Contacts of the helix formed by residues 187 - 193 (chain C) in PDB entry 1QD6
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 ASP 187 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185C ASN 4.0 1.4 - - - -
186C PRO* 1.3 79.6 - - + +
188C ILE* 1.3 64.1 + - - +
189C THR* 3.3 3.8 - - - -
190C LYS* 3.2 52.8 + - + +
191C TYR* 3.4 15.8 + - - -
252C TYR* 2.8 27.1 + - - -
253C ASN* 5.3 1.0 - - - +
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Residues in contact with ILE 188 (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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155C TRP* 3.6 56.5 - - + +
178C VAL* 5.4 0.7 - - + -
182C THR* 5.0 7.0 - - + -
185C ASN* 3.1 39.1 + - - +
186C PRO 3.4 2.5 - - - +
187C ASP* 1.3 77.2 + - - +
189C THR* 1.3 64.0 + - + +
191C TYR* 3.1 7.3 + - - +
192C MET* 2.9 38.9 + - + +
249C LEU* 4.1 15.7 - - + -
252C TYR* 3.7 25.4 - - + -
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Residues in contact with THR 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C TRP* 4.1 5.4 - - + -
178C VAL* 3.3 35.2 - - + -
186C PRO 5.1 3.1 + - - -
187C ASP* 4.8 2.3 - - - -
188C ILE* 1.3 74.8 + - + +
190C LYS* 1.3 56.2 + - - +
191C TYR 3.1 2.0 - - - -
192C MET* 4.6 1.1 - - - -
193C GLY* 2.9 27.7 + - - +
194C TYR* 3.8 32.8 + - + -
215C ASN* 2.8 26.9 + - - -
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Residues in contact with LYS 190 (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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187C ASP* 3.2 43.8 + - + +
189C THR* 1.3 81.2 + - - +
191C TYR* 1.3 75.4 + - + +
215C ASN* 3.8 9.3 - - - +
218C THR* 2.7 38.5 + - + -
220C TYR* 3.3 34.9 - - + +
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Residues in contact with TYR 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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187C ASP* 3.4 25.2 + - - -
188C ILE 3.1 4.5 + - - +
190C LYS* 1.3 111.2 + - + +
192C MET* 1.3 66.2 + - + +
193C GLY 3.5 0.4 - - - -
213C GLN* 5.2 1.0 - - - +
220C TYR* 3.7 43.9 + + - +
221C GLY* 4.0 12.6 + - - -
245C TYR* 3.5 37.6 - + + +
252C TYR* 3.0 34.1 - + + +
253C ASN* 3.4 27.0 + - + +
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Residues in contact with MET 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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143C ASP* 5.4 3.8 - - - +
155C TRP* 3.6 37.0 - - + +
157C ARG* 5.5 2.0 - - - +
176C TRP* 3.7 5.2 - - + -
188C ILE* 2.9 37.2 + - + +
191C TYR* 1.3 81.7 - - + +
193C GLY* 1.3 63.7 + - - +
194C TYR 3.8 0.3 + - - -
195C TYR 4.1 1.0 - - - +
213C GLN* 3.3 52.1 - - - +
214C TYR 5.3 1.3 - - - -
215C ASN* 5.2 0.4 - - - -
245C TYR 4.9 0.9 - - - +
246C GLY* 3.8 38.6 - - - +
248C SER 6.4 0.7 - - - -
249C LEU* 5.3 7.4 - - + -
252C TYR* 5.0 4.5 - - + -
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Residues in contact with GLY 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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176C TRP* 3.1 16.0 + - - -
189C THR* 2.9 27.6 + - - +
191C TYR 3.5 1.4 - - - -
192C MET* 1.3 82.3 - - - +
194C TYR* 1.3 69.9 + - - -
195C TYR 3.7 0.2 - - - -
214C TYR 4.8 2.5 - - - -
215C ASN* 3.9 26.3 - - - +
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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