Contacts of the helix formed by residues 56 - 74 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54D GLN 3.4 1.9 + - - -
55D TYR* 1.3 70.1 - - - +
57D LYS* 1.3 57.5 + - - +
58D GLU* 3.0 12.0 + - - +
59D GLU* 2.8 44.1 + - + +
60D PHE* 3.0 26.3 + - - +
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Residues in contact with LYS 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D LEU 5.6 4.7 - - - +
55D TYR* 2.9 32.3 + - + +
56D ASP* 1.3 69.6 + - - +
58D GLU* 1.3 75.9 + - + +
60D PHE* 3.4 10.7 - - - +
61D ALA* 3.3 18.7 + - - +
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Residues in contact with GLU 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ASP* 3.0 7.0 + - - +
57D LYS* 1.3 87.8 - - + +
59D GLU* 1.3 65.2 + - - +
60D PHE 3.1 1.6 - - - -
61D ALA* 3.2 12.2 + - - +
62D ARG* 3.2 22.9 + - - +
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Residues in contact with GLU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ASP* 2.8 39.1 + - - +
58D GLU* 1.3 77.2 - - - +
60D PHE* 1.3 58.5 + - - +
62D ARG* 3.1 22.8 + - - +
63D ILE* 3.0 26.7 + - + +
199D PHE* 3.7 18.1 - - + -
200D VAL* 2.9 39.8 + - - +
214D PRO* 3.3 28.4 - - + +
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Residues in contact with PHE 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D TYR* 3.7 29.2 - + + -
56D ASP 3.0 14.0 + - - +
57D LYS 3.4 13.0 - - - +
59D GLU* 1.3 75.5 - - - +
61D ALA* 1.3 62.6 + - - +
63D ILE* 3.3 12.4 + - + +
64D GLN* 3.2 37.2 + - - +
217D LEU* 3.7 25.8 - - + -
227D ILE* 3.5 44.6 - - + -
228D GLU* 3.8 24.2 - - + -
231D MSE 3.7 17.3 - - + -
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Residues in contact with ALA 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D LYS 3.3 9.6 + - - +
58D GLU* 3.2 17.2 + - - +
59D GLU 3.2 0.2 - - - -
60D PHE* 1.3 77.5 - - - +
62D ARG* 1.3 64.3 + - + +
64D GLN* 3.3 15.6 + - - +
65D LYS* 3.0 21.5 + - - +
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Residues in contact with ARG 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D GLU 3.2 10.6 + - - +
59D GLU* 3.1 27.8 + - - +
61D ALA* 1.3 77.3 - - + +
63D ILE* 1.3 59.6 + - - +
65D LYS* 3.2 12.6 + - + +
66D CYS* 2.8 36.5 + - - +
197D GLU* 2.8 39.4 + - - +
198D THR 2.8 32.5 + - - +
199D PHE* 3.8 20.3 - - + +
200D VAL* 6.0 1.4 - - - +
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Residues in contact with ILE 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D GLU* 3.0 22.5 + - + +
60D PHE* 3.5 17.7 - - + +
61D ALA 3.2 0.2 - - - -
62D ARG* 1.3 77.3 - - - +
64D GLN* 1.3 58.4 + - - +
66D CYS* 3.8 1.8 - - - +
67D ALA* 2.9 28.2 + - - +
199D PHE* 3.6 24.5 - - + -
214D PRO* 4.0 25.6 - - + -
217D LEU* 4.0 31.4 - - + +
218D LEU* 3.6 33.7 - - + +
221D ALA* 4.6 3.1 - - + -
227D ILE* 4.0 11.9 - - + -
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Residues in contact with GLN 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D PHE* 3.2 26.3 + - - +
61D ALA* 3.6 13.4 - - - +
62D ARG 3.3 0.2 - - - -
63D ILE* 1.3 80.3 - - - +
65D LYS* 1.3 60.6 + - - +
67D ALA* 3.4 7.7 + - - +
68D GLU* 3.1 31.0 + - + +
221D ALA* 5.3 2.2 - - + -
226D ASN* 5.4 0.8 + - - -
227D ILE* 3.8 21.1 - - + +
228D GLU* 3.5 37.6 + - - +
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Residues in contact with LYS 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D ALA 3.0 13.8 + - - +
62D ARG* 3.2 16.6 + - + +
64D GLN* 1.3 72.5 - - - +
66D CYS* 1.3 72.6 + - - +
68D GLU* 3.2 8.7 + - - +
69D LYS* 3.1 20.9 + - + +
197D GLU* 5.9 1.2 + - - -
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Residues in contact with CYS 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D ARG* 2.8 21.2 + - - +
63D ILE 3.8 2.9 - - - +
65D LYS* 1.3 81.8 - - - +
67D ALA* 1.3 64.0 + - - +
69D LYS* 3.1 10.6 + - - +
70D ILE* 3.0 30.0 + - - +
177D TYR* 3.9 23.1 - - + -
197D GLU* 3.7 37.5 - - - -
199D PHE* 3.8 12.8 - - + -
218D LEU* 4.3 6.5 - - + -
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Residues in contact with ALA 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D ILE 2.9 17.5 + - - +
64D GLN* 3.5 7.9 - - - +
65D LYS 3.2 0.2 - - - -
66D CYS* 1.3 77.1 - - - +
68D GLU* 1.3 62.9 + - - +
70D ILE* 3.3 4.0 + - - +
71D LYS* 2.9 34.0 + - - +
218D LEU* 4.2 2.2 - - + +
221D ALA* 3.8 30.1 - - + +
222D VAL* 3.8 23.2 - - + +
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Residues in contact with GLU 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D GLN* 3.1 17.5 + - + +
65D LYS* 3.2 8.3 + - - +
67D ALA* 1.3 76.6 - - - +
69D LYS* 1.3 65.5 + - - +
71D LYS* 3.2 33.5 + - - +
72D ASN* 3.0 39.5 + - - +
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Residues in contact with LYS 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D LYS* 3.1 13.9 + - + +
66D CYS* 3.4 12.6 - - - +
68D GLU* 1.3 75.4 - - - +
70D ILE* 1.3 62.1 + - - +
72D ASN* 3.2 6.9 + - - +
73D ASP* 2.9 53.1 + - - +
171D GLU* 5.7 1.6 + - - -
174D LYS* 2.9 41.4 + - - +
175D ARG* 4.7 4.4 - - - +
177D TYR* 3.4 17.1 + - + +
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Residues in contact with ILE 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D CYS 3.0 22.0 + - - +
67D ALA 3.6 4.0 - - - +
69D LYS* 1.3 74.7 - - - +
71D LYS* 1.3 58.6 + - - +
73D ASP* 3.5 7.0 - - - -
74D SER* 2.9 45.8 + - - +
77D LEU* 4.3 23.8 - - + -
112D PRO* 4.5 1.6 - - + -
139D SER* 4.5 3.6 - - - +
141D ASN* 6.0 0.2 - - + -
177D TYR* 3.5 44.9 - - + +
218D LEU* 4.5 9.2 - - + -
222D VAL* 3.8 37.0 - - + -
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Residues in contact with LYS 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D ALA* 2.9 21.8 + - - +
68D GLU* 3.2 35.8 + - - +
70D ILE* 1.3 75.6 - - - +
72D ASN* 1.3 64.9 - - - +
74D SER 4.1 7.8 - - - +
110D LYS 5.2 5.1 - - - +
111D THR* 4.3 11.1 - - + +
112D PRO* 3.8 18.8 - - + +
221D ALA 3.1 28.3 + - - -
222D VAL* 3.3 22.7 - - - +
224D GLY* 3.8 15.5 - - - -
225D LEU 5.8 0.2 + - - -
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Residues in contact with ASN 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D GLU* 3.0 32.7 + - - +
69D LYS* 3.9 5.3 - - - +
71D LYS* 1.3 85.9 - - - +
73D ASP* 1.3 57.6 + - + +
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Residues in contact with ASP 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D LYS* 2.9 57.1 + - - +
70D ILE* 3.4 5.8 - - - +
72D ASN* 1.3 78.3 - - + +
74D SER* 1.3 74.5 + - - +
137D ASP* 3.6 10.1 - - - +
139D SER* 3.9 2.9 + - - -
175D ARG* 3.0 39.1 + - - +
177D TYR* 4.7 0.3 + - - -
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Residues in contact with SER 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D ILE* 2.9 24.9 + - - +
71D LYS 4.1 5.6 + - - +
72D ASN 3.8 1.2 - - - -
73D ASP* 1.3 96.8 + - - +
75D ASP* 1.3 63.5 + - - +
76D ILE 3.6 20.9 - - - -
112D PRO* 3.7 13.6 - - - +
137D ASP 3.9 5.8 - - - -
138D PHE* 3.8 0.6 - - - -
139D SER* 2.7 21.0 + - - -
175D ARG* 3.3 5.5 + - - -
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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