Contacts of the helix formed by residues 86 - 92 (chain A) in PDB entry 2C3O
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 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ILE* 3.6 8.7 - - + +
31A THR 4.2 13.5 - - - +
33A SER* 4.2 4.3 - - - +
85A THR* 1.3 85.7 + - - +
87A SER* 1.3 72.9 + - - +
88A GLN 3.3 0.2 + - - -
89A GLY* 2.7 16.8 + - - -
90A LEU* 2.9 7.7 + - - -
111A VAL* 4.6 1.8 - - - -
112A THR* 3.1 32.8 - - - +
114A ARG* 4.2 6.5 - - + -
129A ASP* 3.7 4.9 - - - -
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Residues in contact with SER 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE* 4.7 0.2 - - - -
86A ALA* 1.3 68.9 - - - +
88A GLN* 1.3 76.4 + - - +
90A LEU* 2.7 27.7 + - - +
91A LEU* 3.2 10.7 + - - +
114A ARG* 3.3 41.5 + - - +
115A ALA 2.5 21.5 + - - -
116A ILE* 3.9 7.3 - - - +
129A ASP* 2.8 27.8 + - - +
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Residues in contact with GLN 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE* 4.2 1.7 - - + +
87A SER* 1.3 89.2 + - - +
89A GLY* 1.3 60.6 + - - +
91A LEU* 3.5 31.3 + - - +
92A LEU* 3.5 11.6 + - - +
114A ARG* 4.6 8.9 + - - +
115A ALA 4.6 0.2 - - - +
116A ILE* 4.9 0.8 - - - +
117A ALA* 2.8 45.3 + - + +
121A LEU* 5.4 3.8 - - + +
868A LEU* 3.6 25.4 - - + +
870A GLU* 5.0 2.2 + - - +
2236A TPP 3.3 46.9 - - + +
95B PRO* 4.6 6.9 + - - +
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Residues in contact with GLY 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE* 3.5 4.2 - - - +
64A GLU* 3.1 51.1 - - - +
85A THR* 3.3 8.5 - - - -
86A ALA 2.7 16.9 + - - -
88A GLN* 1.3 72.3 - - - +
90A LEU* 1.3 60.8 + - - -
92A LEU 3.4 7.4 + - - -
93A MET* 3.5 7.4 - - - +
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A THR* 3.4 13.8 + - + -
86A ALA* 2.9 13.4 + - - +
87A SER 2.7 13.6 + - - +
89A GLY* 1.3 69.7 - - - -
91A LEU* 1.3 65.9 + - + +
93A MET* 3.1 12.8 + - + +
94A ILE* 3.5 11.6 + - + +
97A MET* 3.9 15.3 - - - -
109A PHE* 4.5 5.4 - - + -
111A VAL* 4.3 15.7 - - + -
129A ASP* 3.7 17.0 - - + +
130A ILE* 3.7 28.9 - - + +
133A ALA* 4.5 5.8 - - + -
168A MET* 3.5 35.4 - - + -
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Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A SER 3.2 10.7 + - - +
88A GLN* 3.6 30.5 - - - +
89A GLY 3.2 0.2 - - - -
90A LEU* 1.3 80.0 - - + +
92A LEU* 1.3 60.8 + - - +
93A MET 3.1 0.2 - - - -
94A ILE* 2.9 29.4 + - + +
95A PRO* 4.2 2.3 - - - +
116A ILE* 3.9 31.4 - - + -
129A ASP* 4.9 3.4 - - - +
132A ALA* 3.9 27.8 - - + -
91B LEU 5.0 5.9 - - - +
94B ILE* 4.5 8.7 - - + +
95B PRO* 4.1 31.1 - - + +
98B TYR* 4.2 11.7 - - + -
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A SER* 4.9 0.7 - - - -
64A GLU* 4.4 3.8 - - + +
65A ALA* 3.5 40.2 - - + +
68A ALA* 4.8 0.7 - - - +
88A GLN 3.5 11.2 + - - +
89A GLY 3.4 7.3 + - - +
90A LEU 3.2 0.6 - - - -
91A LEU* 1.3 75.8 - - - +
93A MET* 1.3 60.7 + - - +
94A ILE 3.5 0.2 - - - -
95A PRO* 4.1 9.0 - - - +
96A ASN* 5.6 1.2 + - - -
870A GLU* 4.0 20.0 - - + +
969A ILE* 4.4 13.0 - - + -
2236A TPP 3.6 22.2 - - + -
92B LEU* 5.8 10.5 - - + +
95B PRO* 3.7 29.4 - - + -
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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