Contacts of the helix formed by residues 56 - 67 (chain C) in PDB entry 2OVL
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 GLY 56 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52C THR* 4.0 4.7 - - - -
55C HIS* 1.3 72.7 - - - +
57C GLY* 1.3 63.2 + - - +
58C ALA 3.4 2.2 - - - -
59C ALA* 3.2 8.5 + - - +
60C VAL* 3.1 26.3 + - - +
99C HIS* 3.9 20.3 - - - -
67D ASP* 2.9 27.7 + - - -
91D LEU* 4.5 2.7 - - - -
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Residues in contact with GLY 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 4.0 6.1 - - - -
32C GLU* 2.8 33.7 + - - -
34C ILE* 3.8 12.2 - - - +
52C THR* 3.5 8.5 - - - -
55C HIS 3.2 1.2 + - - -
56C GLY* 1.3 76.7 - - - +
58C ALA* 1.3 62.3 + - - +
60C VAL* 3.2 4.9 + - - +
61C ALA* 3.1 22.3 + - - +
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Residues in contact with ALA 58 (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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11C LEU* 3.8 19.8 - - + +
32C GLU* 3.9 7.5 + - - +
56C GLY 3.4 0.6 - - - -
57C GLY* 1.3 75.3 - - - +
59C ALA* 1.3 57.0 + - - +
61C ALA* 3.3 3.9 + - - +
62C THR* 2.8 34.0 + - - +
62D THR* 3.7 20.0 - - + -
66D LYS* 4.7 16.2 - - + -
67D ASP* 5.7 2.2 + - - +
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Residues in contact with ALA 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C GLY* 3.2 15.6 + - - +
57C GLY 3.2 0.4 - - - -
58C ALA* 1.3 78.2 - - - +
60C VAL* 1.3 63.9 + - - +
62C THR* 3.0 7.1 + - - -
63C MSE 2.9 39.6 + - + +
99C HIS* 5.1 1.8 - - + -
59D ALA* 4.1 7.7 - - + +
62D THR* 3.9 11.3 - - + +
63D MSE 3.7 30.5 - - + -
67D ASP* 4.7 2.8 + - - +
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Residues in contact with VAL 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ILE* 4.2 11.2 - - + -
50C THR* 3.9 21.8 - - + -
52C THR* 4.2 14.6 - - + -
56C GLY 3.1 14.5 + - - +
57C GLY 3.2 6.5 + - - +
59C ALA* 1.3 75.9 - - - +
61C ALA* 1.3 63.8 + - - +
63C MSE 3.2 20.8 + - + +
64C VAL* 3.2 22.6 + - + +
99C HIS* 4.0 20.4 - - + +
102C SER* 4.3 5.4 - - - -
103C ALA* 3.9 26.5 - - - +
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Residues in contact with ALA 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C THR* 3.7 22.4 - - + +
10C ASP 5.3 0.4 - - - -
11C LEU* 4.4 19.5 - - + -
34C ILE* 4.1 12.1 - - + +
57C GLY 3.1 12.9 + - - +
58C ALA* 3.6 9.2 - - - +
60C VAL* 1.3 76.0 - - - +
62C THR* 1.3 58.1 + - - +
64C VAL* 3.2 2.4 + - - +
65C ASP* 3.0 32.2 + - - +
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Residues in contact with THR 62 (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 ALA* 2.8 22.8 + - - +
59C ALA* 3.0 10.7 + - - -
61C ALA* 1.3 77.0 - - - +
63C MSE 1.3 57.7 + - - +
65C ASP* 4.9 1.6 - - - -
66C LYS* 2.8 43.8 + - + +
67C ASP* 3.9 1.3 - - - +
58D ALA* 3.7 31.6 - - + +
59D ALA* 3.8 13.5 - - + +
62D THR* 3.9 10.9 + - - +
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Residues in contact with MSE 63 (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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59C ALA* 2.9 19.6 + - + +
60C VAL* 3.2 42.6 - - + +
61C ALA 3.3 0.2 - - - -
62C THR* 1.3 75.2 - - - +
64C VAL* 1.3 58.5 + - - +
67C ASP* 2.9 23.4 + - - +
68C LEU* 2.8 28.0 + - - +
91C LEU* 4.1 12.3 - - + -
99C HIS* 3.2 28.7 - - + +
100C ALA* 3.4 35.4 - - - -
103C ALA* 4.0 8.5 - - + -
59D ALA* 3.5 21.3 - - + -
63D MSE 5.8 1.8 - - - -
99D HIS* 5.0 8.7 - - + -
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Residues in contact with VAL 64 (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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7C VAL* 4.9 6.2 - - + +
9C THR* 3.1 23.3 - - + +
34C ILE* 4.9 2.7 - - + -
36C VAL* 4.2 31.2 - - + -
60C VAL* 3.2 17.4 + - + +
61C ALA* 3.2 7.4 + - - +
63C MSE 1.3 79.6 - - - +
65C ASP* 1.3 59.3 + - - +
68C LEU* 3.6 8.4 - - + +
69C ARG* 2.9 30.0 + - - +
72C LEU* 5.6 0.9 - - + -
103C ALA* 3.6 31.4 - - + +
106C ALA* 5.2 0.4 - - + -
107C VAL* 4.2 10.1 - - + -
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Residues in contact with ASP 65 (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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7C VAL* 6.1 0.7 - - - -
9C THR* 3.9 27.5 + - + +
61C ALA 3.0 14.2 + - - +
62C THR* 4.4 1.3 - - - +
64C VAL* 1.3 81.0 - - - +
66C LYS* 1.3 75.9 + - + +
69C ARG* 3.1 60.5 + - - +
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Residues in contact with LYS 66 (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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62C THR* 2.8 39.3 + - + +
65C ASP* 1.3 95.3 + - + +
67C ASP* 1.3 66.7 + - - +
69C ARG* 4.8 8.4 - - - +
70C GLY 5.3 1.0 + - - -
90C ARG* 5.6 0.2 + - - -
13D ARG* 5.5 3.5 + - - -
55D HIS* 5.0 3.6 - - - -
58D ALA* 5.3 7.9 - - + -
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Residues in contact with ASP 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C THR* 3.9 4.0 - - - +
63C MSE 2.9 34.7 + - - +
66C LYS* 1.3 85.1 - - - +
68C LEU* 1.3 60.2 + - - +
69C ARG 3.4 1.7 + - - -
70C GLY 3.8 1.1 + - - -
90C ARG* 2.8 36.3 + - - -
91C LEU* 3.8 20.2 - - + +
13D ARG* 4.7 5.4 + - - -
32D GLU* 5.3 0.2 - - - +
55D HIS* 3.3 16.6 - - + +
56D GLY* 2.9 37.5 + - - -
57D GLY 4.8 0.2 + - - -
58D ALA* 5.7 2.6 + - - +
59D ALA* 4.5 2.9 + - - +
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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