Contacts of the helix formed by residues 115 - 121 (chain C) in PDB entry 2OQH
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 SER 115 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114C GLN* 1.3 77.5 + - - +
116C VAL* 1.3 63.6 + - - +
117C THR* 3.5 11.3 + - - -
118C ASP* 3.0 38.2 + - - +
119C LEU* 3.2 10.4 + - - +
348C PRO 5.3 4.3 - - - -
349C SER* 4.3 10.5 - - - -
350C GLY 3.4 24.9 - - - -
351C PRO* 4.1 1.4 - - - +
352C GLY 3.6 2.5 - - - -
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Residues in contact with VAL 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C TRP* 3.8 39.3 - - + +
114C GLN 3.7 0.8 + - - -
115C SER* 1.3 71.2 - - - +
117C THR* 1.3 62.9 + - - +
119C LEU* 2.9 19.4 + - - +
120C LEU* 3.1 32.9 + - + +
277C ILE* 4.5 8.1 - - + -
311C ALA* 4.1 13.9 - - + -
352C GLY* 2.9 38.8 + - - +
353C LEU* 3.6 18.2 - - + +
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Residues in contact with THR 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C SER* 3.0 11.4 + - - -
116C VAL* 1.3 78.6 - - - +
118C ASP* 1.3 58.5 + - - +
120C LEU* 3.1 15.9 + - - +
122C GLY 3.0 19.9 + - - +
123C ALA* 3.8 22.7 - - + +
311C ALA* 3.4 29.5 - - - +
314C SER* 3.7 24.0 - - - +
315C SER* 3.9 4.3 - - - -
347C VAL* 3.6 16.6 - - + +
348C PRO 5.0 1.4 + - - -
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Residues in contact with ASP 118 (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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114C GLN* 4.3 18.7 - - + +
115C SER* 3.0 29.4 + - - +
117C THR* 1.3 73.9 - - - +
119C LEU* 1.3 62.2 + - + +
120C LEU 3.1 5.3 + - - -
121C GLY* 3.7 6.9 + - - -
122C GLY* 3.6 21.2 + - - +
123C ALA* 4.4 2.8 + - - +
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Residues in contact with LEU 119 (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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73C PHE* 6.4 0.4 - - + -
105C TRP* 3.7 28.2 - - + +
108C MSE 4.1 21.3 - - + -
109C GLY* 3.9 32.8 - - - +
112C THR* 4.0 14.6 - - + +
114C GLN* 4.1 19.3 - - + -
115C SER 3.2 10.0 + - - +
116C VAL* 2.9 11.8 + - - +
118C ASP* 1.3 78.9 - - - +
120C LEU* 1.3 59.7 + - - +
121C GLY 3.5 1.3 + - - -
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Residues in contact with LEU 120 (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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105C TRP* 3.6 28.9 - - + -
116C VAL* 3.2 31.4 - - + +
117C THR 3.1 3.1 + - - +
118C ASP 3.1 0.8 - - - -
119C LEU* 1.3 80.3 - - - +
121C GLY* 1.3 55.8 + - - +
122C GLY 3.6 1.6 - - - -
277C ILE* 3.5 32.8 - - + -
278C ALA* 5.9 0.2 - - - -
281C LYS* 3.1 40.9 + - + +
311C ALA* 4.0 24.9 - - + +
312C VAL* 4.3 6.7 - - + +
315C SER* 3.5 14.8 + - - +
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Residues in contact with GLY 121 (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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118C ASP 3.7 4.6 + - - -
119C LEU 3.5 2.6 - - - -
120C LEU* 1.3 79.4 - - - +
122C GLY* 1.3 65.2 + - - +
124C VAL* 5.8 1.6 - - - +
315C SER* 4.6 2.2 - - - -
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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