.1 + - - +
296A GLU* 2.8 31.4 + - - +
297A LYS* 2.9 27.9 + - - +
299A LEU* 3.9 19.3 + - + +
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Residues in contact with HIS 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 THR* 2.9 17.9 + - + +
62A PHE* 3.8 5.4 - - - +
64A GLN* 1.3 74.0 - - - +
66A LEU* 1.3 62.2 + - - +
68A ASP* 2.9 23.6 + - - +
69A SER* 2.9 22.4 + - - -
334A GLN* 3.0 49.4 + - - -
337A ASP* 4.0 20.9 + - + +
338A MET* 3.5 28.5 - - + +
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Residues in contact with LEU 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 PHE* 3.0 23.8 + - + +
63A TYR* 3.5 4.9 - - + +
65A HIS* 1.3 74.3 - - - +
67A ALA* 1.3 61.9 + - - +
69A SER* 3.4 20.8 - - - +
70A LYS* 3.7 25.5 - - - +
76A ILE* 4.0 21.1 - - + -
78A LEU* 4.0 19.5 - - + -
329A PHE* 3.6 43.7 - - + -
334A GLN* 3.8 28.0 - - + +
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Residues in contact with ALA 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 TYR* 2.7 39.1 + - + +
64A GLN* 3.6 5.6 - - - +
66A LEU* 1.3 74.4 - - - +
68A ASP* 1.3 61.3 + - - +
70A LYS* 2.8 26.5 + - - +
72A ASP* 5.4 0.3 - - - +
76A ILE* 3.8 6.5 - - - +
296A GLU* 3.9 11.0 - - + +
297A LYS* 5.7 1.3 - - - +
425A ARG* 3.6 26.5 + - - +
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Residues in contact with ASP 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 GLN 2.8 20.0 + - - +
65A HIS* 3.2 15.1 - - - +
67A ALA* 1.3 75.3 - - - +
69A SER* 1.3 62.9 + - - +
70A LYS 3.2 4.5 + - - +
297A LYS* 3.6 25.5 + - - +
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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
------------------------------------------------------------
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