Contacts of the helix formed by residues 72 - 82 (chain D) in PDB entry 3ER8
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 SER 72 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70D SER* 2.8 13.2 - - - -
71D ALA* 1.3 78.6 - - - +
73D GLU* 1.3 62.4 + - - +
75D LYS* 3.6 10.5 - - - +
76D ASP* 2.8 29.8 + - - +
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Residues in contact with GLU 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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68D ASN 4.5 0.7 - - - +
69D THR* 3.3 20.6 - - - +
70D SER* 3.0 34.6 + - - +
72D SER* 1.3 74.7 - - - +
74D ILE* 1.3 54.0 + - + +
75D LYS 2.7 15.4 + - - -
76D ASP* 4.2 4.3 - - - +
77D ARG* 2.7 74.3 + - - +
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Residues in contact with ILE 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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53D VAL* 3.6 7.6 - - - +
56D VAL* 3.5 33.0 - - + +
57D LYS* 3.6 23.1 - - + +
60D LYS* 4.7 11.2 - - + -
69D THR* 2.7 35.4 - - - +
70D SER 3.3 15.4 + - - +
71D ALA* 4.0 7.6 - - - -
73D GLU* 1.3 74.7 - - + +
75D LYS* 1.3 55.8 + - - +
78D ILE* 3.4 17.0 - - - +
223D PHE* 3.1 20.9 - - - +
224D ILE* 3.3 24.7 - - + +
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Residues in contact with LYS 75 (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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50D ASP* 5.9 6.6 + - - -
53D VAL* 3.3 27.7 - - + +
57D LYS* 3.8 9.0 - - - +
71D ALA 3.1 20.6 - - - +
72D SER* 3.6 10.3 - - - +
73D GLU 2.7 2.8 + - - -
74D ILE* 1.3 77.3 - - - +
76D ASP* 1.3 61.9 + - + +
78D ILE* 3.7 5.8 - - - +
79D LEU* 3.0 47.6 + - + +
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Residues in contact with ASP 76 (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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72D SER 2.8 19.0 + - - +
73D GLU* 4.0 4.0 - - - +
75D LYS* 1.3 76.6 - - + +
77D ARG* 1.3 70.0 + - - +
78D ILE 2.7 4.6 + - - -
79D LEU* 3.1 6.6 + - - +
80D SER* 2.7 37.2 + - - -
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Residues in contact with ARG 77 (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 THR* 4.2 1.4 - - - +
73D GLU* 2.7 69.1 + - - +
74D ILE* 3.7 5.1 - - - +
76D ASP* 1.3 72.2 - - - +
78D ILE* 1.3 66.8 + - - +
80D SER* 3.3 6.8 - - - -
81D TYR* 3.0 20.3 + - - +
222D LYS* 3.5 18.8 - - + +
223D PHE* 3.2 39.4 + - + +
224D ILE 4.0 1.2 + - - -
225D THR 3.2 18.5 + - - -
226D GLY* 2.9 24.4 - - - -
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Residues in contact with ILE 78 (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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49D LYS 4.8 4.5 - - - +
52D PHE* 3.9 7.2 - - + -
53D VAL* 3.7 31.0 - - + +
56D VAL* 3.4 31.9 - - + -
74D ILE 3.4 26.9 - - - +
75D LYS 3.7 8.0 - - - +
76D ASP 2.7 4.0 + - - -
77D ARG* 1.3 68.9 - - - +
79D LEU* 1.3 56.1 + - + +
80D SER 2.6 16.4 + - - -
81D TYR* 2.6 17.2 + - - -
82D PHE* 3.2 32.5 + - + -
223D PHE* 3.4 30.5 - - + -
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Residues in contact with LEU 79 (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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49D LYS* 3.3 33.4 - - + +
50D ASP* 5.3 5.2 - - - +
53D VAL* 4.2 6.3 - - + -
75D LYS* 3.0 50.5 - - + +
76D ASP* 3.1 8.5 + - - +
78D ILE* 1.3 77.7 - - - +
80D SER* 1.3 61.4 + - - +
82D PHE* 3.4 10.8 + - - +
83D SER* 3.3 24.3 + - - -
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Residues in contact with SER 80 (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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76D ASP* 2.7 33.6 + - - -
77D ARG* 3.3 9.2 - - - -
78D ILE 2.6 4.2 + - - -
79D LEU* 1.3 69.5 - - - +
81D TYR* 1.3 67.6 + - - +
83D SER* 3.5 2.4 + - - -
84D LYS* 3.4 19.1 + - - +
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Residues in contact with TYR 81 (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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77D ARG 3.0 10.9 + - - +
78D ILE 2.6 14.4 + - - +
80D SER* 1.3 70.3 - - - +
82D PHE* 1.3 59.9 - + + +
83D SER 2.5 14.9 + - - -
84D LYS* 2.8 51.6 + - + +
97D ILE* 4.0 19.6 - - + +
100D LEU* 3.5 27.0 - - - +
101D GLN* 3.6 32.9 - - + +
104D LEU* 5.3 0.7 - - + -
219D PHE* 3.3 33.8 - + - -
222D LYS* 4.7 7.4 - - - -
223D PHE* 4.3 11.0 - + + -
472D ILE* 3.3 30.8 + - + +
475D ASP* 6.1 0.3 - - - -
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Residues in contact with PHE 82 (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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21D TYR* 5.2 0.3 - - - -
44D ILE* 5.2 0.2 - - + -
47D PHE* 4.5 13.2 - + - -
49D LYS* 3.1 62.1 + - + +
52D PHE* 3.6 31.6 - + - -
78D ILE* 3.2 36.7 + - + -
79D LEU* 3.8 11.2 - - - +
80D SER 3.4 0.4 - - - -
81D TYR* 1.3 81.2 - + + +
83D SER* 1.3 57.0 + - - +
85D GLN* 3.3 14.9 + - - +
101D GLN* 3.5 19.1 - - + +
104D LEU* 3.6 22.4 - - + -
105D VAL* 5.0 3.6 - - + -
223D PHE* 4.0 13.5 - + - -
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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