Contacts of the helix formed by residues 88 - 95 (chain C) in PDB entry 2AXT
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 88 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C TRP* 3.6 27.4 - - + -
64C ALA 3.7 6.3 - - - +
67C MET* 3.5 37.2 - - + -
68C THR* 3.4 29.6 - - - +
71C GLU* 3.0 12.0 + - - +
87C ILE* 1.3 83.1 - - + +
89C ILE* 1.3 67.8 + - - +
90C PRO* 3.1 1.6 - - - -
91C HIS* 2.8 22.4 + - - +
92C ILE* 3.3 4.2 + - - +
492C CLA 4.4 7.6 - - + -
493C CLA 3.2 40.2 - - - +
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Residues in contact with ILE 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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68C THR* 4.5 11.4 - - + +
71C GLU* 2.7 48.8 + - + +
72C LEU* 3.5 23.3 - - + +
75C PHE* 4.0 18.6 - - + -
81C MET* 4.2 18.4 - - + -
86C LEU* 4.3 7.0 - - + -
88C LEU* 1.3 71.8 - - - +
90C PRO* 1.3 67.3 - - + +
92C ILE* 3.0 12.4 + - - +
93C ALA* 2.9 20.1 + - - +
111C PHE* 3.5 40.8 - - + -
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Residues in contact with PRO 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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81C MET* 4.3 12.1 - - + -
86C LEU* 3.6 26.9 - - + +
87C ILE* 3.3 16.2 - - - +
88C LEU 3.2 4.7 - - - +
89C ILE* 1.3 95.0 - - + +
91C HIS* 1.3 57.9 + - - +
93C ALA* 3.4 2.8 + - + +
94C THR* 3.0 30.7 + - - +
301C PHE* 4.1 25.4 - - + +
302C TYR* 3.8 28.3 - - + -
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Residues in contact with HIS 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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87C ILE 2.8 26.2 + - - -
88C LEU* 2.8 10.5 + - - +
90C PRO* 1.3 76.4 - - - +
92C ILE* 1.3 64.8 + - - +
94C THR* 2.6 24.1 + - - -
95C LEU* 3.5 11.4 + - - +
297C TYR* 4.6 3.8 - + - -
302C TYR* 3.0 27.2 + + - -
426C LEU* 5.0 2.7 - - + -
491C CLA 6.4 1.3 - + + -
492C CLA 2.8 60.3 + + + +
493C CLA 3.4 45.8 - + + +
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Residues in contact with ILE 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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68C THR* 4.2 11.7 - - + -
88C LEU 3.4 14.4 - - - +
89C ILE* 3.0 10.0 + - - +
91C HIS* 1.3 75.9 - - - +
93C ALA* 1.3 62.5 + - - +
95C LEU* 3.2 19.3 + - - +
97C TRP* 3.4 42.5 - - + +
110C PRO 4.8 1.1 - - - +
111C PHE* 3.8 25.1 - - + -
114C VAL* 3.9 39.0 - - + -
493C CLA 3.5 24.5 - - + +
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Residues in contact with ALA 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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81C MET* 4.6 5.2 - - + -
89C ILE 2.9 13.4 + - - +
90C PRO* 3.6 10.3 - - + +
92C ILE* 1.3 74.7 - - - +
94C THR* 1.3 55.8 + - - +
96C GLY* 2.7 28.9 + - - -
97C TRP 3.5 7.6 + - - -
99C VAL* 3.5 31.6 - - + +
111C PHE* 4.1 9.1 - - + -
186C TYR* 4.2 2.9 - - - +
301C PHE* 3.9 19.5 - - + -
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Residues in contact with THR 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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90C PRO 3.0 17.4 + - - +
91C HIS* 2.6 23.4 + - - -
93C ALA* 1.3 76.0 - - - +
95C LEU* 1.3 57.6 + - - +
185C LEU* 3.6 5.9 - - - +
186C TYR* 2.8 34.0 + - - +
296C VAL 4.6 7.9 + - - +
298C PRO* 3.2 39.0 - - + -
301C PHE* 3.7 4.0 - - + -
302C TYR* 4.2 8.7 - - + +
491C CLA 4.3 18.2 + - - +
493C CLA 4.7 2.1 + - - -
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Residues in contact with LEU 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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91C HIS 3.6 11.4 - - - +
92C ILE* 3.2 10.7 + - - +
93C ALA 3.0 1.0 + - - -
94C THR* 1.3 76.2 + - - +
96C GLY* 1.3 51.9 + - - +
97C TRP* 3.9 28.0 - - + -
175C LEU* 3.7 22.2 - - + -
178C LYS* 2.7 17.1 + - + -
184C GLY 2.6 25.2 - - - +
185C LEU* 3.1 15.9 - - + +
491C CLA 3.2 28.9 - - + +
492C CLA 4.5 13.7 - - + -
493C CLA 3.6 33.4 - - + +
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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