Contacts of the helix formed by residues 187 - 192 (chain C) in PDB entry 3G33
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 ALA 187 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C TYR 3.7 2.0 + - - -
186C ARG* 1.3 72.9 - - - +
188C PRO* 1.3 74.4 - - + +
189C GLU* 3.2 26.2 - - - +
190C VAL* 3.0 19.0 + - + +
191C LEU* 3.1 13.2 + - - +
200C VAL* 3.7 34.3 + - + +
203C TRP* 3.7 10.5 - - + -
204C SER* 5.1 0.4 + - - -
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Residues in contact with PRO 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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186C ARG 3.9 0.4 - - - -
187C ALA* 1.3 87.3 - - + +
189C GLU* 1.3 65.1 + - - +
191C LEU* 3.1 13.4 + - + +
192C LEU* 2.9 36.5 + - - +
203C TRP* 3.4 47.8 - - + +
228C LEU* 4.3 10.3 - - + -
231C ILE* 4.5 6.3 - - + -
232C PHE* 5.8 0.4 - - + -
283C PHE* 3.8 33.7 - - + -
288C ARG* 3.9 2.5 - - - +
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Residues in contact with GLU 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C ALA* 3.3 14.4 - - + +
188C PRO* 1.3 78.3 - - - +
190C VAL* 1.3 62.5 + - + +
192C LEU* 3.4 3.4 + - - +
193C GLN 3.1 3.1 + - - -
194C SER* 2.0 62.1 + - - +
195C THR 5.0 6.5 - - - +
196C TYR* 5.2 2.0 - - - -
197C ALA* 6.0 0.2 - - + -
200C VAL* 3.5 25.8 + - + +
244C PRO* 6.2 1.1 - - + -
283C PHE* 3.9 4.0 - - - +
285C PRO* 3.7 27.8 - - + +
288C ARG* 3.0 38.8 + - - -
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Residues in contact with VAL 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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144C ARG* 5.7 2.9 - - - +
186C ARG* 3.9 28.5 - - - +
187C ALA* 3.0 12.7 + - + +
189C GLU* 1.3 76.3 - - + +
191C LEU* 1.3 59.4 + - + +
193C GLN* 3.0 23.9 + - - +
196C TYR* 4.1 38.4 + - + +
200C VAL* 3.7 35.2 - - + -
224C GLU* 5.9 0.3 - - - -
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Residues in contact with LEU 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C LEU* 4.3 13.2 - - + -
186C ARG* 3.6 36.3 - - + +
187C ALA 3.1 13.8 + - - +
188C PRO* 3.1 9.2 + - + +
190C VAL* 1.3 78.1 - - + +
192C LEU* 1.3 60.2 + - - +
193C GLN* 3.2 4.6 + - - +
224C GLU* 3.5 38.2 - - + +
227C GLN* 3.5 30.7 - - + -
228C LEU* 3.6 32.9 - - + +
231C ILE* 4.2 4.3 - - + -
248C SER* 5.5 0.3 + - - -
249C LEU* 4.6 5.7 - - - +
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Residues in contact with LEU 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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188C PRO 2.9 20.6 + - - +
189C GLU* 4.3 3.4 - - - +
191C LEU* 1.3 75.8 - - - +
193C GLN* 1.3 68.9 + - - +
194C SER* 3.0 4.6 + - - +
228C LEU* 3.7 24.9 - - + -
232C PHE* 4.9 0.2 - - + -
243C TRP* 4.0 28.5 - - + +
244C PRO* 5.6 4.9 - - + -
247C VAL* 3.6 29.5 - - + +
248C SER* 4.6 10.4 + - - -
249C LEU* 3.5 39.7 - - + +
254C PHE* 5.4 2.0 - - + -
283C PHE* 4.2 24.0 - - + -
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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