Contacts of the helix formed by residues 188 - 192 (chain A) in PDB entry 3NPC
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 THR 188 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ARG 4.0 9.9 - - - +
151A ASP* 2.6 36.1 + - - +
153A LYS* 2.8 29.7 + - + +
185A TYR* 4.8 0.8 + - - -
187A VAL* 1.3 70.9 - - - +
189A ARG* 1.3 55.2 + - - +
190A TYR 3.2 0.2 - - - -
191A TYR* 2.8 32.6 + - + +
192A ARG* 3.4 39.8 + - + +
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Residues in contact with ARG 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A VAL* 3.3 27.9 - - + +
188A THR* 1.3 76.5 - - - +
190A TYR* 1.3 76.4 + - - +
191A TYR 3.0 1.7 + - - -
192A ARG* 3.2 27.2 + - - +
197A ILE* 5.5 0.2 - - - +
227A GLY 2.8 36.9 + - - -
228A THR* 3.2 21.1 + - - +
229A ASP* 3.8 22.1 - - - +
230A HIS* 4.4 20.9 + - + +
233A GLN* 3.4 30.0 + - + +
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Residues in contact with TYR 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A VAL* 4.0 23.1 - - + -
187A VAL* 3.6 25.3 - - + +
188A THR 3.0 1.4 + - - -
189A ARG* 1.3 89.9 + - - +
191A TYR* 1.3 71.4 + + + +
192A ARG 3.6 0.4 + - - -
209A TRP* 5.0 1.0 + - - -
213A CYS* 3.8 16.1 - - - +
223A VAL* 3.6 27.9 - - + +
225A PHE* 3.6 22.4 + - - +
226A GLN* 3.7 33.8 + - + +
227A GLY 3.4 21.4 + - - -
233A GLN* 3.5 19.0 + - - +
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Residues in contact with TYR 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ARG 6.2 0.2 - - - -
152A LEU 3.3 20.9 - - - +
153A LYS* 3.6 11.0 - - + -
154A PRO* 3.3 26.8 - - + +
186A VAL* 4.0 16.7 - - + +
187A VAL 3.5 25.6 - - - -
188A THR* 2.8 10.5 + - + +
190A TYR* 1.3 92.4 - - + +
192A ARG* 1.3 60.2 + - - +
193A ALA 3.6 0.2 + - - -
209A TRP* 3.6 8.1 - - - -
210A SER* 2.5 31.5 + - - +
213A CYS* 3.7 28.0 - - + -
214A ILE* 4.0 17.9 - - + -
217A GLU* 2.6 36.0 + - - -
223A VAL* 4.3 6.3 - - + +
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Residues in contact with ARG 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ARG* 3.2 46.6 + - - +
151A ASP* 4.2 9.5 + - - -
188A THR* 3.4 39.3 - - + +
189A ARG* 3.2 17.9 + - - +
190A TYR 3.6 0.9 - - - +
191A TYR* 1.3 77.6 - - - +
193A ALA* 1.3 69.6 + - - +
194A PRO 3.8 0.2 - - - -
196A VAL* 3.8 25.2 - - + +
197A ILE* 3.6 21.1 - - + +
209A TRP* 3.2 11.9 + - - -
230A HIS* 3.4 29.2 + - - +
233A GLN* 5.4 1.2 + - - -
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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