Contacts of the helix formed by residues 60 - 71 (chain E) in PDB entry 4S0H
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 GLU 60 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58E LEU 3.6 0.6 + - - -
59E HIS* 1.3 108.3 + - + +
61E ARG* 1.3 64.7 + - - +
62E GLU* 3.4 6.0 + - + -
63E LEU* 3.5 30.1 + - + +
64E TRP* 3.4 23.2 + - + +
85E PRO* 5.7 2.7 - - + +
86E SER 5.5 5.4 + - - +
88E LYS* 6.0 1.4 - - - +
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Residues in contact with ARG 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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58E LEU* 3.6 28.7 + - + +
59E HIS 3.4 0.8 - - - -
60E GLU* 1.3 75.2 - - - +
62E GLU* 1.3 66.5 + - - +
64E TRP* 3.2 7.7 + - - +
65E LEU* 3.0 48.1 + - + +
206E PHE* 5.9 0.9 - - - -
208E GLU* 3.4 28.0 + - + +
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Residues in contact with GLU 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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60E GLU* 5.2 4.0 - - + -
61E ARG* 1.3 78.9 - - - +
63E LEU* 1.3 65.9 + - + +
65E LEU* 3.4 12.8 + - - +
66E LYS* 3.0 34.7 + - + +
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Residues in contact with LEU 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E GLU* 3.5 34.9 + - + +
61E ARG 3.2 0.2 - - - -
62E GLU* 1.3 84.2 - - + +
64E TRP* 1.3 62.1 + - - +
66E LYS* 3.2 25.4 + - + +
67E PHE* 3.1 35.5 + - + -
84E PHE* 4.3 18.8 - - + -
85E PRO* 4.1 20.2 - - + -
225E LEU* 6.1 0.2 - - + -
229E ASN* 3.4 35.0 - - + +
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Residues in contact with TRP 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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58E LEU* 3.5 36.6 - - + +
59E HIS 4.1 3.0 + - - -
60E GLU* 3.4 22.0 + - + +
61E ARG 3.2 7.7 + - - +
63E LEU* 1.3 77.6 - - - +
65E LEU* 1.3 53.5 + - - +
67E PHE* 3.1 6.9 + - + +
68E HIS* 2.8 33.6 + - - +
72E THR* 4.7 9.6 - - + -
74E MET* 3.5 28.3 - - + -
83E MET* 4.6 8.7 - - + -
85E PRO* 3.1 53.6 - - + +
86E SER 3.8 14.6 + - - -
87E TYR* 4.4 8.1 - + - -
208E GLU* 3.8 16.9 - - + +
209E THR* 3.7 43.7 - - + -
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Residues in contact with LEU 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E ARG* 3.0 49.9 + - + +
62E GLU* 3.5 13.9 - - + +
64E TRP* 1.3 77.7 - - - +
66E LYS* 1.3 61.1 + - - +
68E HIS* 3.3 15.6 - - + +
69E GLU* 3.2 23.9 + - - +
208E GLU* 4.0 22.4 - - + -
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Residues in contact with LYS 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 GLU* 3.0 29.0 + - + +
63E LEU* 3.2 20.8 + - + +
65E LEU* 1.3 74.8 - - - +
67E PHE* 1.3 64.1 + - + +
69E GLU* 3.6 9.5 + - - +
70E VAL* 3.6 17.8 + - - +
225E LEU* 3.8 28.9 - - + +
229E ASN* 5.0 8.1 + - - +
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Residues in contact with PHE 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 LEU* 3.1 44.7 + - + -
64E TRP* 3.1 9.7 + - + +
66E LYS* 1.3 76.4 - - + +
68E HIS* 1.3 66.6 + - - +
70E VAL 3.4 1.2 + - - -
71E GLY 3.1 15.8 + - - -
72E THR* 3.1 31.4 + - + +
84E PHE* 4.0 14.6 - + - -
85E PRO* 3.7 24.0 - - + -
222E ILE* 3.9 19.9 - - + +
225E LEU* 3.5 38.6 - - + -
226E LYS* 3.4 36.6 - - + -
229E ASN* 4.7 0.2 - - - -
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Residues in contact with HIS 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 TRP 2.8 13.3 + - - +
65E LEU* 3.3 23.8 - - + +
66E LYS 3.2 0.2 - - - -
67E PHE* 1.3 76.4 - - - +
69E GLU* 1.3 68.9 + - + +
71E GLY* 2.9 16.3 + - - -
72E THR* 3.4 11.0 + - - -
178E LYS* 5.7 4.5 - - - -
207E PRO* 3.5 26.0 + - - +
208E GLU* 3.8 24.0 + - + +
210E ALA* 4.6 10.4 + - + -
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Residues in contact with GLU 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 LEU 3.2 12.2 + - - +
66E LYS* 3.6 4.4 + - - +
67E PHE 3.3 0.2 - - - -
68E HIS* 1.3 84.2 - - + +
70E VAL* 1.3 63.0 + - + +
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Residues in contact with VAL 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 LYS 3.6 13.4 + - - +
67E PHE 3.4 6.4 + - - +
68E HIS 3.2 0.6 - - - -
69E GLU* 1.3 80.5 - - + +
71E GLY* 1.3 56.4 + - - +
121E TRP* 5.5 2.9 - - - -
219E ASN* 3.4 31.2 + - - +
221E LYS* 3.9 36.3 - - + +
222E ILE* 3.6 24.2 - - + +
225E LEU* 3.9 14.1 - - + -
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Residues in contact with GLY 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 PHE 3.1 3.0 + - - -
68E HIS 2.9 13.2 + - - -
70E VAL* 1.3 77.6 - - - +
72E THR* 1.3 65.6 + - - +
73E GLU* 3.3 21.0 - - - +
121E TRP* 4.3 13.6 + - - -
212E ILE* 5.5 4.5 - - - -
219E ASN* 5.4 0.2 - - - +
222E ILE* 3.6 7.2 - - - +
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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