Contacts of the helix formed by residues 54 - 75 (chain A) in PDB entry 3R7G
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 ASN 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A PRO 4.0 0.4 + - - -
53A ILE* 1.3 78.9 - - - +
55A GLU* 1.3 65.0 + - - +
56A GLU* 3.0 13.3 + - - +
57A GLN* 2.9 52.1 + - - +
58A ALA 3.2 15.2 + - - -
137A LEU* 4.0 2.2 - - - +
147A ARG* 3.8 8.5 - - - +
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Residues in contact with GLU 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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54A ASN* 1.3 75.7 - - - +
56A GLU* 1.3 63.9 + - - +
58A ALA* 3.0 13.2 + - - +
59A TRP* 3.1 25.4 + - + -
137A LEU* 4.3 4.0 - - + -
147A ARG* 3.9 16.5 + - - +
148A GLU 4.1 3.6 - - - +
149A LEU* 3.4 12.1 - - + +
150A SER* 2.8 49.0 + - - -
153A LEU* 3.8 25.1 - - + +
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Residues in contact with GLU 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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54A ASN* 3.0 10.3 + - - +
55A GLU* 1.3 78.1 - - - +
57A GLN* 1.3 58.6 + - - +
59A TRP* 3.4 6.9 + - - +
60A ALA* 3.0 28.4 + - - +
206A HIS* 2.7 39.3 + - - -
207A LEU* 3.9 2.3 - - - +
216A HIS* 2.6 39.5 + - + +
217A TYR* 3.8 3.1 - - - -
220A VAL* 4.1 15.5 - - + -
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Residues in contact with GLN 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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53A ILE* 3.4 21.7 - - + +
54A ASN* 2.9 51.1 + - - +
56A GLU* 1.3 74.1 - - + +
58A ALA* 1.3 58.7 + - - +
60A ALA* 3.8 0.2 - - - +
61A VAL* 2.9 34.5 + - + +
220A VAL* 3.9 22.4 + - + +
221A CYS* 6.2 0.2 - - - -
224A LEU* 3.6 44.6 - - + +
227A GLU* 6.4 0.4 - - - -
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Residues in contact with ALA 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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53A ILE* 3.9 11.8 - - + +
54A ASN 3.2 11.7 + - - +
55A GLU 3.0 10.5 + - - +
57A GLN* 1.3 73.7 - - - +
59A TRP* 1.3 66.2 + - - +
61A VAL* 3.5 2.5 + - - +
62A CYS* 3.1 25.1 + - - +
133A ILE* 3.8 26.0 - - + +
137A LEU* 3.9 21.8 - - + -
153A LEU* 4.3 10.3 - - + -
156A LEU* 6.0 0.4 - - - -
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Residues in contact with TRP 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 GLU* 3.1 38.5 + - + +
56A GLU* 3.5 8.5 - - - +
58A ALA* 1.3 75.6 - - - +
60A ALA* 1.3 58.1 + - - +
62A CYS* 3.4 5.3 - - - +
63A TYR* 3.0 29.8 + - - +
150A SER* 5.1 2.4 + - - -
152A PRO* 3.7 29.8 - - + -
153A LEU* 3.7 38.8 - - + +
156A LEU* 3.9 24.9 - - + -
202A LEU* 3.8 21.5 - - + -
203A CYS* 3.7 21.6 - - - +
206A HIS* 3.4 51.5 - + + -
217A TYR* 3.7 16.4 - - + +
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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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56A GLU 3.0 18.2 + - - +
57A GLN 3.8 2.2 - - - +
58A ALA 3.2 0.4 - - - -
59A TRP* 1.3 75.1 - - - +
61A VAL* 1.3 60.7 + - - +
63A TYR* 3.8 0.2 - - - +
64A GLN* 2.9 36.4 + - - +
217A TYR* 3.5 27.4 - - + +
220A VAL* 3.7 25.4 - - + -
221A CYS* 3.8 12.3 - - - -
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Residues in contact with VAL 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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42A LEU* 5.0 10.3 - - + -
53A ILE* 5.4 2.7 - - + -
57A GLN* 2.9 22.9 + - + +
58A ALA 4.1 2.5 - - - +
60A ALA* 1.3 75.4 - - - +
62A CYS* 1.3 54.4 + - - +
65A CYS* 2.8 40.9 + - + +
88A ILE* 4.1 26.7 - - + -
90A VAL* 5.0 6.5 - - + -
96A VAL* 4.2 9.8 - - + +
129A LEU* 5.4 1.1 - - + -
133A ILE* 3.7 25.8 - - + -
221A CYS* 4.2 16.6 - - - -
224A LEU* 4.6 16.4 - - + -
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Residues in contact with CYS 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 ALA 3.1 18.4 + - - +
59A TRP* 3.4 6.3 - - - +
60A ALA 3.2 0.2 - - - -
61A VAL* 1.3 75.2 - - - +
63A TYR* 1.3 65.7 + - - +
65A CYS* 4.1 0.2 - - - +
66A CYS* 3.1 30.9 + - - -
129A LEU* 4.6 12.1 - - - -
133A ILE* 4.9 8.7 - - + +
156A LEU* 4.1 11.4 - - + -
157A ILE* 6.1 0.2 - - - -
160A MET* 3.6 27.6 - - - -
199A VAL* 3.4 28.5 - - - -
203A CYS* 4.0 4.7 - - - -
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Residues in contact with TYR 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 TRP 3.0 16.7 + - - +
60A ALA 3.8 2.5 - - - +
62A CYS* 1.3 75.7 - - - +
64A GLN* 1.3 79.1 + - - +
66A CYS* 3.8 1.9 - - - +
67A GLY* 3.0 25.2 + - - -
200A MET* 3.7 53.7 - - + +
203A CYS* 3.8 23.0 - - + -
204A ALA* 4.6 2.9 - - + -
213A ALA* 3.8 19.8 - - + +
214A PRO* 3.7 38.0 - - + +
217A TYR* 3.4 27.4 - + + -
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Residues in contact with GLN 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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60A ALA 2.9 21.2 + - - +
63A TYR* 1.3 98.8 - - - +
65A CYS* 1.3 60.4 + - - +
67A GLY* 3.3 3.7 + - - -
68A SER* 3.2 24.3 + - - -
94A GLY 2.8 27.3 + - - +
95A ALA* 4.0 6.9 - - - +
96A VAL* 3.5 23.1 + - + +
214A PRO* 4.4 4.0 - - - +
217A TYR* 3.8 17.9 - - + +
218A GLN* 3.7 27.6 + - - +
221A CYS* 3.9 2.7 - - - -
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Residues in contact with CYS 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 VAL* 2.8 24.4 + - + +
62A CYS 4.1 1.8 - - - +
64A GLN* 1.3 70.5 - - - +
66A CYS* 1.3 60.3 + - - +
68A SER* 3.2 4.9 + - - -
69A LEU* 2.9 47.2 + - - +
82A VAL* 6.0 0.4 - - - -
88A ILE* 5.1 3.8 - - - -
96A VAL* 3.7 24.6 - - + +
97A THR 4.7 4.9 - - - -
98A LEU* 4.3 24.0 - - - -
129A LEU* 4.3 25.8 - - + -
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Residues in contact with CYS 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 CYS 3.1 22.6 + - - +
65A CYS* 1.3 75.6 - - - +
67A GLY* 1.3 56.7 + - - +
69A LEU* 3.8 7.4 - - - +
70A ARG* 2.9 32.6 + - - +
126A ILE* 5.3 1.8 - - - -
129A LEU* 4.0 18.8 - - - -
196A TYR* 3.9 23.1 - - + +
199A VAL* 3.8 31.2 - - + -
200A MET* 3.7 23.1 - - + -
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Residues in contact with GLY 67 (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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63A TYR* 3.0 15.3 + - - -
64A GLN* 3.3 5.1 + - - -
65A CYS 3.2 0.4 - - - -
66A CYS* 1.3 75.8 - - - +
68A SER* 1.3 60.5 + - - +
70A ARG* 3.5 5.7 + - - +
71A ALA* 3.1 21.8 + - - +
74A ARG* 5.3 1.0 + - - -
200A MET* 3.7 20.7 - - - -
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Residues in contact with SER 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 GLN 3.2 6.5 + - - -
65A CYS 3.2 4.0 + - - -
67A GLY* 1.3 73.0 - - - +
69A LEU* 1.3 61.9 + - - +
71A ALA* 3.2 8.3 + - - +
72A ALA* 3.0 27.7 + - - +
95A ALA* 5.3 2.6 - - - +
96A VAL 2.5 32.0 + - - -
97A THR* 4.0 19.1 - - - +
98A LEU 5.4 1.1 - - - -
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Residues in contact with LEU 69 (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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65A CYS* 2.9 38.3 + - - +
66A CYS* 3.8 5.4 - - - +
68A SER* 1.3 77.2 - - - +
70A ARG* 1.3 57.8 + - - +
72A ALA* 3.3 9.0 + - + +
73A ALA* 2.9 29.3 + - - +
80A HIS 6.4 0.2 - - - +
98A LEU* 3.9 28.9 - - + +
125A VAL* 3.9 15.3 - - + -
129A LEU* 5.0 8.5 - - + -
196A TYR* 3.8 42.1 - - + +
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Residues in contact with ARG 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 CYS 2.9 13.9 + - - +
67A GLY* 3.5 7.9 + - - +
69A LEU* 1.3 74.7 - - - +
71A ALA* 1.3 63.8 + - - +
73A ALA* 3.4 4.8 + - + +
74A ARG* 3.3 39.1 + - - +
196A TYR* 3.9 14.7 - - + -
197A ARG* 3.7 42.6 - - - +
200A MET* 4.0 29.7 - - - +
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Residues in contact with ALA 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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67A GLY 3.1 15.6 + - - +
68A SER* 3.2 10.1 + - - +
70A ARG* 1.3 74.5 - - - +
72A ALA* 1.3 61.1 + - - +
74A ARG* 3.3 44.4 + - - +
75A ARG* 3.8 10.4 + - - +
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Residues in contact with ALA 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 SER 3.0 15.6 + - - +
69A LEU* 3.7 12.1 - - + +
70A ARG 3.2 0.2 - - - -
71A ALA* 1.3 76.1 - - - +
73A ALA* 1.3 58.5 + - - +
75A ARG* 3.1 16.6 + - - -
77A GLN* 3.1 45.8 + - + +
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Residues in contact with ALA 73 (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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69A LEU 2.9 17.0 + - - +
70A ARG* 3.4 7.4 + - + +
72A ALA* 1.3 72.3 - - - +
74A ARG* 1.3 65.7 + - - +
76A ARG* 3.0 22.8 + - - +
77A GLN 4.7 5.4 - - - +
79A ARG* 5.7 9.2 - - + +
122A GLU* 5.1 5.2 - - - +
196A TYR* 4.4 15.7 - - + -
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Residues in contact with ARG 74 (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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67A GLY 5.3 0.6 + - - -
70A ARG* 3.3 28.3 + - - +
71A ALA* 3.3 51.8 + - - +
73A ALA* 1.3 79.0 - - - +
75A ARG* 1.3 95.2 + - - +
76A ARG* 3.3 6.2 + - - +
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Residues in contact with ARG 75 (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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71A ALA 4.1 10.2 + - - +
72A ALA* 3.1 9.8 + - - +
74A ARG* 1.3 112.7 + - - +
76A ARG* 1.3 72.2 + - - +
77A GLN* 3.1 23.6 + - + +
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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