Contacts of the helix formed by residues 81 - 92 (chain C) in PDB entry 2AG1
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 ALA 81 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50C GLU* 4.5 5.4 - - + +
54C GLY* 5.7 0.7 - - - -
72C VAL* 4.3 22.4 - - + -
77C GLY 3.5 9.9 + - - +
78C PHE* 2.7 18.0 + - + +
80C ASN* 1.3 73.1 - - - +
82C VAL* 1.3 65.3 + - - +
83C THR 3.3 2.0 - - - -
84C PRO* 3.1 18.6 - - - +
85C ILE* 3.2 20.3 + - + +
97C PHE* 4.6 17.5 - - + -
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Residues in contact with VAL 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C PHE* 3.9 36.6 - - + +
79C THR* 3.3 22.3 + - + +
80C ASN 3.3 0.4 - - - -
81C ALA* 1.3 76.8 - - - +
83C THR* 1.3 65.1 + - - +
85C ILE* 3.1 9.7 + - + +
86C ALA* 2.9 24.1 + - + +
121C MSE 5.4 9.0 - - + +
122C ALA* 6.2 0.2 - - - -
125C ILE* 4.2 16.4 - - + -
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Residues in contact with THR 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C ALA* 5.3 4.5 - - - -
55C HIS* 3.9 16.8 - - + +
79C THR 5.0 0.2 + - - -
80C ASN 4.6 1.7 + - - -
82C VAL* 1.3 80.3 - - - +
84C PRO* 1.3 66.2 - - - +
86C ALA* 3.3 5.9 + - + +
87C ASN* 2.9 30.4 + - + +
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Residues in contact with PRO 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C ALA* 3.2 37.2 - - - +
54C GLY* 3.6 28.0 - - - -
55C HIS* 3.4 14.1 - - + +
58C GLU* 3.4 15.1 - - - +
80C ASN 4.2 0.7 - - - +
81C ALA* 3.1 15.7 - - - +
83C THR* 1.3 90.9 - - - +
85C ILE* 1.3 65.9 + - - +
87C ASN* 3.3 0.4 + - + -
88C ALA* 2.9 25.8 + - - +
97C PHE* 3.7 7.2 - - + -
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Residues in contact with ILE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C PHE* 4.0 28.3 - - + -
81C ALA* 3.2 16.8 + - + +
82C VAL* 3.1 13.9 + - + +
84C PRO* 1.3 76.6 - - - +
86C ALA* 1.3 58.2 + - - +
88C ALA* 3.4 0.3 + - - +
89C TRP* 2.9 27.5 + - - +
97C PHE* 3.7 30.5 - - + -
122C ALA* 4.6 5.6 - - + -
125C ILE* 3.4 30.5 - - + +
126C THR* 3.6 17.7 - - + -
156C PRO* 3.5 8.0 - - + +
158C LEU* 4.1 16.4 - - + -
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Residues in contact with ALA 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C VAL* 2.9 17.5 + - + +
83C THR* 3.8 6.1 - - + +
85C ILE* 1.3 76.4 - - - +
87C ASN* 1.3 64.1 + - - +
89C TRP* 3.3 8.3 + - - +
90C LEU* 3.0 32.4 + - + +
125C ILE* 3.8 24.0 - - + +
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Residues in contact with ASN 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C HIS* 4.5 8.8 + - + -
58C GLU* 3.0 23.0 - - - +
62C ARG* 4.6 6.4 + - - -
83C THR* 2.9 20.9 + - + +
84C PRO* 3.7 2.2 - - + +
86C ALA* 1.3 75.4 - - - +
88C ALA* 1.3 58.8 + - - +
90C LEU* 3.1 8.0 + - - +
91C ASP* 2.8 49.2 + - - +
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Residues in contact with ALA 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C GLU* 3.3 18.9 + - + +
84C PRO 2.9 17.9 + - - +
85C ILE 3.7 3.4 - - - +
87C ASN* 1.3 74.9 - - - +
89C TRP* 1.3 57.1 + - - +
92C ARG* 2.9 26.3 + - - -
93C THR* 3.0 38.1 + - + +
95C VAL* 4.5 4.9 - - + -
97C PHE* 4.5 1.6 - - + -
156C PRO* 3.6 17.4 - - + +
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Residues in contact with TRP 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C ILE 2.9 7.8 + - - +
86C ALA 3.4 9.4 - - - +
88C ALA* 1.3 78.4 - - - +
90C LEU* 1.3 91.0 + - + +
92C ARG* 3.5 11.8 + - - +
124C PRO 3.8 19.1 + - - -
125C ILE* 3.2 50.6 - - + +
126C THR* 3.5 25.6 - - - -
127C LYS* 3.9 15.3 - - + -
154C ARG 5.4 0.2 - - - +
155C GLY* 5.7 0.7 - - - -
156C PRO* 3.5 14.4 - - + +
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Residues in contact with LEU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ALA* 3.0 20.6 + - + +
87C ASN* 3.9 8.1 - - - +
89C TRP* 1.3 101.8 - - + +
91C ASP* 1.3 66.4 + - - +
92C ARG* 3.6 6.6 + - - -
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Residues in contact with ASP 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C GLU* 4.5 0.3 - - - +
62C ARG* 4.0 21.4 + - - -
87C ASN* 2.8 37.2 + - - +
89C TRP 3.2 0.2 - - - -
90C LEU* 1.3 82.2 - - - +
92C ARG* 1.3 69.9 + - - +
93C THR* 3.1 21.3 - - + +
213C SER* 3.7 9.0 + - - -
217C ARG* 2.9 14.9 + - - +
240C GLU* 5.2 5.0 - - - +
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Residues in contact with ARG 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ALA 2.9 6.2 + - - -
89C TRP 3.5 6.8 + - - +
90C LEU 3.3 8.4 - - - -
91C ASP* 1.3 79.3 - - - +
93C THR* 1.3 57.2 - - - +
153C PRO* 3.5 32.9 - - + +
154C ARG* 3.0 34.5 - - - +
155C GLY* 4.5 0.2 - - - -
213C SER* 3.7 16.9 + - - +
214C GLU* 3.9 24.7 - - - +
217C ARG* 2.8 20.3 + - - +
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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