Contacts of the helix formed by residues 50 - 71 (chain A) in PDB entry 1WKB
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A HIS 3.8 3.1 + - - +
49A LEU* 1.3 75.0 - - - +
51A VAL* 1.3 60.6 + - - +
52A GLY* 3.0 26.9 + - - -
53A HIS* 2.8 69.0 + + - +
54A ALA* 2.9 11.3 + - - +
644A GLY 5.7 0.4 - - - -
651A MET* 3.5 29.5 + - + +
658A VAL* 4.9 9.4 - - + -
659A LEU 3.2 20.6 - - - +
660A ASN* 4.0 4.7 - - - +
661A PHE* 3.9 5.6 - - - +
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A HIS* 1.3 70.7 - - - +
52A GLY* 1.3 67.0 + - - +
54A ALA* 3.1 22.4 - - + +
55A ARG 3.3 5.5 + - - -
644A GLY 6.3 0.2 - - - -
645A THR 5.5 0.9 - - - +
646A LEU* 5.4 0.4 - - + -
651A MET* 4.2 17.7 - - + -
659A LEU* 3.0 32.9 + - + +
661A PHE* 4.3 6.1 - - + -
664A ALA* 3.7 30.5 - - + -
673A VAL* 5.2 0.2 - - + -
677A ILE* 3.7 3.8 - - + +
687A PHE* 3.5 14.2 - - + -
689A TRP* 4.0 37.2 - - + -
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Residues in contact with GLY 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A HIS* 3.0 17.7 + - - -
51A VAL* 1.3 80.2 - - - +
53A HIS* 1.3 62.8 + - - +
55A ARG* 3.2 17.5 + - - +
56A THR* 3.6 8.4 + - - -
641A ASN* 5.1 0.9 + - - -
642A GLY 5.3 1.7 - - - +
643A PHE* 5.7 0.8 - - - -
644A GLY 4.4 12.3 + - - -
651A MET* 4.0 5.0 - - - +
687A PHE* 4.1 14.7 - - - -
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Residues in contact with HIS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A HIS 4.8 2.4 + - - -
49A LEU* 3.4 35.7 - - + +
50A HIS* 2.8 62.3 + + - +
52A GLY* 1.3 78.3 - - - +
54A ALA* 1.3 61.7 + - - +
56A THR* 3.1 17.5 + - - -
57A TYR* 3.1 34.1 - - + -
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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
----------------------------------------------------------
50A HIS 2.9 5.1 + - - -
51A VAL* 3.1 24.9 - - - +
53A HIS* 1.3 77.7 - - - +
55A ARG* 1.3 58.2 + - - +
57A TYR* 3.5 2.4 + - - +
58A THR* 2.7 32.7 + - - -
142A PHE* 4.5 0.2 - - - -
661A PHE* 3.6 41.9 - - + -
677A ILE* 3.6 17.3 - - + -
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Residues in contact with ARG 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A VAL 3.3 1.6 + - - -
52A GLY 3.2 10.6 + - - +
53A HIS 3.1 0.8 - - - -
54A ALA* 1.3 80.4 - - - +
56A THR* 1.3 65.4 + - - +
58A THR* 3.2 0.7 + - - -
59A ILE* 3.1 37.0 + - + +
641A ASN* 3.9 9.0 - - - +
642A GLY 3.3 30.6 + - - -
643A PHE 3.7 8.3 + - - -
677A ILE* 3.5 30.3 + - + +
678A MET* 4.1 7.7 - - + +
681A ALA* 3.5 34.6 + - - -
682A GLU* 3.5 3.8 - - - +
683A HIS 3.0 23.8 + - - +
685A SER 2.7 24.4 + - - -
686A ASP* 3.8 3.6 - - - +
687A PHE* 3.6 24.0 - - + -
749A THR* 5.7 0.2 + - - -
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Residues in contact with THR 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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40A VAL* 3.5 21.8 - - + +
41A ALA* 5.5 2.2 - - + +
52A GLY 3.6 9.0 + - - -
53A HIS* 3.1 12.7 + - - -
55A ARG* 1.3 79.5 - - - +
57A TYR* 1.3 65.6 + - + +
59A ILE* 4.3 0.9 - - - +
60A PRO* 2.9 21.8 - - - +
608A CYS* 5.1 1.6 - - - +
609A SER* 4.0 4.0 - - - -
610A GLY* 3.9 19.4 + - - +
641A ASN* 3.2 36.1 + - - +
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Residues in contact with TYR 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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40A VAL* 3.6 26.0 - - + -
41A ALA 2.6 29.3 + - - -
42A PHE 3.9 0.2 + - - -
43A PRO* 3.1 30.2 - - + +
49A LEU* 4.2 10.8 - - + -
53A HIS* 3.1 40.7 + + + +
54A ALA* 4.2 2.0 - - - +
56A THR* 1.3 82.9 - - + +
58A THR* 1.3 61.0 + - - +
60A PRO* 3.2 19.3 - - - +
61A ASP* 3.7 6.1 + - - +
76A PHE* 4.2 6.4 - + + -
78A MET* 4.0 9.6 - - + -
137A PHE* 3.6 31.9 - + - -
142A PHE* 3.5 29.4 - + + -
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Residues in contact with THR 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* 2.7 24.2 + - - +
55A ARG 3.2 0.2 + - - -
57A TYR* 1.3 74.3 - - - +
59A ILE* 1.3 67.9 + - - +
61A ASP* 3.0 2.6 + - - +
62A VAL* 2.9 27.3 + - + +
142A PHE* 3.5 20.6 - - - -
661A PHE* 4.3 6.1 - - - -
674A ARG* 4.1 34.1 - - + +
677A ILE* 5.4 2.6 - - - +
678A MET* 3.8 34.3 - - + -
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Residues in contact with ILE 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 ARG* 3.1 23.7 + - + +
56A THR* 4.6 0.4 - - - +
58A THR* 1.3 76.7 - - - +
60A PRO* 1.3 71.4 - - + +
62A VAL* 3.2 3.4 + - - +
63A ILE* 3.1 23.8 + - + +
608A CYS* 5.2 3.1 - - + -
640A VAL 5.5 1.1 - - - +
641A ASN* 3.3 44.0 - - + +
678A MET* 3.9 23.1 - - + -
682A GLU* 6.6 0.2 - - - -
683A HIS 6.0 1.8 - - - +
747A PHE* 3.7 33.4 - - + +
749A THR* 4.3 18.8 - - + +
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Residues in contact with PRO 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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38A ILE* 3.7 33.2 - - + +
40A VAL* 3.6 29.4 - - + -
56A THR 2.9 23.6 - - - +
57A TYR 3.2 16.6 - - - +
59A ILE* 1.3 88.9 - - + +
61A ASP* 1.3 54.1 + - - +
63A ILE* 3.3 1.9 + - + +
64A ALA* 2.8 31.0 + - - +
76A PHE* 4.0 14.4 - - + -
608A CYS* 4.1 11.2 - - + -
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Residues in contact with ASP 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 TYR 3.7 1.9 + - - +
58A THR 3.0 9.4 + - - +
60A PRO* 1.3 77.5 - - - +
62A VAL* 1.3 67.4 + - - +
64A ALA* 3.3 0.9 + - - +
65A ARG* 2.9 37.4 + - - +
76A PHE* 3.6 12.9 - - + -
141A GLY 3.3 1.2 - - - +
142A PHE* 3.5 21.9 - - + -
143A SER* 2.7 43.4 + - - -
674A ARG* 2.8 33.6 + - - +
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Residues in contact with VAL 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 THR* 2.9 32.1 + - + +
59A ILE* 3.5 8.7 - - - +
61A ASP* 1.3 76.6 - - - +
63A ILE* 1.3 59.4 + - + +
65A ARG 3.3 0.2 + - - -
66A PHE* 2.9 27.7 + - - +
674A ARG* 4.1 2.2 - - + +
678A MET* 4.0 17.3 - - + -
744A LEU* 3.9 20.6 - - + -
749A THR* 5.1 4.3 - - + -
796A PRO* 3.5 33.8 - - + +
797A PHE* 3.9 27.4 - - + -
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Residues in contact with ILE 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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36A PHE* 3.7 27.6 - - + -
38A ILE* 4.2 4.9 - - + -
59A ILE* 3.1 19.3 + - + +
60A PRO 3.7 3.6 - - - +
62A VAL* 1.3 74.7 - - + +
64A ALA* 1.3 60.0 + - - +
66A PHE* 3.2 6.5 + - + +
67A LYS* 2.8 37.9 + - + +
744A LEU* 3.5 45.5 - - + +
747A PHE* 3.8 44.4 - - + -
749A THR* 5.6 1.3 - - + -
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Residues in contact with ALA 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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36A PHE* 4.7 5.1 - - - -
38A ILE* 4.3 3.6 - - + -
60A PRO 2.8 20.9 + - - +
61A ASP 3.3 5.1 + - - +
63A ILE* 1.3 73.7 - - - +
65A ARG* 1.3 56.8 + - - +
67A LYS* 3.2 6.3 + - - +
68A ARG* 3.0 34.6 + - - +
74A VAL* 3.8 23.8 - - + +
76A PHE* 4.2 16.2 - - + -
143A SER* 4.1 13.5 - - - +
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Residues in contact with ARG 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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17A TRP* 3.5 29.9 - - - +
23A PHE* 3.8 24.5 - - - -
61A ASP* 2.9 39.7 + - - +
62A VAL 3.9 3.4 - - - +
64A ALA* 1.3 72.8 - - - +
66A PHE* 1.3 66.5 + - - +
68A ARG* 3.3 20.4 + - - +
69A MET* 3.1 30.8 + - + +
141A GLY 2.8 22.0 + - - -
143A SER* 3.8 7.5 - - - +
674A ARG* 4.0 1.3 - - - +
795A ALA 4.4 1.5 + - - +
796A PRO* 3.9 27.1 - - + -
799A PRO* 3.4 25.5 - - - +
803A GLU* 5.1 5.3 + - - -
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Residues in contact with PHE 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 VAL 2.9 18.6 + - - +
63A ILE* 3.4 11.2 - - + +
65A ARG* 1.3 76.1 - - - +
67A LYS* 1.3 74.5 + - - +
69A MET* 3.2 10.4 + - + +
70A GLN* 3.1 54.9 + - + +
740A THR* 6.3 0.2 - - + -
741A THR* 3.8 37.5 - - + -
744A LEU* 3.7 45.1 - - + -
745A GLU* 3.8 24.9 - - - -
796A PRO* 4.0 12.0 - - + +
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Residues in contact with LYS 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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36A PHE* 3.7 41.7 - - + -
63A ILE* 2.8 27.4 + - - +
64A ALA 3.6 4.7 - - - +
66A PHE* 1.3 80.7 - - - +
68A ARG* 1.3 66.6 + - - +
70A GLN* 2.7 36.8 + - - +
71A GLY 3.1 0.5 + - - -
72A TYR* 3.1 46.1 + - + -
74A VAL* 3.9 15.5 - - + -
745A GLU* 2.8 28.5 + - - +
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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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22A ILE 5.6 0.4 + - - -
23A PHE* 3.4 33.3 + - - +
64A ALA* 3.0 22.3 + - - +
65A ARG* 3.3 23.9 + - - +
67A LYS* 1.3 76.5 - - - +
69A MET* 1.3 60.3 + - + +
71A GLY* 3.0 19.2 + - - -
72A TYR 3.9 11.2 + - - +
74A VAL* 3.5 41.7 + - + +
76A PHE* 4.6 3.8 - - - +
143A SER* 2.9 49.5 + - - -
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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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65A ARG* 3.1 12.4 + - + +
66A PHE* 3.5 10.1 - - + +
67A LYS 3.2 0.2 - - - -
68A ARG* 1.3 77.4 - - + +
70A GLN* 1.3 62.0 + - + +
71A GLY 3.4 0.9 + - - -
792A ARG* 3.3 48.2 - - + +
795A ALA* 3.9 15.3 - - - -
796A PRO* 3.9 18.2 - - - -
806A TRP* 3.9 24.7 - - + -
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Residues in contact with GLN 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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66A PHE* 3.1 38.4 + - + +
67A LYS* 2.7 51.6 + - - +
69A MET* 1.3 78.0 - - + +
71A GLY* 1.3 58.3 + - - +
72A TYR* 3.4 16.0 + - + -
741A THR* 4.0 8.4 - - + +
745A GLU* 3.0 19.0 + - - +
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Residues in contact with GLY 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LYS* 3.3 28.5 + - - +
34A LYS* 4.2 12.0 - - - +
68A ARG 3.0 11.9 + - - -
69A MET 3.2 1.0 - - - -
70A GLN* 1.3 80.4 - - - +
72A TYR* 1.3 63.1 + - - +
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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