Contacts of the helix formed by residues 46 - 55 (chain C) in PDB entry 2OVI
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 LYS 46 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42C VAL* 4.0 18.8 - - + -
43C PRO* 3.4 21.5 - - + +
44C GLY 3.0 1.0 + - - -
45C ASP* 1.3 91.1 + - - +
47C PHE* 1.3 65.6 + - - +
48C ASP 3.3 1.8 - - - -
49C THR* 2.8 29.8 + - - +
50C VAL* 2.9 15.8 + - + +
107C ILE* 3.9 3.1 - - + -
160C LEU* 3.4 37.4 - - + +
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Residues in contact with PHE 47 (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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44C GLY 2.9 17.3 + - - +
45C ASP* 3.1 1.9 - - - -
46C LYS* 1.3 77.3 - - - +
48C ASP* 1.3 71.8 + - - +
50C VAL* 2.9 10.1 - - - +
51C TRP* 2.9 46.9 + + + +
82C HIS* 4.1 3.1 - - - -
87C PHE* 3.5 51.4 - + + -
99C ILE* 4.5 13.7 - - + -
101C ALA* 3.8 31.9 - - + +
104C CYS* 4.8 7.0 - - + -
107C ILE* 3.6 3.4 - - + +
124C PHE* 3.8 33.7 - + + -
133C LEU* 6.3 0.2 - - + -
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Residues in contact with ASP 48 (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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45C ASP 4.7 4.3 + - - +
46C LYS 3.3 0.8 - - - -
47C PHE* 1.3 87.2 - - - +
49C THR* 1.3 65.2 + - - +
51C TRP* 4.5 2.5 - - - -
52C ASP* 3.0 38.9 + - - +
82C HIS* 2.7 37.2 + - - -
87C PHE* 4.0 6.6 - - - -
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Residues in contact with THR 49 (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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45C ASP 5.5 0.2 + - - -
46C LYS* 2.8 29.1 + - + +
48C ASP* 1.3 78.9 - - - +
50C VAL* 1.3 60.0 + - - +
52C ASP* 4.0 1.4 - - - +
53C THR* 2.6 40.5 + - - +
156C LEU* 4.5 7.6 - - + -
159C SER* 6.3 1.3 - - - -
160C LEU* 4.5 16.2 - - + -
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Residues in contact with VAL 50 (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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46C LYS* 2.9 13.8 + - + +
47C PHE* 2.9 19.5 - - - +
49C THR* 1.3 75.0 - - - +
51C TRP* 1.3 63.0 + - - +
53C THR* 3.1 3.5 + - - -
54C VAL* 3.0 28.3 + - + +
107C ILE* 3.4 28.9 - - + -
109C LEU* 5.5 1.1 - - + -
122C ILE* 3.9 40.8 - - + -
124C PHE* 4.0 13.2 - - + -
156C LEU* 4.3 18.6 - - + -
160C LEU* 5.3 7.1 - - + +
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Residues in contact with TRP 51 (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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47C PHE* 2.9 47.2 + + + +
48C ASP* 4.1 3.8 - - - +
50C VAL* 1.3 73.7 - - - +
52C ASP* 1.3 70.0 + - - +
54C VAL* 3.0 13.8 + - - +
55C CYS* 3.1 29.1 + - - -
62C THR* 5.2 1.3 - - + -
77C LEU* 3.3 39.2 - - + +
78C PRO 2.7 20.9 + - - -
79C SER* 4.0 2.4 - - - +
87C PHE* 3.6 29.2 - + + -
89C LEU* 3.6 28.5 - - + -
95C MET* 5.3 0.4 - - + -
99C ILE* 4.6 7.0 - - + -
124C PHE* 4.0 18.8 - + - -
133C LEU* 3.7 30.7 - - + -
135C ILE* 4.4 2.2 - - + -
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Residues in contact with ASP 52 (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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48C ASP* 3.0 26.9 + - - +
49C THR* 4.2 1.8 - - - +
51C TRP* 1.3 86.0 - - - +
53C THR* 1.3 63.8 + - - +
55C CYS* 3.5 18.8 + - - +
56C GLU* 3.6 13.3 - - - +
79C SER* 5.6 4.0 - - - -
80C GLY 5.5 2.3 + - - +
87C PHE* 5.1 5.4 - - - -
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Residues in contact with THR 53 (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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49C THR* 2.6 33.6 + - - +
50C VAL 3.5 4.3 - - - -
52C ASP* 1.3 78.5 - - - +
54C VAL* 1.3 62.9 + - - +
56C GLU* 3.0 27.5 + - - +
57C TRP* 3.4 36.6 - - + +
152C ALA* 5.6 0.7 - - + +
156C LEU* 4.0 19.4 - - + +
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Residues in contact with VAL 54 (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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50C VAL* 3.0 17.8 + - + +
51C TRP 3.0 5.8 + - - +
53C THR* 1.3 71.7 - - - +
55C CYS* 1.3 58.4 + - - +
56C GLU 2.9 11.4 + - - -
57C TRP* 3.0 42.6 + - + +
58C GLY 4.4 4.3 + - - +
60C VAL* 4.4 9.0 - - + -
77C LEU* 3.8 27.4 + - + +
122C ILE* 3.7 29.2 - - + -
135C ILE* 4.3 23.6 - - + -
156C LEU* 4.7 1.3 - - + -
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Residues in contact with CYS 55 (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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51C TRP* 3.1 31.9 + - - -
52C ASP* 3.6 13.9 - - - +
53C THR 3.2 0.6 - - - -
54C VAL* 1.3 75.6 - - - +
56C GLU* 1.3 61.1 + - + +
58C GLY 4.9 2.2 + - - -
76C GLU* 4.9 10.6 - - - +
77C LEU* 3.3 33.3 + - - +
78C PRO 3.5 15.7 - - - -
79C SER* 3.7 16.2 - - - +
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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