Contacts of the helix formed by residues 50 - 72 (chain A) in PDB entry 1WXI
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 GLY 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 SER* 3.2 7.9 + - - -
49A GLY* 1.3 80.6 - - - +
51A GLN* 1.3 65.3 + - - -
53A SER* 3.9 0.2 + - - -
54A THR* 2.8 26.5 + - - -
205A LEU 4.1 3.4 - - - -
500A DPO 3.0 27.0 + - - -
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Residues in contact with GLN 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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50A GLY* 1.3 70.7 - - - +
52A ASP* 1.3 75.7 + - - +
54A THR* 3.3 3.1 + - - -
55A LEU* 3.0 24.4 + - + +
189A LYS* 3.1 40.8 + - - +
192A GLY* 3.9 7.3 - - - -
193A LYS* 2.7 48.3 + - - +
196A LEU* 3.6 22.2 - - + +
205A LEU 3.8 11.3 + - - -
206A TYR* 4.0 10.5 - - + +
500A DPO 3.4 15.2 + - - +
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Residues in contact with ASP 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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51A GLN* 1.3 86.3 + - - +
53A SER* 1.3 57.9 + - - +
55A LEU* 3.4 2.9 + - - +
56A ALA* 3.0 28.9 + - - +
160A THR* 3.9 19.7 - - - +
162A HIS* 2.9 30.9 + - + -
165A GLU* 3.0 2.9 - - - +
184A LEU* 3.7 11.5 - - + +
189A LYS* 2.9 18.7 + - - -
500A DPO 3.0 12.2 + - - +
600A MG 2.4 26.8 - - - -
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Residues in contact with SER 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 3.7 5.1 - - - +
46A GLY 3.5 24.7 - - - -
47A ILE* 4.0 6.0 - - - +
48A SER* 3.1 23.7 + - - -
49A GLY 3.9 1.9 + - - -
50A GLY 3.6 4.2 + - - -
52A ASP* 1.3 70.9 - - - +
54A THR* 1.3 61.6 + - - +
56A ALA* 4.4 0.9 - - - -
57A GLY* 2.9 26.0 + - - -
101A ILE* 4.4 3.0 - - - +
160A THR* 3.8 9.8 - - - +
400A AMP 3.6 11.2 - - - -
500A DPO 2.6 26.2 + - - -
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Residues in contact with THR 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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47A ILE* 5.5 1.2 - - - +
49A GLY* 4.1 6.8 + - - -
50A GLY 2.8 25.2 + - - -
51A GLN* 3.6 5.4 - - - -
53A SER* 1.3 77.0 + - - +
55A LEU* 1.3 63.0 + - - +
57A GLY* 3.8 0.7 - - - -
58A LYS* 3.1 23.2 + - - +
97A ALA* 3.7 22.1 - - + +
100A PHE* 3.8 28.5 - - + -
101A ILE* 3.9 10.3 - - + +
196A LEU* 4.3 4.5 - - + -
201A CYS* 4.1 15.3 - - - -
205A LEU* 4.5 12.7 + - + +
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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 GLN* 3.0 18.1 + - - +
52A ASP* 3.7 4.9 - - - +
54A THR* 1.3 74.8 - - - +
56A ALA* 1.3 66.7 + - - +
58A LYS* 3.2 4.9 + - - +
59A LEU* 3.1 35.7 + - + +
184A LEU* 3.9 28.3 - - + -
187A LEU* 4.8 2.2 - - + -
192A GLY* 3.8 31.2 - - - +
195A LEU* 3.9 28.3 - - + -
196A LEU* 3.7 17.9 - - + +
199A LEU* 3.9 20.2 - - + -
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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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45A LEU* 3.8 13.2 - - + -
52A ASP 3.0 17.8 + - - +
53A SER 4.1 0.2 - - - +
55A LEU* 1.3 76.4 - - - +
57A GLY* 1.3 57.8 + - - +
59A LEU* 3.3 7.5 + - - +
60A CYS* 2.9 31.9 + - - -
158A VAL* 4.9 6.3 - - + -
159A GLY 4.7 5.6 - - - +
160A THR* 3.9 19.7 - - + -
183A PRO* 4.9 3.7 - - + +
184A LEU* 4.3 19.5 - - + +
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Residues in contact with GLY 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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45A LEU* 3.3 17.9 - - - +
47A ILE* 5.3 0.2 - - - -
53A SER 2.9 16.5 + - - -
54A THR 3.8 0.9 - - - -
55A LEU 3.2 0.2 - - - -
56A ALA* 1.3 77.7 - - - +
58A LYS* 1.3 60.6 + - - +
60A CYS* 3.3 2.4 + - - +
61A GLN* 3.0 19.4 + - - +
78A PHE* 3.8 11.2 - - - -
101A ILE* 3.6 21.8 - - - +
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Residues in contact with LYS 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 THR 3.1 14.0 + - - +
55A LEU* 3.2 7.8 + - - +
57A GLY* 1.3 75.9 - - - +
59A LEU* 1.3 63.7 + - - +
61A GLN* 3.3 3.8 + - + +
62A MET* 3.0 45.5 + - + +
100A PHE* 2.9 58.8 + - + +
101A ILE* 3.9 20.3 + - + +
102A GLN* 4.7 8.1 + - - -
199A LEU* 4.0 27.1 - - + -
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Residues in contact with LEU 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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23A ILE* 4.0 32.1 - - + +
26A SER* 3.9 21.3 - - - +
27A VAL* 4.1 16.7 - - + +
30A LEU* 4.0 11.1 - - + +
55A LEU* 3.1 22.7 + - + +
56A ALA* 3.6 7.2 - - - +
58A LYS* 1.3 76.6 - - - +
60A CYS* 1.3 62.9 + - - +
62A MET* 3.4 11.2 + - - +
63A ALA* 3.0 24.3 + - - +
183A PRO* 5.2 3.6 - - + -
184A LEU* 3.8 29.2 - - + -
195A LEU* 5.0 4.9 - - + -
199A LEU* 4.5 11.9 - - + -
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Residues in contact with CYS 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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30A LEU* 4.0 14.6 - - - -
43A LEU* 4.1 11.0 - - + -
45A LEU* 4.7 1.6 - - - -
56A ALA* 2.9 20.6 + - - +
57A GLY 3.6 7.4 - - - +
59A LEU* 1.3 77.2 - - - +
61A GLN* 1.3 62.0 + - - +
63A ALA* 3.2 2.9 + - - +
64A ILE* 2.8 30.0 + - - +
78A PHE* 3.6 27.6 - - + -
158A VAL* 3.8 40.4 - - - -
183A PRO* 5.4 0.7 - - - -
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Residues in contact with GLN 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 GLY 3.0 16.0 + - - +
58A LYS* 3.8 4.9 - - + +
60A CYS* 1.3 76.7 - - - +
62A MET* 1.3 58.8 - - + +
64A ILE* 3.3 3.6 + - - +
65A ASN* 2.8 61.6 + - - +
68A ARG* 4.1 0.7 + - - -
78A PHE* 3.3 20.6 - - + +
101A ILE* 3.7 17.3 - - + +
102A GLN* 3.6 17.3 - - + +
103A PRO* 3.1 8.5 - - - +
104A ASP* 3.0 46.9 + - - +
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Residues in contact with MET 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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23A ILE* 4.2 18.8 - - + -
24A ARG* 4.2 18.6 - - - +
27A VAL* 4.3 8.7 - - + -
58A LYS* 3.0 41.2 + - + +
59A LEU* 3.7 13.7 - - - +
61A GLN* 1.3 76.2 - - + +
63A ALA* 1.3 62.9 + - - +
65A ASN* 3.3 8.7 + - - +
66A GLU* 3.0 36.6 + - - +
199A LEU* 4.1 24.0 - - + -
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Residues in contact with ALA 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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27A VAL* 3.9 15.0 - - + +
30A LEU* 3.8 30.5 - - + -
31A LYS* 3.8 14.1 - - + +
34A LEU* 5.9 0.4 - - + -
43A LEU* 4.8 4.7 - - + -
59A LEU 3.0 14.7 + - - +
60A CYS* 3.5 8.3 - - - +
61A GLN 3.2 0.2 - - - -
62A MET* 1.3 77.1 - - - +
64A ILE* 1.3 61.0 + - - +
66A GLU* 3.5 0.5 + - - +
67A LEU* 3.0 31.2 + - + +
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Residues in contact with ILE 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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34A LEU* 4.9 8.1 - - + -
43A LEU* 3.3 32.8 - - + +
60A CYS 2.8 30.0 + - - +
61A GLN* 3.8 5.2 - - - +
63A ALA* 1.3 72.8 - - - +
65A ASN* 1.3 67.8 + - - +
67A LEU* 3.2 7.0 + - + +
68A ARG* 3.0 56.0 + - + +
76A LEU* 4.0 8.7 - - + +
77A GLN* 3.9 17.3 - - - +
78A PHE* 3.4 25.8 - - + -
104A ASP* 3.7 8.1 - - - +
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Residues in contact with ASN 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 GLN* 2.8 51.6 + - - +
62A MET* 3.6 8.8 - - - +
64A ILE* 1.3 74.8 - - - +
66A GLU* 1.3 63.5 + - + +
68A ARG* 3.5 22.3 + - - +
69A LEU* 3.3 30.6 + - + +
104A ASP* 4.5 0.6 + - - -
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Residues in contact with GLU 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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24A ARG* 2.8 38.9 + - - -
27A VAL* 4.1 5.2 - - - +
31A LYS* 2.8 33.7 + - - +
62A MET* 3.0 26.2 + - - +
63A ALA 3.9 1.1 - - - +
65A ASN* 1.3 76.6 - - + +
67A LEU* 1.3 63.3 + - - +
69A LEU* 3.4 8.2 + - + +
70A GLU* 2.9 35.6 + - - +
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Residues in contact with LEU 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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31A LYS* 3.9 20.9 - - + -
34A LEU* 3.6 41.7 - - + -
35A GLN* 3.8 35.4 - - + +
63A ALA* 3.0 21.7 + - + +
64A ILE* 3.2 5.1 + - - +
66A GLU* 1.3 76.2 - - - +
68A ARG* 1.3 57.8 + - - +
70A GLU* 4.4 9.4 - - - +
71A THR* 2.8 48.0 + - + +
76A LEU* 3.8 18.2 - - + -
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Residues in contact with ARG 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 ILE* 3.0 25.9 + - + +
65A ASN* 3.6 24.7 - - - +
67A LEU* 1.3 77.9 - - - +
69A LEU* 1.3 58.8 + - + +
71A THR* 4.4 0.4 - - - -
72A GLY* 2.6 34.3 + - - -
73A ASN 3.6 23.6 - - - +
74A GLU* 4.5 23.1 + - - +
76A LEU* 2.9 31.1 + - + -
77A GLN* 3.5 5.7 - - - +
104A ASP* 2.4 49.2 + - - +
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Residues in contact with LEU 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 ASN* 3.3 19.8 + - + +
66A GLU* 3.8 8.7 - - + +
68A ARG* 1.3 83.7 - - + +
70A GLU* 1.3 63.2 + - + +
72A GLY* 4.3 3.1 + - - -
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Residues in contact with GLU 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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31A LYS* 2.7 38.9 + - - -
35A GLN* 4.9 5.4 + - - +
66A GLU* 2.9 26.4 + - - +
67A LEU* 4.0 9.8 - - - +
69A LEU* 1.3 81.1 - - + +
71A THR* 1.3 65.0 + - + +
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Residues in contact with THR 71 (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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35A GLN* 4.9 9.9 - - + +
67A LEU* 2.8 37.9 + - + +
70A GLU* 1.3 80.8 - - + +
72A GLY* 1.3 62.8 + - - +
73A ASN* 3.1 24.2 + - - +
76A LEU* 4.5 3.1 - - + +
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Residues in contact with GLY 72 (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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68A ARG 2.6 23.6 + - - -
69A LEU 4.3 3.0 + - - -
70A GLU 3.7 1.2 - - - -
71A THR* 1.3 73.3 - - - +
73A ASN* 1.3 56.9 + - - +
74A GLU* 3.1 24.6 + - - +
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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