Contacts of the helix formed by residues 54 - 77 (chain M) in PDB entry 1YST
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 SER 54 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28M ASN* 4.8 1.9 + - - +
53M GLY* 1.3 73.9 - - - +
55M LEU* 1.3 67.2 + - - +
56M GLY 3.0 7.1 + - - +
57M VAL* 3.6 10.9 + - - +
58M LEU* 4.1 2.9 + - - +
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Residues in contact with LEU 55 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54M SER* 1.3 81.1 - - - +
56M GLY* 1.3 71.4 + - - +
58M LEU* 3.4 29.3 - - + +
59M SER* 3.6 9.0 + - - -
128M SER* 4.0 9.6 - - - +
131M GLY* 3.7 24.7 - - - -
132M ARG* 3.7 14.8 - - + +
135M LEU* 3.5 35.4 - - + -
136M ARG* 5.8 5.4 - - - +
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Residues in contact with GLY 56 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52M LEU* 6.1 1.6 - - - -
53M GLY 4.0 7.6 + - - -
54M SER 3.0 2.8 + - - -
55M LEU* 1.3 79.1 - - - +
57M VAL* 1.3 68.6 + - - +
59M SER* 2.7 24.9 + - - -
60M LEU* 3.6 3.0 + - - +
129M TRP* 5.0 2.8 - - - -
132M ARG* 3.9 34.1 - - - -
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Residues in contact with VAL 57 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52M LEU* 5.0 18.6 - - + +
53M GLY 3.1 24.3 + - - +
54M SER 3.6 5.1 + - - +
56M GLY* 1.3 73.2 - - - +
58M LEU* 1.3 65.1 + - - +
59M SER 3.1 0.3 + - - -
60M LEU* 3.3 7.1 + - - +
61M PHE* 3.0 25.7 + - + +
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Residues in contact with LEU 58 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54M SER 4.1 2.1 + - - +
55M LEU* 3.4 23.0 - - + +
56M GLY 2.9 0.8 + - - -
57M VAL* 1.3 79.2 - - - +
59M SER* 1.3 55.3 + - - +
61M PHE* 3.4 16.9 + - + +
62M SER* 2.7 36.3 + - - +
124M VAL* 5.1 13.0 - - + -
128M SER* 4.1 22.4 - - - +
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Residues in contact with SER 59 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55M LEU 3.7 2.8 + - - -
56M GLY* 2.7 18.4 + - - -
58M LEU* 1.3 71.5 - - - +
60M LEU* 1.3 56.2 + - - -
62M SER* 2.8 12.2 + - - -
63M GLY* 2.8 31.1 + - - -
125M ALA* 3.9 11.8 - - - +
128M SER* 3.2 39.8 + - - -
129M TRP* 3.5 23.7 + - - -
309M BPH 4.4 6.3 - - - -
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Residues in contact with LEU 60 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52M LEU* 6.3 3.4 - - + -
56M GLY 3.6 2.8 + - - +
57M VAL* 3.3 9.0 + - - +
59M SER* 1.3 78.6 - - - +
61M PHE* 1.3 57.3 + - - +
63M GLY 3.8 0.4 - - - -
64M LEU* 2.9 58.7 + - + +
129M TRP* 5.1 12.1 - - + -
309M BPH 4.1 32.9 - - + +
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Residues in contact with PHE 61 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57M VAL* 3.0 19.4 + - + +
58M LEU* 3.4 21.5 - - + +
59M SER 2.9 1.6 + - - -
60M LEU* 1.3 77.5 - - - +
62M SER* 1.3 66.4 + - - +
64M LEU* 3.7 3.4 - - - +
65M MET* 2.9 37.4 + - + +
121M PHE* 5.9 9.2 - + - -
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Residues in contact with SER 62 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58M LEU* 2.7 22.0 + - - +
59M SER* 2.8 11.4 + - - -
61M PHE* 1.3 79.7 - - - +
63M GLY* 1.3 52.0 + - - +
65M MET* 3.1 10.2 + - - +
66M TRP* 2.6 36.9 + - - +
121M PHE* 3.9 39.2 - - - +
124M VAL* 4.6 5.7 - - - +
125M ALA* 3.9 10.1 + - - -
128M SER* 4.7 0.5 + - - -
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Residues in contact with GLY 63 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59M SER 2.8 18.2 + - - -
62M SER* 1.3 74.3 - - - +
64M LEU* 1.3 59.1 + - - +
65M MET 3.0 0.2 - - - -
66M TRP* 3.2 12.8 + - - +
67M PHE* 3.0 23.4 + - - +
125M ALA* 4.0 11.9 - - - +
309M BPH 3.8 28.0 - - - +
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Residues in contact with LEU 64 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60M LEU* 2.9 45.1 + - + +
61M PHE* 3.7 3.8 - - - +
63M GLY* 1.3 72.1 - - - -
65M MET* 1.3 57.9 + - - +
67M PHE* 3.4 6.3 - - - +
68M PHE* 2.8 28.4 + - + +
309M BPH 3.8 55.8 - - + +
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Residues in contact with MET 65 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61M PHE* 2.9 30.2 + - + +
62M SER* 3.4 3.1 - - - +
64M LEU* 1.3 76.1 - - - +
66M TRP* 1.3 67.5 + - - +
67M PHE 2.9 3.8 - - - -
68M PHE* 2.8 9.5 + - + +
69M THR* 2.5 70.9 + - + +
117M ILE* 4.7 3.6 - - + -
118M ALA* 4.5 6.7 - - - -
121M PHE* 2.8 64.2 - - + -
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Residues in contact with TRP 66 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62M SER 2.6 19.6 + - - +
63M GLY* 3.4 13.2 - - - +
65M MET* 1.3 78.1 - - - +
67M PHE* 1.3 81.0 + + + +
69M THR* 3.1 14.5 + - - -
70M ILE* 3.2 37.5 - - + +
118M ALA* 3.3 29.5 - - + +
121M PHE* 4.6 0.4 - - + -
122M MET* 3.3 62.7 - - + +
177M TYR* 3.5 35.8 - + - -
307M BCL 5.9 1.1 - - + -
308M BCL 4.3 24.7 - - + -
309M BPH 5.6 1.6 - - + -
310M SPO 3.8 26.2 - - + -
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Residues in contact with PHE 67 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277L U10 4.8 17.3 - - + -
63M GLY 3.0 14.9 + - - +
64M LEU* 3.4 10.1 - - - +
65M MET 2.8 0.2 + - - -
66M TRP* 1.3 91.0 - + + +
68M PHE* 1.3 68.9 + - - +
70M ILE* 2.9 10.7 + - - +
71M GLY* 2.9 18.2 + - - -
308M BCL 5.3 6.3 - - + -
309M BPH 3.6 61.2 - - + -
310M SPO 3.4 61.4 - - + +
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Residues in contact with PHE 68 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64M LEU* 2.8 25.5 + - + +
65M MET* 2.8 14.8 + - + +
67M PHE* 1.3 71.4 - - - +
69M THR* 1.3 51.9 + - - +
71M GLY* 3.0 2.1 + - - -
72M ILE* 2.7 62.8 + - + +
309M BPH 6.1 0.7 - - + -
310M SPO 3.4 31.6 - - - -
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Residues in contact with THR 69 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65M MET* 2.5 52.0 + - + +
66M TRP* 3.1 8.2 + - - -
68M PHE* 1.3 73.6 - - - +
70M ILE* 1.3 53.9 + - - +
72M ILE* 2.9 8.7 + - + +
73M TRP* 2.5 68.2 + - + +
117M ILE* 4.8 8.5 - - + -
118M ALA* 4.6 9.3 - - + +
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Residues in contact with ILE 70 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66M TRP* 3.2 57.9 + - + +
67M PHE* 2.9 10.0 + - - +
69M THR* 1.3 74.8 - - - +
71M GLY* 1.3 51.9 + - - +
73M TRP* 3.4 7.7 - - - -
74M PHE* 2.6 56.4 + - + -
94M LEU* 6.2 2.0 - - + -
114M LEU* 5.0 8.3 - - + -
118M ALA* 4.6 7.2 - - + -
177M TYR* 3.8 31.9 - - + -
310M SPO 3.6 30.1 - - + -
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Residues in contact with GLY 71 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67M PHE 2.9 13.2 + - - -
68M PHE 3.3 4.3 - - - -
70M ILE* 1.3 74.2 - - - +
72M ILE* 1.3 52.9 + - - +
74M PHE* 3.1 12.8 + - - +
75M TRP* 2.6 46.8 + - - -
310M SPO 4.1 24.1 - - - +
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Residues in contact with ILE 72 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68M PHE* 2.7 57.0 + - + +
69M THR* 3.5 6.5 - - + +
71M GLY* 1.3 72.2 - - - -
73M TRP* 1.3 60.5 + - + +
75M TRP* 3.0 13.4 + - + -
76M TYR* 2.5 51.0 + - + +
310M SPO 5.2 1.5 + - - -
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Residues in contact with TRP 73 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69M THR* 2.5 52.4 + - + +
70M ILE 3.4 3.4 - - - +
72M ILE* 1.3 74.3 - - + +
74M PHE* 1.3 63.9 + - - +
76M TYR* 4.4 14.3 + + + +
77M GLN* 4.9 10.3 + - - +
94M LEU* 3.4 47.1 - - + +
109M LEU* 4.3 22.7 + - + +
114M LEU* 3.3 65.7 - - + -
117M ILE* 3.6 23.6 - - + -
118M ALA* 5.1 1.3 - - + -
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Residues in contact with PHE 74 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70M ILE* 2.6 37.3 + - + -
71M GLY* 3.1 9.2 - - - +
73M TRP* 1.3 76.7 - - - +
75M TRP* 1.3 60.7 - - - +
76M TYR 3.6 0.2 + - - -
77M GLN* 3.7 1.4 + - - +
78M ALA* 2.7 32.5 + - - +
85M PHE* 4.3 14.8 - + + -
89M LEU* 4.3 17.0 - - + -
92M PHE* 3.0 54.7 - + + -
93M SER* 4.4 3.8 - - - -
94M LEU* 5.1 4.6 - - + +
177M TYR 5.7 0.2 - - - -
178M GLY* 4.3 17.5 - - - -
179M ILE* 5.3 1.1 - - + -
310M SPO 3.3 49.1 - - + -
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Residues in contact with TRP 75 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71M GLY* 2.6 43.8 + - - +
72M ILE* 3.0 14.8 + - + +
74M PHE* 1.3 74.7 - - - +
76M TYR* 1.3 53.9 + - - +
77M GLN 2.6 15.9 + - - -
78M ALA* 2.7 18.4 + - - +
80M TRP* 3.0 45.1 + + - +
82M PRO* 3.6 38.8 - - + -
85M PHE* 3.3 50.4 - + + -
310M SPO 3.8 27.6 - - + +
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Residues in contact with TYR 76 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72M ILE* 2.5 38.6 + - + +
73M TRP* 4.7 11.9 - + + +
74M PHE 3.6 0.4 + - - -
75M TRP* 1.3 68.9 - - - +
77M GLN* 1.3 84.5 + - - +
80M TRP* 3.3 42.1 - + - +
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Residues in contact with GLN 77 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73M TRP* 4.9 12.7 + - - +
74M PHE 3.7 3.2 + - - +
75M TRP 2.6 6.1 + - - -
76M TYR* 1.3 114.2 - - - +
78M ALA* 1.3 50.1 + - - +
79M GLY* 2.5 21.4 + - - -
80M TRP* 4.5 1.5 + - - -
94M LEU* 6.0 5.6 - - + -
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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