Contacts of the helix formed by residues 50 - 70 (chain B) in PDB entry 1WZ2
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 HIS 50 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B HIS 3.4 2.9 + - - +
49B LEU* 1.3 76.4 - - - +
51B VAL* 1.3 65.1 + - - +
52B GLY* 2.6 43.8 + - - -
53B HIS* 2.9 43.4 + + - -
54B ALA* 2.9 18.4 + - - +
109B TYR* 5.7 4.0 - - - -
644B GLY 5.3 1.3 - - - -
650B LYS* 5.1 6.1 + - - -
651B MET* 3.2 27.4 + - + +
658B VAL* 4.0 21.8 - - + -
659B LEU 3.0 17.9 - - - +
660B ASN* 3.9 0.9 - - - +
661B PHE* 3.7 6.6 - - - +
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B HIS* 1.3 72.6 - - - +
52B GLY* 1.3 61.2 + - - +
54B ALA* 2.6 30.6 - - + +
55B ARG 3.3 2.8 + - - -
645B THR 5.7 0.2 - - - +
646B LEU* 5.1 0.7 - - + -
651B MET* 4.4 8.3 - - + -
659B LEU* 2.9 51.3 + - + +
660B ASN 4.4 3.8 - - - +
661B PHE* 4.1 3.7 - - + +
664B ALA* 4.7 2.9 - - + -
673B VAL* 5.6 2.2 - - + -
677B ILE* 3.8 11.7 - - + -
687B PHE* 3.9 11.5 - - + -
689B TRP* 3.2 39.9 - - + -
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Residues in contact with GLY 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B HIS* 2.6 28.3 + - - -
51B VAL* 1.3 74.3 - - - +
53B HIS* 1.3 62.5 + - - -
54B ALA 3.0 0.9 + - - -
55B ARG* 3.1 17.3 + - - +
56B THR* 3.7 5.6 + - - -
641B ASN* 5.6 0.2 + - - -
642B GLY 5.5 1.9 - - - +
643B PHE* 5.3 2.7 - - - -
644B GLY 4.7 11.4 - - - -
651B MET* 3.6 6.8 - - - +
687B PHE* 4.4 10.7 - - - -
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Residues in contact with HIS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B HIS 4.7 1.6 + - - -
49B LEU* 3.4 23.8 - - + -
50B HIS* 2.9 61.1 + + - +
52B GLY* 1.3 72.2 - - - +
54B ALA* 1.3 60.5 + - - +
55B ARG 3.2 0.2 - - - -
56B THR* 3.2 13.8 + - - -
57B TYR* 2.7 43.3 - - + -
109B TYR* 5.8 1.2 + - - -
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU* 5.2 1.1 - - - +
50B HIS 2.9 6.0 + - - -
51B VAL* 2.6 28.9 + - + +
53B HIS* 1.3 80.4 - - - +
55B ARG* 1.3 58.9 + - - +
57B TYR* 3.0 14.0 + - - +
58B THR* 3.2 17.4 + - - +
142B PHE* 4.6 2.1 - - - -
661B PHE* 3.0 44.2 - - + -
677B ILE* 5.0 6.1 - - + -
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Residues in contact with ARG 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B VAL 3.3 0.2 + - - -
52B GLY 3.1 10.4 + - - +
54B ALA* 1.3 75.7 - - - +
56B THR* 1.3 59.0 + - - +
57B TYR 2.9 4.1 + - - -
58B THR* 3.4 6.0 + - - -
59B ILE* 2.7 46.3 + - + +
641B ASN* 4.0 9.4 - - - +
642B GLY 3.8 19.1 + - - -
643B PHE 3.4 10.9 + - - -
677B ILE* 3.8 24.9 + - + +
678B MET* 5.4 0.2 - - - -
681B ALA* 3.4 31.8 + - - +
682B GLU* 3.6 4.4 - - - +
683B HIS 3.5 16.6 + - - +
685B SER 2.7 29.7 + - - -
686B ASP 4.0 0.2 - - - -
687B PHE* 3.2 46.3 - - + +
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Residues in contact with THR 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B VAL* 3.6 25.5 - - + +
41B ALA* 5.6 1.8 - - + +
52B GLY 3.7 7.0 + - - -
53B HIS* 3.2 15.5 + - - -
55B ARG* 1.3 79.0 - - - +
57B TYR* 1.3 70.0 + - + +
59B ILE* 4.4 0.2 - - - +
60B PRO* 2.8 19.6 - - - +
608B CYS* 4.7 2.6 - - - +
609B SER* 4.3 13.9 - - - -
610B GLY* 4.5 6.2 + - - +
641B ASN* 3.2 32.3 + - - +
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Residues in contact with TYR 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 3.5 19.3 - - + -
41B ALA 2.9 21.5 + - - -
43B PRO* 3.3 25.5 - - + +
49B LEU* 3.9 20.4 - - + -
53B HIS* 2.7 35.7 - - + -
54B ALA* 3.0 7.2 + - - +
55B ARG 2.9 0.4 - - - -
56B THR* 1.3 87.9 - - + +
58B THR* 1.3 61.5 + - - +
60B PRO* 2.6 27.3 - - - +
61B ASP* 3.3 8.0 + - - +
76B PHE* 4.3 2.6 - + + -
78B MET* 3.5 34.3 - - + -
137B PHE* 3.8 12.8 - + + -
142B PHE* 3.8 22.6 - - + -
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Residues in contact with THR 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ALA* 3.2 17.8 + - - +
55B ARG* 3.4 5.3 + - - -
57B TYR* 1.3 75.5 - - - +
59B ILE* 1.3 51.4 + - - +
61B ASP* 2.6 10.0 + - - +
62B VAL* 2.6 55.8 + - + +
142B PHE* 3.5 19.5 - - - -
661B PHE* 4.8 5.7 - - - -
674B ARG* 4.5 30.9 - - + +
677B ILE* 5.2 3.8 - - - +
678B MET* 3.4 25.1 - - + -
797B PHE* 5.8 0.7 - - - +
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Residues in contact with ILE 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ARG* 2.7 39.9 - - + +
58B THR* 1.3 73.5 - - - +
60B PRO* 1.3 70.4 - - + +
62B VAL* 3.7 0.3 - - - +
63B ILE* 3.1 31.1 + - + +
608B CYS* 5.3 2.9 - - + -
641B ASN* 3.4 32.3 - - + +
678B MET* 3.5 25.1 - - + +
747B PHE* 4.0 28.7 - - + +
749B THR* 4.3 12.3 - - + +
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Residues in contact with PRO 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 4.1 16.5 - - + +
39B THR 4.8 1.3 - - - +
40B VAL* 4.1 14.1 - - + -
56B THR 2.8 25.4 - - - +
57B TYR* 2.6 31.0 - - - +
59B ILE* 1.3 82.5 - - + +
61B ASP* 1.3 54.5 + - - +
63B ILE* 3.6 1.9 + - - +
64B ALA* 2.9 27.9 + - - +
76B PHE* 3.3 28.9 - - + -
608B CYS* 4.1 20.8 - - + -
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Residues in contact with ASP 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B TYR 3.3 5.1 + - - +
58B THR* 2.6 15.0 + - - +
60B PRO* 1.3 68.8 - - - +
62B VAL* 1.3 55.3 + - - +
63B ILE 2.9 1.3 - - - -
64B ALA* 2.6 25.9 + - - -
65B ARG* 2.6 29.5 + - - +
76B PHE* 4.0 6.8 - - + -
141B GLY 3.3 1.7 - - - +
142B PHE* 3.3 22.1 - - + -
143B SER* 2.6 42.7 + - - -
674B ARG* 2.9 34.5 + - - +
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Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B THR* 2.6 29.4 + - + +
59B ILE 3.7 5.4 - - - +
61B ASP* 1.3 71.8 - - - +
63B ILE* 1.3 62.8 + - + +
65B ARG* 4.0 0.9 - - - -
66B PHE* 3.0 28.4 + - - +
674B ARG* 4.8 0.7 - - - +
678B MET* 3.2 36.8 - - + -
744B LEU* 4.2 17.9 - - + -
749B THR* 5.0 2.7 - - + -
796B PRO* 3.5 38.1 - - + +
797B PHE* 4.6 13.9 - - + -
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Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B PHE* 4.2 11.4 - - + -
38B ILE* 4.3 3.1 - - + -
59B ILE* 3.1 19.5 + - + +
60B PRO 3.9 3.4 - - - +
61B ASP 2.9 0.8 - - - -
62B VAL* 1.3 84.2 - - + +
64B ALA* 1.3 60.4 + - - +
66B PHE* 4.0 7.4 - - + -
67B LYS* 2.9 55.8 + - + +
744B LEU* 3.5 31.4 - - + +
747B PHE* 3.8 52.7 - - + -
749B THR* 5.8 2.2 - - + -
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Residues in contact with ALA 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B PHE* 5.4 2.0 - - - -
38B ILE* 4.4 7.6 - - + +
60B PRO 2.9 19.6 + - - +
61B ASP* 2.6 17.1 + - - +
63B ILE* 1.3 69.6 - - - +
65B ARG* 1.3 66.3 + - - +
67B LYS* 4.4 1.5 - - - -
68B ARG* 3.0 37.7 + - - +
74B VAL* 3.7 11.9 - - + +
76B PHE* 4.0 25.4 - - + -
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Residues in contact with ARG 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B TRP* 4.1 8.3 - - - -
23B PHE* 3.4 34.2 - - - -
61B ASP* 2.6 37.7 + - - +
62B VAL 3.9 3.4 - - - +
64B ALA* 1.3 69.6 - - - +
66B PHE* 1.3 57.5 + - - +
68B ARG* 2.5 41.8 + - - +
69B MET* 2.9 13.9 + - + +
141B GLY 2.8 24.9 + - - -
143B SER* 2.9 25.1 + - - +
674B ARG* 3.5 5.7 - - - +
795B ALA 4.3 1.7 + - - -
796B PRO* 3.8 34.3 - - + -
799B PRO* 3.5 21.9 - - - +
816B SER* 3.4 21.5 + - - +
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Residues in contact with PHE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B VAL 3.0 18.6 + - - +
63B ILE* 3.6 8.1 - - + +
65B ARG* 1.3 78.7 - - - +
67B LYS* 1.3 74.8 + - + +
69B MET* 3.1 8.9 + - - +
70B GLN* 2.8 54.8 + - - +
741B THR* 3.6 14.6 - - - -
744B LEU* 3.3 45.3 - - + -
745B GLU* 3.6 18.8 - - - -
796B PRO* 3.9 10.8 - - + +
820B TRP* 3.7 45.1 - + - -
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Residues in contact with LYS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B PHE* 3.7 41.5 - - + -
63B ILE* 2.9 44.0 + - + +
64B ALA 4.5 1.6 - - - +
66B PHE* 1.3 85.5 - - + +
68B ARG* 1.3 61.8 + - - +
70B GLN* 3.2 21.0 + - - +
72B TYR* 2.9 72.3 + - + +
74B VAL* 5.3 1.3 - - + -
745B GLU* 3.0 24.8 + - - +
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Residues in contact with ARG 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ILE 5.1 2.6 + - - -
23B PHE* 3.5 30.5 + - - +
64B ALA* 3.1 21.2 + - - +
65B ARG* 2.5 46.0 + - - +
67B LYS* 1.3 72.0 - - - +
69B MET* 1.3 55.0 + - - +
71B GLY* 2.9 21.1 + - - -
72B TYR 3.7 12.7 + - - +
74B VAL* 3.2 41.9 + - + +
76B PHE* 4.7 1.8 - - - +
143B SER* 2.9 50.3 + - - -
816B SER 4.0 14.5 + - - +
817B LEU* 4.5 23.0 - - + +
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Residues in contact with MET 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ARG* 2.9 13.9 + - + +
66B PHE* 3.5 6.1 - - - +
68B ARG* 1.3 71.5 - - - +
70B GLN* 1.3 55.6 + - - +
71B GLY* 2.8 17.5 + - - -
792B ARG* 3.2 31.9 - - + +
795B ALA* 3.6 23.8 - - + -
796B PRO* 4.3 10.3 - - - -
815B VAL* 4.3 6.1 - - + +
816B SER* 3.6 21.8 - - - +
817B LEU 4.8 3.2 - - - +
818B ALA 2.9 30.5 - - - +
819B LYS* 3.3 19.4 - - - +
820B TRP* 3.3 41.6 + - + +
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Residues in contact with GLN 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B PHE* 2.8 44.4 + - - +
67B LYS* 3.2 34.4 - - - +
68B ARG 3.1 0.2 - - - -
69B MET* 1.3 77.0 - - - +
71B GLY* 1.3 57.0 + - - +
72B TYR* 3.3 24.6 + - + +
741B THR* 4.4 2.5 - - - +
745B GLU* 3.1 19.2 - - - +
820B TRP* 4.0 12.8 - - + +
822B GLU* 4.1 17.3 - - + +
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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
------------------------------------------------------------
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