Contacts of the helix formed by residues 91 - 100 (chain C) in PDB entry 2AXZ
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 LEU 91 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84C LYS* 3.6 19.7 - - - +
85C ILE* 3.3 29.7 - - + +
88C ASN* 2.9 38.0 + - + +
90C ASP* 1.3 86.2 - - + +
92C PHE* 1.3 64.2 + - - +
93C ASP* 3.7 2.0 - - - -
94C LYS* 4.3 3.9 + - - +
95C ASN* 3.6 20.4 + - - +
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Residues in contact with PHE 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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85C ILE* 3.6 21.6 - - + +
89C PRO* 3.0 17.9 + - + +
90C ASP 3.3 0.2 - - - -
91C LEU* 1.3 76.9 - - - +
93C ASP* 1.3 71.2 + - - +
95C ASN* 2.9 7.1 + - - +
96C PHE* 2.9 50.5 + + + -
116C TYR* 2.9 50.0 - + - -
119C ILE* 3.4 16.6 - - + -
120C ALA* 3.5 24.5 - - + -
123C TYR* 6.3 0.4 - + + -
125C ILE* 4.0 27.4 - - + -
127C VAL* 4.4 4.0 - - + -
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Residues in contact with ASP 93 (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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89C PRO 4.6 0.2 - - - +
90C ASP 2.6 29.8 - - - +
91C LEU* 3.8 0.7 - - - -
92C PHE* 1.3 81.4 + - - +
94C LYS* 1.3 80.0 + - - +
96C PHE* 3.4 2.7 + - - +
97C GLN* 3.1 36.4 + - - +
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Residues in contact with LYS 94 (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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91C LEU* 4.8 5.6 - - - +
92C PHE 3.0 1.6 + - - -
93C ASP* 1.3 90.1 - - - +
95C ASN* 1.3 64.7 + - + +
97C GLN* 2.7 38.2 + - - +
98C ARG* 3.3 28.7 + - - +
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Residues in contact with ASN 95 (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 GLU* 5.2 3.5 + - - +
81C LEU* 3.2 25.9 - - + +
85C ILE* 5.0 0.9 - - + -
91C LEU 3.6 16.0 + - - +
92C PHE 2.9 5.8 + - - +
94C LYS* 1.3 75.5 - - + +
96C PHE* 1.3 67.3 + - - +
98C ARG* 2.9 27.9 + - - +
99C ILE* 3.0 20.9 + - - +
116C TYR* 2.5 48.4 + - + -
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Residues in contact with PHE 96 (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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92C PHE* 2.9 46.3 + + + +
93C ASP* 3.8 3.6 - - - +
95C ASN* 1.3 66.4 - - - +
97C GLN* 1.3 61.4 + - + +
98C ARG 2.8 10.9 + - - -
99C ILE* 3.0 5.0 + - + +
100C GLU* 2.8 51.0 + - + +
113C TYR* 4.2 17.3 - + - -
116C TYR* 3.3 39.3 - + + -
117C ILE* 3.6 30.7 - - + -
127C VAL* 4.4 10.3 - - + -
129C THR* 4.5 15.9 - - + -
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Residues in contact with GLN 97 (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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93C ASP* 3.1 25.3 + - - +
94C LYS* 2.7 34.4 + - - +
95C ASN 3.3 0.2 - - - -
96C PHE* 1.3 78.6 - - + +
98C ARG* 1.3 56.9 + - - +
100C GLU* 2.9 23.3 - - - +
101C PRO* 3.3 10.0 - - - +
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Residues in contact with ARG 98 (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 GLU* 5.1 8.9 + - - -
94C LYS* 3.3 34.1 - - - +
95C ASN* 2.9 21.8 + - - +
96C PHE 2.8 1.8 + - - -
97C GLN* 1.3 80.3 - - + +
99C ILE* 1.3 64.3 + - + +
101C PRO* 3.1 18.0 - - - +
102C LYS* 3.8 33.8 - - - +
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Residues in contact with ILE 99 (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 GLU* 4.1 26.0 - - + +
95C ASN* 3.0 21.5 + - - +
96C PHE* 3.0 5.9 + - + +
98C ARG* 1.3 79.7 - - - +
100C GLU* 1.3 66.7 + - - +
101C PRO* 3.1 3.6 - - - -
102C LYS* 2.7 23.8 + - - +
103C ARG* 3.3 7.5 + - - -
109C TYR* 4.3 17.9 - - + +
112C ILE* 3.8 30.7 - - + -
113C TYR* 4.1 21.8 - - + +
116C TYR* 3.7 23.1 - - + -
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Residues in contact with GLU 100 (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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96C PHE* 2.8 43.0 + - + +
97C GLN* 2.9 30.1 - - - +
99C ILE* 1.3 73.3 - - - +
101C PRO* 1.3 90.9 - - + +
103C ARG* 3.1 42.8 + - - +
113C TYR* 4.7 12.6 - - + -
129C THR* 5.2 9.0 - - + +
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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