Contacts of the helix formed by residues 82 - 92 (chain C) in PDB entry 1OVM
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 82 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52C GLU* 3.9 19.3 - - + +
53C LEU* 4.4 0.4 - - - +
56C SER* 4.0 4.7 - - - -
71C LEU* 3.9 27.8 - - + -
73C THR* 4.5 0.9 - - + -
78C GLY 3.4 7.8 + - - +
79C GLU 3.0 10.1 + - - +
81C SER* 1.3 79.6 - - - +
83C MET* 1.3 63.6 + - - +
84C ASN 3.3 2.7 - - - -
85C GLY* 2.9 15.1 + - - -
86C ILE* 3.1 14.1 + - + +
98C HIS* 4.2 7.4 - - + -
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Residues in contact with MET 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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79C GLU* 3.3 9.9 + - + +
80C LEU* 3.2 46.5 + - + +
81C SER 3.5 0.2 - - - -
82C ALA* 1.3 76.2 - - - +
84C ASN* 1.3 58.6 + - - +
85C GLY 3.1 0.3 + - - -
86C ILE* 3.2 6.9 + - + +
87C ALA* 2.9 30.1 + - - +
98C HIS* 6.1 2.5 - - + +
126C PHE 4.9 1.8 - - - +
129C MET* 4.1 5.8 - - - +
130C SER* 3.3 38.1 - - - +
133C ILE* 3.6 17.7 - - + +
164C TYR* 5.9 0.2 - - + -
80D LEU* 4.1 15.9 - - + +
83D MET* 4.3 14.4 - - + +
129D MET* 3.6 26.0 - - - -
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Residues in contact with ASN 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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53C LEU* 4.1 8.9 - - + +
57C TYR* 3.2 10.4 + - - -
81C SER 5.0 1.0 + - - +
82C ALA 3.3 0.6 - - - -
83C MET* 1.3 78.8 - - - +
85C GLY* 1.3 62.2 + - - +
87C ALA* 3.7 1.3 - - - +
88C GLY* 3.1 15.9 + - - -
407C TRP* 2.8 46.3 + - - +
409C SER* 2.9 23.4 + - - -
77D VAL* 3.6 13.2 - - - +
80D LEU* 3.9 9.3 + - - +
81D SER* 3.0 37.8 + - - +
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Residues in contact with GLY 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C LEU* 4.0 2.8 - - - +
56C SER* 3.2 28.7 + - - +
57C TYR* 4.2 17.3 - - - -
60C ASP* 4.6 1.9 - - - +
82C ALA 2.9 6.1 + - - -
84C ASN* 1.3 76.6 - - - +
86C ILE* 1.3 66.6 + - - +
88C GLY* 3.1 3.5 + - - -
89C SER* 2.9 26.0 + - - -
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Residues in contact with ILE 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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56C SER* 4.8 2.5 - - - -
71C LEU* 4.1 15.5 - - + -
82C ALA 3.1 15.3 + - - +
83C MET* 3.7 7.0 - - + +
85C GLY* 1.3 76.1 - - - +
87C ALA* 1.3 58.4 + - - +
89C SER* 3.0 6.6 + - - +
90C TYR* 2.8 27.5 + - - +
96C VAL* 4.2 22.4 - - + +
98C HIS* 3.8 39.7 - - + +
130C SER* 5.1 3.4 - - - +
133C ILE* 3.5 33.4 - - + +
134C THR* 4.2 7.9 - - + -
162C PRO* 3.7 11.2 - - + +
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Residues in contact with ALA 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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83C MET 2.9 17.5 + - - +
84C ASN 3.7 2.0 - - - +
86C ILE* 1.3 78.4 - - - +
88C GLY* 1.3 57.1 + - - +
90C TYR* 3.2 2.8 + - - +
91C ALA* 2.8 29.1 + - - +
133C ILE* 3.9 22.9 - - + +
407C TRP* 3.7 18.4 - - + -
80D LEU* 3.5 26.2 - - + -
118D LEU* 4.3 5.0 - - + +
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Residues in contact with GLY 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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60C ASP* 4.3 3.4 - - - -
84C ASN 3.1 9.2 + - - -
85C GLY* 3.1 3.6 + - - -
87C ALA* 1.3 78.8 - - - +
89C SER* 1.3 63.0 + - - +
91C ALA* 3.2 0.9 + - - +
92C GLU* 2.9 30.7 + - - +
404C GLN* 4.1 8.1 - - - -
407C TRP* 3.3 31.6 - - - +
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Residues in contact with SER 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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56C SER 4.8 1.2 + - - -
60C ASP* 2.9 26.6 + - - +
85C GLY 2.9 13.5 + - - -
86C ILE* 3.0 11.7 + - - +
88C GLY* 1.3 76.1 - - - +
90C TYR* 1.3 56.6 + - - +
92C GLU 3.6 0.2 - - - -
93C HIS* 3.0 9.7 + - - -
94C VAL* 2.7 39.7 + - - +
96C VAL* 3.7 17.1 - - - +
162C PRO* 3.4 16.6 - - - -
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Residues in contact with TYR 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 ILE 2.8 7.6 + - - +
87C ALA 3.5 7.4 - - - +
89C SER* 1.3 77.4 - - - +
91C ALA* 1.3 63.9 + - - +
92C GLU 3.4 0.2 + - - -
93C HIS 3.4 4.5 + - - -
132C PRO 3.7 14.9 + - - -
133C ILE* 3.2 35.7 - - - +
134C THR* 3.5 26.0 - - - -
135C VAL* 4.0 5.4 - - + +
161C ARG* 2.8 73.1 + - - +
162C PRO* 3.4 14.5 - - + +
118D LEU* 3.7 28.7 - - + -
120D ASP* 5.7 2.8 + - + -
125D HIS* 6.2 0.4 - + - -
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Residues in contact with ALA 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 ALA 2.8 17.4 + - - +
88C GLY 3.2 4.7 + - - +
90C TYR* 1.3 81.3 - - - +
92C GLU* 1.3 59.3 + - + +
93C HIS* 3.8 9.4 + - - -
218C PHE* 4.8 1.7 - - - -
406C LEU* 3.4 22.0 - - + +
407C TRP* 4.0 20.9 - - + -
117D THR 3.9 22.2 - - - +
118D LEU* 4.0 17.8 - - - +
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Residues in contact with GLU 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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64C ARG* 2.9 32.2 + - - +
88C GLY 2.9 17.7 + - - +
91C ALA* 1.3 82.0 - - + +
93C HIS* 1.3 59.6 + - - +
94C VAL* 3.6 3.6 - - + -
218C PHE* 3.4 10.6 - - - -
222C ARG* 2.7 37.3 + - - +
245C MET* 3.5 14.8 - - + +
403C VAL 3.6 3.6 - - - +
404C GLN* 3.2 28.0 - - + +
406C LEU* 2.8 34.2 + - + +
407C TRP* 3.0 9.3 + - + +
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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