Contacts of the helix formed by residues 206 - 218 (chain A) in PDB entry 3GNI
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 HIS 206 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A LEU 4.9 0.7 - - - -
162A TRP* 3.4 50.0 + + - -
167A TYR* 3.5 28.5 - + - +
202A PHE* 2.7 55.1 + + + +
203A LEU 3.8 1.6 - - - -
205A GLN* 1.3 86.7 - - + +
207A TYR* 1.3 65.8 + - - +
208A ASP 3.1 3.3 + - - -
209A ARG* 3.3 6.0 + - + -
210A PHE* 3.0 21.8 + - + +
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Residues in contact with TYR 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 LEU 2.9 20.1 + - - +
204A GLU* 3.8 10.7 + - - +
205A GLN 3.5 2.2 + - - -
206A HIS* 1.3 77.2 - - - +
208A ASP* 1.3 77.1 + - - +
210A PHE* 3.8 1.3 - - - +
211A PHE* 2.9 73.4 + + + +
245A ILE* 3.8 28.0 - - + -
248A LYS* 3.8 40.2 - - + +
249A TYR* 3.1 37.2 + - - +
252A LYS* 5.1 8.1 - - + +
255A ASN* 4.6 2.6 + - - -
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Residues in contact with ASP 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A HIS 3.3 1.2 - - - -
207A TYR* 1.3 94.2 + - - +
209A ARG* 1.3 63.9 + - - +
211A PHE* 4.0 0.8 - - - +
212A SER* 3.0 27.0 + - - -
248A LYS* 5.0 7.8 + - - -
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Residues in contact with ARG 209 (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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164A GLU* 2.8 44.3 + - - -
167A TYR* 3.6 56.0 - - + +
206A HIS* 3.3 7.8 + - + +
208A ASP* 1.3 77.8 - - - +
210A PHE* 1.3 63.3 + - - +
212A SER* 3.4 5.3 + - - -
213A GLU* 3.0 33.1 + - + +
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Residues in contact with PHE 210 (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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166A PHE* 4.0 10.3 - + - -
167A TYR* 4.3 7.5 - - + -
170A PHE* 3.8 22.7 - + - -
188A PHE* 4.1 0.7 - + - -
192A LEU* 3.8 38.6 - - + -
202A PHE* 3.6 28.9 - + + -
203A LEU* 3.6 21.3 - - + -
206A HIS 3.0 19.5 + - - +
207A TYR* 3.8 2.7 - - - +
209A ARG* 1.3 77.7 - - - +
211A PHE* 1.3 75.5 + + + +
213A GLU* 3.3 6.7 + - - +
214A TYR* 2.7 63.7 + + - +
236A LEU* 4.8 5.6 - - + -
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Residues in contact with PHE 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LEU* 4.5 10.8 - - + -
207A TYR* 2.9 70.3 + + + +
208A ASP* 4.6 0.9 - - - +
210A PHE* 1.3 101.6 - + - +
212A SER* 1.3 60.8 + - - +
214A TYR* 3.9 10.4 - + + +
215A GLU* 2.9 29.3 + - - +
233A LEU* 3.9 26.5 - - + -
236A LEU* 5.7 4.5 - - + -
237A LEU* 5.0 4.9 - - + -
245A ILE* 3.7 19.5 - - + -
249A TYR* 4.0 25.6 - + + -
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Residues in contact with SER 212 (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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208A ASP 3.0 20.9 + - - -
209A ARG* 3.6 7.0 - - - -
211A PHE* 1.3 78.5 - - - +
213A GLU* 1.3 63.5 + - - +
215A GLU* 3.6 19.9 - - - +
216A LYS* 3.7 20.9 + - - +
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Residues in contact with GLU 213 (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 TYR* 4.2 22.8 - - + +
170A PHE* 3.6 51.0 - - + +
209A ARG* 3.0 26.6 + - + +
210A PHE 3.5 6.7 - - - +
212A SER* 1.3 74.0 - - - +
214A TYR* 1.3 65.5 + - - +
216A LYS* 3.1 40.7 + - - +
217A LEU* 3.6 4.0 + - - +
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Residues in contact with TYR 214 (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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170A PHE* 3.6 13.9 - + - -
188A PHE* 4.1 18.1 - + - -
210A PHE* 2.7 51.9 + + - +
211A PHE* 3.9 17.0 - + + +
212A SER 3.4 0.2 - - - -
213A GLU* 1.3 70.2 - - - +
215A GLU* 1.3 65.6 + - - +
217A LEU* 3.1 18.0 + - + +
218A LEU* 3.3 30.5 + - + +
229A SER* 2.5 44.7 + - - -
232A LEU* 3.4 23.4 - - + +
233A LEU* 3.5 23.1 + - + -
236A LEU* 4.9 3.6 - - + -
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Residues in contact with GLU 215 (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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211A PHE 2.9 18.9 + - - +
212A SER* 3.6 13.2 - - - +
213A GLU 3.3 0.2 - - - -
214A TYR* 1.3 77.4 - - - +
216A LYS* 1.3 61.3 + - + +
218A LEU* 3.3 18.0 + - - +
219A HIS* 3.2 39.9 + - + +
254A GLU* 5.0 17.0 - - - +
255A ASN* 5.1 10.0 - - - +
258A LEU* 5.1 11.2 - - + +
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Residues in contact with LYS 216 (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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174A GLU* 4.3 5.1 - - - +
212A SER* 3.7 20.0 + - - +
213A GLU* 3.1 31.7 + - - +
215A GLU* 1.3 79.4 - - + +
217A LEU* 1.3 62.5 + - + +
219A HIS* 3.2 17.1 + - - +
220A SER* 3.3 11.4 + - - -
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Residues in contact with LEU 217 (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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170A PHE* 3.6 44.0 - - + +
173A VAL* 3.7 29.8 - - + -
174A GLU* 3.8 16.8 - - - +
185A PHE* 5.4 0.9 - - + -
188A PHE* 4.6 8.1 - - + -
213A GLU 4.0 0.9 - - - +
214A TYR* 3.1 26.4 + - + +
216A LYS* 1.3 73.8 - - + +
218A LEU* 1.3 58.8 + - - +
219A HIS 3.1 4.9 - - - -
220A SER* 3.2 25.8 + - - -
225A THR* 4.0 7.6 - - + +
226A LYS* 3.9 12.8 - - - -
229A SER* 3.7 23.8 - - - +
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Residues in contact with LEU 218 (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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214A TYR* 3.3 31.1 + - + +
215A GLU* 3.6 13.2 - - - +
216A LYS 3.3 0.4 - - - -
217A LEU* 1.3 75.8 - - - +
219A HIS* 1.3 61.3 + - - +
220A SER 3.4 0.7 - - - -
226A LYS* 3.6 25.2 + - + +
229A SER* 4.0 4.0 - - - -
230A LEU* 3.9 43.1 - - + +
233A LEU* 3.8 22.9 - - + -
249A TYR* 4.2 4.5 - - + +
258A LEU* 3.6 32.6 - - + +
259A MET* 4.0 3.1 - - + -
262A LEU* 4.3 13.6 - - + +
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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