Contacts of the helix formed by residues 80 - 89 (chain E) in PDB entry 4XCS
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 80 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47C ASP* 5.4 6.6 + - - -
49C THR* 5.9 2.1 - - - +
79C ASP* 5.6 0.5 + - - -
83C SER* 4.9 3.1 + - - -
201D CPS 4.4 24.9 - - - -
78E VAL 3.8 0.8 + - - -
79E ASP* 1.3 79.3 - - - +
81E HIS* 1.3 60.0 + - - +
82E PHE* 3.3 21.7 + - - +
83E SER* 3.1 27.1 + - - -
84E HIS* 3.1 24.4 + - - -
106E SER* 3.6 3.6 - - - -
108E PRO* 4.3 11.9 - - - +
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Residues in contact with HIS 81 (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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169A HIS* 3.3 36.6 - + - -
201D CPS 4.1 18.8 + - + +
18E THR* 3.5 35.9 + - + +
20E VAL* 3.3 17.8 - - + +
26E PHE* 3.5 37.6 - + + -
80E SER* 1.3 70.7 - - - +
82E PHE* 1.3 81.2 + + - +
84E HIS* 4.4 1.8 - - - -
85E LEU* 2.9 26.9 + - - +
106E SER* 3.4 17.8 - - - +
108E PRO* 5.9 1.1 - - + -
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Residues in contact with PHE 82 (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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165A PHE* 4.0 12.8 - + - -
169A HIS* 3.3 31.6 - + - -
80C SER* 3.8 17.9 - - - +
82C PHE* 3.9 23.6 - - + -
83C SER* 3.6 34.8 - - - -
86C ALA* 4.0 11.4 - - + -
201D CPS 4.3 12.1 - - + -
26E PHE* 4.5 11.4 - + - -
80E SER* 3.4 14.4 - - - +
81E HIS* 1.3 101.3 - + - +
83E SER* 1.3 59.8 + - - +
85E LEU* 3.4 6.8 + - + +
86E ALA* 2.9 29.3 + - - +
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Residues in contact with SER 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ASP* 4.3 18.7 + - - +
78C VAL 5.3 4.5 + - - -
79C ASP* 5.4 4.7 + - - -
80C SER* 5.8 1.6 + - - +
110C ARG* 5.5 5.4 + - - -
47E ASP* 3.6 6.0 - - - +
48E PHE* 3.8 7.0 - - - -
79E ASP* 3.7 24.0 + - - -
80E SER* 3.1 18.5 + - - -
82E PHE* 1.3 75.7 - - - +
84E HIS* 1.3 69.4 + - - +
86E ALA* 3.2 8.3 + - - +
87E TRP* 2.9 24.1 + - - +
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Residues in contact with HIS 84 (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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20E VAL* 3.6 14.8 - - + -
44E TYR* 3.3 17.8 + + - -
47E ASP* 2.6 27.5 + - - -
76E ALA 5.0 0.2 - - - -
77E SER* 3.1 28.0 - - - -
79E ASP* 3.7 5.4 - - + -
80E SER 3.1 8.5 + - - -
81E HIS* 3.7 4.3 - - - +
83E SER* 1.3 78.3 - - - +
85E LEU* 1.3 63.0 + - - +
87E TRP* 3.1 3.9 + - - +
88E VAL* 2.9 27.4 + - - +
97E LEU* 6.0 0.2 - - - -
104E LEU* 3.3 40.3 + - + +
105E VAL 2.7 28.2 + - - -
106E SER* 3.7 16.1 - - - -
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Residues in contact with LEU 85 (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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69A LEU* 6.6 0.4 - - + -
20E VAL* 3.8 9.4 - - + +
24E GLY* 3.8 24.7 - - - +
26E PHE* 3.6 29.4 - - + -
81E HIS 2.9 18.4 + - - +
82E PHE* 3.8 5.4 - - + +
84E HIS* 1.3 76.6 - - - +
86E ALA* 1.3 66.3 + - - +
88E VAL* 3.1 17.6 + - + +
89E ASN* 2.9 44.6 + - - +
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Residues in contact with ALA 86 (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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80C SER* 4.8 8.5 - - - +
108C PRO* 4.0 26.7 - - + -
109C LYS* 4.8 2.4 + - - -
110C ARG* 5.6 0.4 - - - +
48E PHE* 3.8 8.5 - - + -
82E PHE 2.9 17.2 + - - +
83E SER* 3.2 8.3 + - - +
85E LEU* 1.3 79.6 - - - +
87E TRP* 1.4 59.0 + - - +
89E ASN* 3.5 6.5 + - - +
90E THR* 2.8 26.3 + - - -
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Residues in contact with TRP 87 (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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47E ASP* 3.5 21.3 - - + -
48E PHE* 3.2 74.4 - + + -
51E VAL* 3.5 33.7 - - + -
53E PRO* 3.7 28.5 - - + -
56E ILE* 4.0 4.0 - - + -
83E SER 2.9 11.9 + - - +
84E HIS 3.8 3.4 - - - +
86E ALA* 1.4 73.3 - - - +
88E VAL* 1.3 67.0 + - - +
90E THR* 3.2 9.9 + - - +
95E GLY 2.7 28.6 + - - -
96E GLY* 3.5 9.5 - - - -
97E LEU* 3.0 50.5 + - + -
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Residues in contact with VAL 88 (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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68A LYS* 5.6 1.5 - - - -
20E VAL* 4.8 11.9 - - + -
24E GLY* 5.6 5.2 - - - -
84E HIS 2.9 21.1 + - - +
85E LEU* 3.1 21.1 + - + +
87E TRP* 1.3 78.2 - - - +
89E ASN* 1.3 69.2 + - - +
90E THR 3.1 2.1 + - - +
97E LEU* 4.0 12.3 - - + -
98E GLY* 3.3 39.6 - - - +
99E PRO* 4.0 5.0 - - + +
100E MET* 3.9 24.2 - - + +
104E LEU* 4.2 9.2 - - + -
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Residues in contact with ASN 89 (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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68A LYS* 3.1 36.7 + - - +
109C LYS* 3.5 16.9 + - - +
85E LEU* 2.9 43.3 + - - +
86E ALA* 3.7 8.0 - - - +
88E VAL* 1.3 81.4 - - - +
90E THR* 1.3 57.7 + - - +
91E PRO* 3.6 8.0 - - - +
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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