Contacts of the helix formed by residues 188 - 196 (chain A) in PDB entry 3N7T
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
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Residue Dist Surf HB Arom Phob DC
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114A LEU* 5.2 0.2 - - - -
167A PHE 5.8 0.4 - - - -
169A THR* 3.5 41.1 + - + +
172A GLU* 4.9 3.4 - - + -
178A ILE* 4.1 11.9 - - + -
181A MET* 4.0 22.0 - - + -
186A LEU 4.2 0.4 + - - +
187A HIS* 1.3 77.1 - - - +
189A ILE* 1.3 65.7 + - - +
190A ALA* 3.7 0.9 + - - +
191A ASP* 3.2 34.3 + - - +
192A MET* 3.0 21.2 + - - +
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Residues in contact with ILE 189 (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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114A LEU* 3.9 11.6 - - + +
141A CYS 3.7 13.2 - - - +
142A HIS* 3.7 43.3 - - + +
144A PRO* 4.1 15.7 - - + -
145A ALA* 3.8 23.1 - - + +
164A VAL* 6.1 0.9 - - + -
165A THR 4.6 1.1 - - - +
166A GLY* 4.0 22.2 - - - -
167A PHE 3.7 17.7 + - - +
172A GLU* 5.4 1.9 + - - +
187A HIS 3.8 0.2 + - - -
188A THR* 1.3 72.3 - - - +
190A ALA* 1.3 57.0 + - - +
192A MET* 3.3 6.7 + - + +
193A ALA* 2.9 30.8 + - + +
200A TYR* 4.3 9.2 - - + -
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Residues in contact with ALA 190 (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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167A PHE 4.8 2.2 + - - +
169A THR* 4.2 17.0 + - - +
188A THR* 3.2 2.7 + - - +
189A ILE* 1.3 78.7 - - - +
191A ASP* 1.3 62.3 + - - +
193A ALA* 3.4 2.8 + - - +
194A GLN* 3.0 28.4 + - - +
200A TYR* 3.5 44.7 - - + +
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Residues in contact with ASP 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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187A HIS* 4.6 12.5 + - + +
188A THR* 3.2 30.5 + - - +
190A ALA* 1.3 78.0 - - - +
192A MET* 1.3 63.5 + - - +
194A GLN* 3.4 11.7 + - - +
195A THR* 3.0 30.6 + - - +
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Residues in contact with MET 192 (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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114A LEU* 4.0 15.0 - - + +
118A PRO* 3.8 24.7 - - + -
144A PRO 5.6 0.7 - - - +
145A ALA* 3.5 32.8 - - + +
148A PRO* 3.7 19.4 - - + +
186A LEU* 5.5 0.2 - - - -
187A HIS* 3.4 49.1 - - + +
188A THR 3.0 13.6 + - - +
189A ILE* 3.6 14.1 - - + +
191A ASP* 1.3 77.5 - - - +
193A ALA* 1.3 60.9 + - - +
195A THR* 3.4 6.2 + - - -
196A ALA* 3.1 23.6 + - - +
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Residues in contact with ALA 193 (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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148A PRO* 5.3 0.2 - - - -
159A ILE* 4.4 11.9 - - + -
164A VAL* 3.8 29.4 - - + -
189A ILE* 2.9 18.8 + - + +
190A ALA 3.7 4.7 - - - +
192A MET* 1.3 75.1 - - - +
194A GLN* 1.3 59.9 + - - +
196A ALA* 3.1 7.8 + - - -
198A ALA* 2.9 30.4 + - + +
200A TYR* 4.0 14.8 - - + +
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Residues in contact with GLN 194 (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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190A ALA 3.0 18.1 + - - +
191A ASP* 3.8 12.1 - - - +
193A ALA* 1.3 74.9 - - - +
195A THR* 1.3 60.0 + - - +
197A ASN* 2.9 24.4 + - - +
198A ALA 3.9 10.5 - - - +
200A TYR* 5.4 2.0 - - + +
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Residues in contact with THR 195 (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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191A ASP* 3.0 19.3 + - - +
192A MET* 3.8 6.9 - - - -
194A GLN* 1.3 76.7 - - - +
196A ALA* 1.3 56.8 + - - +
197A ASN* 3.1 11.5 + - - -
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Residues in contact with ALA 196 (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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148A PRO* 4.0 19.0 - - + +
157A SER* 4.0 12.0 + - - -
159A ILE* 4.0 23.3 - - + -
160A LYS* 3.6 17.0 + - - +
192A MET 3.1 16.1 + - - +
193A ALA 3.6 5.4 - - - +
194A GLN 3.1 1.0 - - - -
195A THR* 1.3 74.7 - - - +
197A ASN* 1.3 71.8 + - - +
198A ALA 3.2 0.9 + - - -
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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