Contacts of the helix formed by residues 190 - 195 (chain C) in PDB entry 3OQN
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 GLU 190 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76C TYR* 5.5 1.0 + - - -
101C GLN* 4.0 27.7 - - - +
126C GLY* 3.7 18.2 - - - +
127C ASN* 5.3 2.0 - - + -
187C PRO* 2.7 33.5 + - + +
188C MET 3.4 2.8 - - - +
189C ALA* 1.3 77.7 - - + +
191C PRO* 1.3 63.0 - - - +
192C ILE* 2.8 27.0 + - + +
193C ASN* 2.9 16.4 + - - +
194C ARG 3.4 9.4 + - - -
222C TYR* 2.8 31.6 + - - -
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Residues in contact with PRO 191 (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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126C GLY 3.4 14.1 - - - +
127C ASN* 3.1 29.6 - - - +
128C ILE 5.4 4.3 - - - +
149C VAL* 3.9 26.8 - - + +
151C GLU* 4.3 21.3 - - + +
189C ALA 3.5 3.6 - - - +
190C GLU* 1.3 79.2 - - - +
192C ILE* 1.3 58.3 + - - +
193C ASN 3.3 0.2 - - - -
194C ARG* 5.3 2.5 - - + -
195C SER* 3.3 31.1 + - - +
196C LYS 3.7 1.9 + - - -
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Residues in contact with ILE 192 (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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126C GLY* 5.0 5.8 + - - +
147C ALA 5.1 5.6 - - - +
149C VAL* 3.4 27.9 - - + +
162C TYR* 3.8 44.4 - - + -
190C GLU* 2.8 27.9 + - + +
191C PRO* 1.3 78.0 - - - +
193C ASN* 1.3 67.4 + - - +
196C LYS* 3.6 2.7 - - - +
197C LYS* 3.1 39.3 + - + +
222C TYR* 4.6 2.2 - - - +
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Residues in contact with ASN 193 (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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185C SER* 4.6 1.0 - - - -
186C GLY* 2.8 43.4 - - - +
187C PRO 3.1 13.4 - - - +
188C MET* 3.9 17.5 - - + +
190C GLU* 2.9 8.6 + - - +
192C ILE* 1.3 84.7 - - - +
194C ARG* 1.3 60.6 + - - +
195C SER 3.4 0.3 + - - -
197C LYS* 3.5 29.6 + - - +
198C LEU* 2.8 33.3 + - - +
222C TYR* 3.4 19.5 + - - -
247C ALA* 4.8 0.4 - - - +
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Residues in contact with ARG 194 (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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188C MET* 3.3 43.9 - - - +
190C GLU 3.4 5.3 + - - +
191C PRO* 5.3 1.3 - - + -
193C ASN* 1.3 80.0 - - - +
195C SER* 1.3 67.6 + - - +
198C LEU* 3.6 13.3 - - + +
199C GLN* 3.5 19.2 - - - +
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Residues in contact with SER 195 (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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151C GLU* 3.5 22.9 + - - -
163C GLU* 4.8 1.0 - - - +
191C PRO* 3.3 20.4 + - - +
193C ASN 3.3 0.4 - - - -
194C ARG* 1.3 89.9 + - - +
196C LYS* 1.3 75.6 + - - +
199C GLN* 3.0 24.2 - - - +
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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