Contacts of the helix formed by residues 195 - 208 (chain A) in PDB entry 3NIA
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 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A ASP* 3.0 40.0 + - + +
194A LEU* 1.3 72.1 - - - +
196A SER* 1.3 56.2 + - - +
197A THR* 3.7 8.0 + - - -
198A SER* 3.1 14.9 + - - -
199A THR* 2.7 34.1 + - - -
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Residues in contact with SER 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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194A LEU 3.8 0.6 + - - -
195A THR* 1.3 73.0 - - - +
197A THR* 1.3 62.5 + - - +
199A THR* 3.6 7.1 - - - -
200A HIS* 2.9 32.1 + - - +
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Residues in contact with THR 197 (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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195A THR* 3.1 7.8 + - - -
196A SER* 1.3 81.8 + - - +
198A SER* 1.3 64.2 + - - +
200A HIS* 3.3 6.2 + - - +
201A THR* 3.0 33.3 + - - +
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Residues in contact with SER 198 (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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75A PHE* 3.4 40.2 + - - -
78A ILE* 5.2 2.6 - - - +
79A ASP* 2.7 28.5 + - - -
194A LEU* 4.1 7.2 - - - +
195A THR* 3.1 12.4 + - - -
197A THR* 1.3 76.7 - - - +
199A THR* 1.3 66.8 + - - +
201A THR* 3.3 5.3 + - - -
202A ILE* 3.1 24.4 + - - +
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Residues in contact with THR 199 (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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188A VAL 4.1 4.6 + - - +
189A LEU* 3.5 36.1 - - + +
194A LEU* 3.4 22.4 + - - +
195A THR 2.7 24.9 + - - -
196A SER* 3.6 7.9 - - - -
198A SER* 1.3 77.7 - - - +
200A HIS* 1.3 62.6 + - - +
202A ILE* 3.0 10.7 - - - +
203A GLU* 2.9 37.5 + - - +
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Residues in contact with HIS 200 (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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196A SER 2.9 19.1 + - - +
197A THR* 3.3 6.0 + - - +
199A THR* 1.3 74.4 - - - +
201A THR* 1.3 66.3 + - - +
203A GLU* 3.3 15.1 + - - +
204A ARG* 2.9 59.4 + - + +
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Residues in contact with THR 201 (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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75A PHE* 3.7 29.2 - - + -
115A LEU* 5.7 0.9 - - + -
197A THR* 3.0 23.3 + - - +
198A SER* 3.7 5.8 - - - -
199A THR 3.2 0.2 - - - -
200A HIS* 1.3 79.8 - - - +
202A ILE* 1.3 60.5 + - - +
204A ARG* 3.4 4.7 + - - +
205A TRP* 3.1 45.8 + - + +
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Residues in contact with ILE 202 (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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68A PHE* 3.5 45.1 - - + +
71A ALA* 3.8 21.1 - - + -
72A ALA* 3.9 14.4 - - + +
75A PHE* 4.7 8.0 - - + -
122A VAL* 5.3 3.1 - - + -
188A VAL* 4.7 1.3 - - + -
189A LEU* 3.9 18.8 - - + -
194A LEU* 4.6 7.2 - - + -
198A SER 3.1 15.4 + - - +
199A THR* 3.0 22.9 - - - +
201A THR* 1.3 74.6 - - - +
203A GLU* 1.3 61.5 + - - +
205A TRP* 3.2 14.8 + - + +
206A LEU* 2.9 36.3 + - + +
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Residues in contact with GLU 203 (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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189A LEU* 3.6 43.6 - - + +
190A TYR* 4.4 9.4 - - - -
199A THR* 2.9 28.4 + - - +
200A HIS* 3.3 17.3 + - - +
202A ILE* 1.3 79.4 - - - +
204A ARG* 1.3 62.0 - - + +
206A LEU* 3.2 4.4 + - - +
207A ILE* 3.0 30.5 + - + +
243A PHE* 3.9 26.5 - - + -
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Residues in contact with ARG 204 (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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123A GLN* 4.2 1.0 + - - -
200A HIS* 2.9 51.9 + - + +
201A THR* 3.9 5.8 - - - +
203A GLU* 1.3 73.2 - - + +
205A TRP* 1.3 69.7 + - + +
207A ILE* 3.3 32.2 + - - +
208A GLY* 3.0 20.3 + - - -
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Residues in contact with TRP 205 (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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71A ALA* 4.7 1.6 - - + -
75A PHE* 3.5 34.8 - + - -
115A LEU* 3.9 15.9 - - + -
118A ALA* 3.7 15.9 - - + -
119A GLN* 3.4 71.4 + - + +
122A VAL* 4.1 27.0 - - + +
123A GLN* 3.0 20.8 + - + +
201A THR* 3.1 36.1 + - + +
202A ILE* 3.2 13.4 + - + +
204A ARG* 1.3 79.3 - - + +
206A LEU* 1.3 55.9 + - - +
209A ASN* 2.9 25.5 + - - +
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Residues in contact with LEU 206 (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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68A PHE* 3.6 44.6 - - + -
122A VAL* 3.9 20.2 - - + -
189A LEU* 4.7 2.0 - - + -
202A ILE* 2.9 23.4 + - + +
203A GLU* 3.6 7.2 - - - +
205A TRP* 1.3 73.6 - - - +
207A ILE* 1.3 66.6 + - - +
209A ASN* 3.3 15.3 - - - +
217A ARG* 3.7 2.1 + - - -
227A GLY* 3.4 7.8 - - - -
228A GLU* 3.3 47.5 + - - +
229A LYS* 4.0 11.0 - - + +
242A GLY* 5.4 0.2 - - - -
243A PHE* 3.9 19.1 - - + -
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Residues in contact with ILE 207 (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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203A GLU* 3.0 20.5 + - + +
204A ARG* 3.3 35.9 + - - +
206A LEU* 1.3 75.7 - - - +
208A GLY* 1.3 59.8 + - - +
209A ASN 3.2 0.6 - - - +
217A ARG* 2.9 34.0 + - - +
225A VAL* 4.0 23.6 - - + -
226A VAL 3.6 24.0 - - - +
243A PHE* 3.8 16.6 - - + -
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Residues in contact with GLY 208 (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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123A GLN* 3.4 20.0 + - - -
204A ARG 3.0 12.5 + - - -
207A ILE* 1.3 75.8 - - - +
209A ASN* 1.3 67.7 + - - +
210A GLN* 3.4 11.1 + - - +
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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