Contacts of the helix formed by residues 50 - 69 (chain a) in PDB entry 5W97
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 ASP 50 (chain a).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48a LEU* 2.7 23.3 + - - +
49a GLY* 1.3 70.1 - - - -
51a ASP* 1.3 65.3 + - - +
52a GLN* 3.5 16.7 + - - +
53a ILE* 3.5 47.5 + - + +
54a TYR* 3.7 7.1 + - - +
120a ALA* 6.0 1.0 - - - +
202b SER* 5.3 1.4 + - - -
43l GLN* 5.1 2.6 - - - +
44l LEU* 4.7 4.9 - - + -
41m LYS* 5.8 0.2 - - - +
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Residues in contact with ASP 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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40a GLU* 5.1 1.6 - - - +
46a THR* 4.4 9.2 + - - -
48a LEU* 5.9 0.2 - - - +
49a GLY 3.8 12.4 + - - +
50a ASP* 1.3 74.5 + - - +
52a GLN* 1.3 65.5 + - - +
53a ILE 3.2 1.1 - - - -
54a TYR* 3.2 8.0 + - + +
55a ASN* 3.1 28.4 + - - +
441a SER* 3.1 27.5 + - - +
202b SER* 3.3 26.8 - - - +
203b ASN* 5.0 2.1 - - - +
206b PHE* 3.0 32.4 - - - -
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Residues in contact with GLN 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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50a ASP* 3.5 15.1 + - - +
51a ASP* 1.3 76.7 - - - +
53a ILE* 1.3 57.6 + - + +
55a ASN* 3.8 4.4 + - - +
56a VAL* 2.9 33.5 + - - +
120a ALA* 2.8 43.6 + - + +
121a GLY 3.1 16.0 + - - -
123a GLY* 3.6 12.2 - - - +
138a HIS* 3.3 26.2 + - - -
201b GLY* 5.0 2.1 - - - -
202b SER* 3.8 30.4 + - - +
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Residues in contact with ILE 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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48a LEU* 4.3 9.2 - - + +
50a ASP* 3.5 36.6 + - + +
51a ASP 3.2 1.0 - - - -
52a GLN* 1.3 77.4 - - + +
54a TYR* 1.3 64.8 + - - +
56a VAL* 3.2 11.1 + - + +
57a VAL* 3.0 31.0 + - + +
120a ALA 5.8 0.7 - - - +
40l VAL* 4.3 22.7 - - + -
43l GLN* 3.4 52.0 - - + +
44l LEU* 3.9 17.3 - - + +
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Residues in contact with TYR 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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37a ILE* 3.5 35.5 - - + +
40a GLU* 3.6 24.2 - - + +
41a LEU* 3.1 17.4 - - + +
48a LEU* 4.3 15.8 - - + +
50a ASP 3.7 4.7 + - - +
51a ASP* 3.2 12.6 + - - +
53a ILE* 1.3 75.7 - - - +
55a ASN* 1.3 61.2 + - - +
57a VAL* 2.6 28.0 + - + +
58a VAL* 2.8 27.3 + - + +
439a ARG 4.2 2.2 - - - -
440a TYR 3.0 32.6 + - - -
441a SER* 3.8 23.8 - - - -
601a HEA 2.5 29.4 + - - -
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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 ASP* 3.1 15.2 + - - +
52a GLN* 3.8 5.6 + - - +
54a TYR* 1.3 87.6 - - - +
56a VAL* 1.3 60.9 + - - +
58a VAL* 4.0 7.3 - - - +
59a THR* 2.9 31.2 + - - -
123a GLY* 3.7 22.2 + - - +
439a ARG* 4.0 12.8 + - - +
199b ILE* 3.9 23.4 - - + +
201b GLY* 3.2 35.8 + - - -
202b SER* 4.1 3.0 + - - +
204b HIS* 5.0 1.6 - - - +
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Residues in contact with VAL 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 GLN* 2.9 28.9 + - - +
53a ILE* 3.5 13.5 - - + +
54a TYR 3.1 0.4 - - - -
55a ASN* 1.3 75.7 - - - +
57a VAL* 1.3 60.3 + - + +
59a THR* 3.8 1.7 - - - -
60a ALA* 3.0 28.1 + - + +
116a SER* 4.0 28.5 - - - +
120a ALA 3.2 24.9 - - - +
121a GLY* 3.7 17.3 - - - -
122a ALA 3.7 11.0 - - - +
123a GLY 3.8 5.6 - - - +
39l ILE* 5.7 3.1 - - + -
43l GLN* 5.9 4.5 - - + -
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Residues in contact with VAL 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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33a LEU* 3.3 45.8 - - + +
36a LEU* 4.1 13.7 - - + -
37a ILE* 3.7 11.9 - - + +
48a LEU* 4.9 5.8 - - + -
53a ILE* 3.0 29.6 + - + +
54a TYR* 2.6 20.0 + - + +
56a VAL* 1.3 72.2 - - + +
58a VAL* 1.3 64.5 + - - +
60a ALA 3.3 1.2 + - - -
61a HIS* 2.8 22.7 + - - +
40l VAL* 4.3 17.0 - - + -
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Residues in contact with VAL 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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37a ILE* 4.2 12.3 - - + -
54a TYR* 2.8 42.6 + - + +
55a ASN* 4.0 7.6 - - - +
57a VAL* 1.3 70.2 - - - +
59a THR* 1.3 66.8 + - - +
61a HIS* 3.0 14.2 + - - +
62a ALA* 3.2 12.6 + - - +
125a GLY* 5.5 1.1 - - - -
439a ARG* 4.6 9.2 - - + -
601a HEA 3.5 71.5 - - + +
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Residues in contact with THR 59 (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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55a ASN 2.9 19.4 + - - -
56a VAL 3.8 0.4 - - - -
58a VAL* 1.3 80.3 - - - +
60a ALA* 1.3 61.7 + - - +
62a ALA* 3.3 4.6 + - - +
63a PHE* 3.3 40.0 + - + -
112a LEU* 6.1 0.7 - - + -
122a ALA* 3.4 23.1 - - + +
124a THR* 3.3 7.6 + - - +
125a GLY* 2.6 50.4 + - - +
126a TRP* 4.5 1.3 - - - +
601a HEA 4.9 0.9 - - - -
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Residues in contact with ALA 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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33a LEU* 3.9 19.7 - - + -
56a VAL* 3.0 21.5 + - + +
57a VAL 4.0 2.2 - - - +
59a THR* 1.3 75.0 - - - +
61a HIS* 1.3 65.4 + - - +
63a PHE* 3.8 7.4 - - - +
64a VAL* 2.9 35.0 + - + +
112a LEU* 5.1 12.3 - - + +
113a LEU* 6.6 0.4 - - + -
116a SER* 5.7 6.5 - - - -
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Residues in contact with HIS 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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30a GLY 3.3 16.2 + - - -
33a LEU* 4.0 15.0 - - + +
34a SER* 3.7 11.2 + - - -
37a ILE* 3.6 17.5 - - + -
57a VAL 2.8 14.3 + - - +
58a VAL 3.0 8.7 + - - +
60a ALA* 1.3 76.3 - - - +
62a ALA* 1.3 62.5 + - - +
64a VAL* 3.9 1.4 - - - +
65a MET* 3.1 38.9 + - + +
601a HEA 1.9 98.8 + + + -
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Residues in contact with ALA 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 VAL 3.2 2.6 + - - -
59a THR 3.3 3.6 + - - +
61a HIS* 1.3 80.9 - - - +
63a PHE* 1.3 64.0 + - - +
65a MET* 4.0 0.2 - - - -
66a ILE* 3.1 30.8 + - - +
126a TRP* 3.6 24.7 - - + -
601a HEA 3.4 51.6 - - + -
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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 THR* 3.3 42.7 + - + +
60a ALA* 4.2 0.9 - - - +
61a HIS 3.4 0.2 - - - -
62a ALA* 1.3 75.9 - - - +
64a VAL* 1.3 63.5 + - - +
67a PHE* 3.1 47.3 + + + +
68a PHE* 3.5 13.1 - - + -
112a LEU* 4.0 34.8 - - + -
124a THR* 5.2 0.2 - - - -
126a TRP* 3.3 44.4 - + + -
128a VAL* 3.7 14.1 - - + -
146a THR* 3.9 18.2 - - + -
150a LEU* 4.2 19.1 - - + -
235a PHE* 6.1 0.7 - + - -
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Residues in contact with VAL 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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26a ALA* 3.1 35.2 - - + +
29a VAL* 4.0 3.1 - - + -
30a GLY* 3.9 13.5 - - - +
33a LEU* 3.9 14.6 - - + -
60a ALA* 2.9 28.9 + - + +
61a HIS 4.0 2.5 - - - +
63a PHE* 1.3 75.0 - - - +
65a MET* 1.3 58.6 + - + +
68a PHE* 3.1 11.6 + - + +
69a MET* 2.8 25.1 + - - +
109a PHE* 3.9 31.9 - - + -
112a LEU* 4.0 10.1 - - + -
113a LEU* 5.7 1.6 - - + -
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Residues in contact with MET 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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26a ALA 4.2 2.5 - - - +
27a GLY* 3.8 12.6 - - - +
30a GLY* 3.7 33.0 - - - +
31a THR* 4.3 3.1 - - - +
61a HIS* 3.1 36.1 + - + +
62a ALA 4.1 1.1 - - - +
64a VAL* 1.3 78.1 - - - +
66a ILE* 1.3 54.7 + - - +
69a MET* 3.2 35.7 + - + +
70a VAL* 2.7 35.7 + - - +
601a HEA 3.4 53.8 - - + -
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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 ALA 3.1 15.6 + - - +
65a MET* 1.3 79.9 - - - +
67a PHE* 1.3 78.9 + - + +
70a VAL 3.7 0.2 + - - -
71a MET* 3.2 29.1 + - - +
126a TRP* 3.8 29.6 - - + -
242a GLU* 3.2 29.2 - - + +
246a LEU* 3.7 27.4 - - + +
381a LEU* 5.2 2.7 - - + -
601a HEA 3.7 41.3 - - + -
602a HEA 5.5 2.0 - - + -
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Residues in contact with PHE 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 PHE* 3.1 46.5 + + + +
66a ILE* 1.3 93.6 - - + +
68a PHE* 1.3 79.0 + + + +
71a MET* 4.1 25.7 - - + +
72a PRO* 3.2 18.9 - - - +
105a LEU* 4.5 6.4 - - - +
126a TRP* 4.2 12.1 - + - -
150a LEU* 3.8 22.0 - - + -
153a ALA* 4.5 19.4 - - + +
154a GLY 6.1 0.4 - - - -
199a LEU* 5.1 6.7 - - + -
202a LEU* 4.9 6.5 - - + -
238a PHE* 4.0 30.3 - + - -
242a GLU* 4.8 0.4 - - - -
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Residues in contact with PHE 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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22a PHE* 3.4 30.1 - + + -
23a GLY* 3.8 3.5 - - - -
26a ALA* 3.3 25.2 - - + +
63a PHE* 3.5 23.1 - - + -
64a VAL* 3.1 19.9 + - + +
67a PHE* 1.3 90.5 - + + +
69a MET* 1.3 61.3 + - - +
72a PRO* 3.3 15.8 - - - +
105a LEU* 3.8 14.1 - - + -
108a SER* 3.3 33.9 - - - -
109a PHE* 3.8 26.2 - + + -
112a LEU* 3.8 20.6 - - + -
149a SER* 3.5 13.2 - - - -
150a LEU* 6.1 2.9 - - + -
153a ALA* 4.8 3.1 - - + -
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Residues in contact with MET 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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23a GLY 3.8 11.2 - - - +
27a GLY* 3.6 20.4 - - - +
64a VAL 2.8 5.3 + - - +
65a MET* 3.2 45.1 + - + +
68a PHE* 1.3 79.3 - - - +
70a VAL* 1.3 87.7 + - + +
71a MET 3.6 0.2 - - - -
72a PRO* 3.4 1.4 - - - +
73a ILE* 3.1 44.4 + - + +
386a VAL* 4.3 10.1 - - + -
389a ILE* 4.2 8.1 - - - -
601a HEA 3.9 39.9 - - + -
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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