Contacts of the helix formed by residues 56 - 74 (chain E) in PDB entry 3IFS
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 56 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54E GLN 3.5 2.1 + - - -
55E TYR* 1.3 72.2 - - - +
57E LYS* 1.3 58.3 + - - +
58E GLU* 2.8 36.3 + - - +
59E GLU* 3.1 32.5 + - + +
60E PHE* 3.1 26.0 + - - +
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Residues in contact with LYS 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E LEU 2.5 30.8 + - - -
54E GLN* 3.4 7.7 + - - +
55E TYR* 2.7 56.5 + - + +
56E ASP* 1.3 72.5 + - - +
58E GLU* 1.3 76.5 + - - +
60E PHE* 3.4 7.5 + - - +
61E ALA* 3.2 22.2 + - - +
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Residues in contact with GLU 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E ASP* 2.8 25.5 - - - +
57E LYS* 1.3 83.4 + - - +
59E GLU* 1.3 62.6 + - - +
61E ALA* 3.6 7.3 + - - +
62E ARG* 3.3 21.0 + - - +
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Residues in contact with GLU 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E ASP* 3.1 35.8 + - - +
58E GLU* 1.3 74.0 - - - +
60E PHE* 1.3 60.9 + - - +
62E ARG* 3.0 20.6 + - - +
63E ILE* 2.9 33.0 + - + +
199E PHE* 3.7 20.3 - - + -
200E VAL* 2.8 42.1 + - - +
214E PRO* 3.5 26.6 - - + +
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Residues in contact with PHE 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E TYR* 3.7 32.1 - + + -
56E ASP 3.1 18.8 + - - +
57E LYS 3.5 6.7 - - - +
58E GLU 3.3 0.2 - - - -
59E GLU* 1.3 78.2 - - - +
61E ALA* 1.3 61.7 + - - +
63E ILE* 3.2 13.4 + - + +
64E GLN* 3.2 46.2 + - - +
217E LEU* 3.8 18.2 - - + -
227E ILE* 3.5 44.2 - - + -
228E GLU* 3.7 14.6 - - + -
231E MSE 3.7 23.3 - - + -
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Residues in contact with ALA 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E LYS 3.2 11.0 + - - +
58E GLU* 3.8 10.5 - - - +
59E GLU 3.3 0.2 - - - -
60E PHE* 1.3 79.2 - - - +
62E ARG* 1.3 57.8 + - - +
64E GLN* 3.2 18.3 + - - +
65E LYS* 2.9 27.1 + - - +
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Residues in contact with ARG 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E GLU 3.3 9.3 + - - +
59E GLU* 3.0 25.8 + - - +
61E ALA* 1.3 75.3 - - - +
63E ILE* 1.3 61.2 + - - +
65E LYS* 4.1 12.8 - - + -
66E CYS* 2.8 34.5 + - - -
197E GLU* 2.5 42.2 + - - +
198E THR 2.8 30.1 + - - +
199E PHE* 3.6 24.1 - - + +
200E VAL* 6.3 0.4 - - - +
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Residues in contact with ILE 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E GLU* 2.9 21.4 + - + +
60E PHE* 3.2 18.6 + - + +
62E ARG* 1.3 75.0 - - - +
64E GLN* 1.3 59.7 + - - +
66E CYS* 3.3 1.8 + - - +
67E ALA* 2.8 27.9 + - - +
199E PHE* 3.6 25.4 - - + -
214E PRO* 4.0 32.1 - - + -
217E LEU* 4.0 20.9 - - + +
218E LEU* 3.6 36.8 - - + +
221E ALA* 4.8 2.0 - - + -
227E ILE* 4.1 11.0 - - + -
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Residues in contact with GLN 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E PHE* 3.2 20.6 + - - +
61E ALA* 3.4 21.5 - - - +
62E ARG 3.2 0.2 - - - -
63E ILE* 1.3 80.8 - - - +
65E LYS* 1.3 62.0 + - - +
67E ALA* 3.4 7.0 + - - +
68E GLU* 3.0 28.1 + - - +
221E ALA* 5.5 1.8 - - + -
227E ILE* 4.0 20.7 - - + +
228E GLU* 2.9 43.2 + - - +
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Residues in contact with LYS 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E ALA 2.9 16.5 + - - +
62E ARG* 3.2 14.8 + - + +
64E GLN* 1.3 76.6 - - - +
66E CYS* 1.3 63.8 + - - +
68E GLU* 3.4 6.3 + - - +
69E LYS* 3.1 20.4 + - - +
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Residues in contact with CYS 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E ARG* 2.8 25.9 + - - +
63E ILE 3.8 3.6 - - - +
65E LYS* 1.3 70.9 - - - +
67E ALA* 1.3 66.3 + - - +
69E LYS* 3.2 9.2 + - - +
70E ILE* 2.9 29.6 + - - +
177E TYR* 4.0 17.0 - - + -
197E GLU* 3.6 30.7 - - - -
199E PHE* 3.5 24.7 - - + -
218E LEU* 4.2 7.6 - - + -
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Residues in contact with ALA 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E ILE 2.8 17.8 + - - +
64E GLN* 3.6 7.0 - - - +
66E CYS* 1.3 77.4 - - - +
68E GLU* 1.3 57.6 + - + +
70E ILE* 3.3 2.8 + - - +
71E LYS* 2.9 37.1 + - - +
218E LEU* 3.9 3.5 - - + +
221E ALA* 3.7 30.7 - - + +
222E VAL* 3.9 23.2 - - + +
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Residues in contact with GLU 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E GLN 3.0 19.5 + - - +
65E LYS* 3.4 5.8 + - - +
67E ALA* 1.3 77.2 - - + +
69E LYS* 1.3 63.4 + - - +
71E LYS* 3.5 34.2 + - - +
72E ASN* 3.0 24.4 + - - +
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Residues in contact with LYS 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E LYS 3.1 13.7 + - - +
66E CYS* 3.5 11.0 - - - +
68E GLU* 1.3 75.0 - - - +
70E ILE* 1.3 64.4 + - - +
72E ASN* 3.1 12.4 + - - +
73E ASP* 2.7 50.3 + - - +
171E GLU* 5.3 1.0 + - - -
174E LYS* 2.8 40.3 + - - +
175E ARG* 4.7 4.2 - - - +
177E TYR* 3.2 17.7 + - + +
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Residues in contact with ILE 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E CYS 2.9 23.0 + - - +
67E ALA 3.7 4.0 - - - +
69E LYS* 1.3 76.4 - - - +
71E LYS* 1.3 58.0 + - - +
73E ASP* 3.3 6.7 + - - -
74E SER* 2.9 48.4 + - - +
77E LEU* 4.3 18.6 - - + -
112E PRO* 4.7 1.3 - - + -
139E SER* 4.4 7.9 - - - +
177E TYR* 3.5 47.1 - - + +
218E LEU* 4.4 10.3 - - + -
222E VAL* 3.8 36.8 - - + -
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Residues in contact with LYS 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E ALA* 2.9 22.3 + - - +
68E GLU* 3.6 33.4 + - - +
70E ILE* 1.3 77.5 - - - +
72E ASN* 1.3 60.2 + - - +
74E SER 4.1 7.9 - - - +
110E LYS 5.8 0.4 - - - +
111E THR* 4.5 11.8 - - + +
112E PRO* 3.7 19.6 - - + +
221E ALA 3.2 26.4 + - - -
222E VAL* 3.6 21.8 - - - +
224E GLY* 4.1 15.9 + - - -
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Residues in contact with ASN 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E GLU 3.0 17.9 + - - +
69E LYS* 3.2 11.4 + - - +
70E ILE 3.0 0.2 - - - -
71E LYS* 1.3 80.2 - - - +
73E ASP* 1.3 69.4 + - - +
74E SER 3.7 0.2 - - - -
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Residues in contact with ASP 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E LYS* 2.7 53.5 + - - +
70E ILE* 3.3 5.5 - - - +
72E ASN* 1.3 85.9 + - - +
74E SER* 1.3 72.8 + - - +
137E ASP* 3.5 9.8 - - - +
139E SER* 3.8 2.3 + - - -
171E GLU* 5.3 0.5 - - - +
175E ARG* 3.0 40.4 + - - +
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Residues in contact with SER 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E ILE* 2.9 20.7 + - - +
71E LYS 4.1 5.7 - - - +
72E ASN 3.7 1.0 - - - -
73E ASP* 1.3 89.9 + - - +
75E ASP* 1.3 63.4 + - - +
76E ILE 3.6 19.7 - - - -
112E PRO* 3.4 18.6 - - - +
137E ASP* 3.9 6.5 - - - -
138E PHE* 4.2 0.7 - - - -
139E SER* 2.6 27.9 + - - -
175E ARG* 3.2 7.1 + - - -
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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
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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