Contacts of the helix formed by residues 198 - 210 (chain A) in PDB entry 2RG8
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 SER 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A GLU 3.1 12.3 + - - -
197A LYS* 1.3 78.7 - - - +
199A GLY* 1.3 59.0 + - - +
200A VAL 3.3 0.4 - - - -
201A PRO* 3.4 1.6 - - - +
202A VAL* 3.5 7.4 - - - +
235A ASP* 3.2 34.0 + - - +
238A LYS* 3.4 25.0 - - - +
239A SER* 2.6 33.4 + - - -
242A LYS* 4.1 15.0 - - - -
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Residues in contact with GLY 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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164A PHE* 3.5 17.0 - - - -
196A MSE 2.7 27.5 + - - +
198A SER* 1.3 78.4 - - - +
200A VAL* 1.3 61.8 + - - +
202A VAL* 3.8 8.4 - - - +
203A LEU* 3.1 25.5 + - - +
242A LYS* 4.9 3.8 - - - +
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Residues in contact with VAL 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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164A PHE* 3.8 18.6 - - + -
168A LEU* 4.8 7.6 - - + -
172A ILE* 4.3 9.7 - - + +
184A VAL* 5.2 5.4 - - + -
188A LEU* 3.8 43.5 - - + -
193A LEU* 4.0 8.1 - - + -
196A MSE 4.2 0.2 - - - +
197A LYS* 3.2 13.4 + - + +
199A GLY* 1.3 74.5 - - - +
201A PRO* 1.3 70.2 - - + +
203A LEU* 3.2 4.9 + - - +
204A ALA* 2.8 30.9 + - + +
222A LEU* 5.4 2.2 - - + -
223A LEU* 6.0 0.9 - - + -
226A LEU* 4.4 13.5 - - + -
231A MSE 5.3 2.5 - - - -
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Residues in contact with PRO 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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197A LYS 3.6 7.2 - - - +
198A SER 3.4 2.0 - - - +
200A VAL* 1.3 95.4 - - + +
202A VAL* 1.3 55.9 + - - +
204A ALA* 3.3 2.1 + - + +
205A VAL* 2.8 38.1 + - + +
223A LEU* 3.6 38.6 - - + -
231A MSE 3.7 22.0 - - + -
236A VAL* 5.2 3.1 - - + -
239A SER* 3.3 33.9 - - - +
240A PHE* 5.8 2.7 - - + -
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Residues in contact with VAL 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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198A SER 3.5 16.6 - - - +
199A GLY* 3.6 8.0 + - - +
200A VAL 3.2 0.4 - - - -
201A PRO* 1.3 77.2 - - - +
203A LEU* 1.3 54.7 + - - +
205A VAL* 3.8 1.8 - - - +
206A SER* 2.7 44.8 + - - +
239A SER* 3.2 28.9 - - - +
242A LYS* 3.6 18.6 - - + -
243A LEU* 4.2 19.0 - - + +
246A ASP* 3.6 24.2 - - - +
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Residues in contact with LEU 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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164A PHE* 4.4 8.1 - - + -
165A GLU* 4.0 29.6 - - + +
168A LEU* 3.6 31.4 - - + -
169A THR* 3.8 25.8 - - - +
172A ILE* 3.7 11.0 - - + -
199A GLY 3.1 15.9 + - - +
200A VAL* 3.8 3.1 - - - +
202A VAL* 1.3 76.6 - - - +
204A ALA* 1.3 67.5 + - - +
206A SER* 3.2 8.6 + - - -
207A LEU* 2.9 37.7 + - + +
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Residues in contact with ALA 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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172A ILE* 3.7 26.3 - - + +
176A PHE* 4.0 2.3 - - - -
200A VAL* 2.8 18.6 + - + +
201A PRO* 3.7 7.2 - - + +
203A LEU* 1.3 77.2 - - - +
205A VAL* 1.3 56.7 + - - +
207A LEU* 3.4 1.9 + - - +
208A ALA* 2.9 29.6 + - - +
219A THR* 3.9 21.6 + - + +
222A LEU* 4.5 15.9 - - + -
223A LEU* 5.1 1.1 - - + -
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Residues in contact with VAL 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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201A PRO* 2.8 26.4 + - + +
202A VAL 3.8 3.1 - - - +
204A ALA* 1.3 71.6 - - - +
206A SER* 1.3 57.9 + - - +
208A ALA* 3.1 4.7 + - - +
209A LEU* 2.8 39.1 + - + +
219A THR* 4.0 18.8 - - + -
223A LEU* 4.5 9.4 - - + -
240A PHE* 5.5 1.1 - - + -
243A LEU* 3.6 37.7 - - + -
261A VAL* 4.6 1.8 - - + -
264A PHE* 3.7 36.3 - - + -
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Residues in contact with SER 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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202A VAL* 2.7 32.0 + - - +
203A LEU* 3.5 12.6 - - - -
205A VAL* 1.3 79.4 - - - +
207A LEU* 1.3 62.1 + - - +
209A LEU* 3.5 22.9 + - - +
210A GLU* 3.9 13.3 + - - +
243A LEU* 4.4 0.7 - - - +
246A ASP* 5.3 0.5 + - - -
250A LEU* 3.6 28.5 - - - +
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Residues in contact with LEU 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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169A THR* 4.1 31.2 - - + +
172A ILE* 3.8 28.9 - - + -
173A GLN* 4.5 13.7 - - + +
176A PHE* 4.2 14.5 - - + -
203A LEU* 2.9 40.3 + - + +
204A ALA 3.9 2.9 - - - +
206A SER* 1.3 74.4 - - - +
208A ALA* 1.3 64.3 + - - +
210A GLU* 3.2 16.6 + - - +
211A GLY* 3.4 8.7 + - - -
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Residues in contact with ALA 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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176A PHE* 3.9 12.3 - - + -
204A ALA 2.9 18.3 + - - +
205A VAL 3.6 4.5 - - - +
207A LEU* 1.3 75.5 - - - +
209A LEU* 1.3 60.5 + - - +
211A GLY* 2.9 19.4 + - - +
212A LYS 4.2 0.5 - - - +
215A HIS* 4.0 9.0 - - - +
216A ARG* 3.0 34.5 + - + +
219A THR* 3.4 21.8 - - - +
264A PHE* 4.3 2.7 - - + -
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Residues in contact with LEU 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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205A VAL* 2.8 28.0 + - + +
206A SER* 3.6 13.2 - - - +
207A LEU 3.2 0.4 - - - -
208A ALA* 1.3 78.2 - - - +
210A GLU* 1.3 59.0 + - + +
211A GLY 3.3 0.6 - - - +
216A ARG* 3.5 15.7 + - - +
250A LEU* 4.0 32.1 - - + -
254A THR* 3.6 25.7 + - - +
257A ALA* 4.1 22.7 - - + +
260A LEU* 3.4 40.6 - - + +
261A VAL* 4.4 6.7 - - + -
264A PHE* 4.6 9.9 - - + -
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Residues in contact with GLU 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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206A SER 3.9 11.6 + - - +
207A LEU* 3.2 10.8 + - - +
208A ALA 3.1 0.8 - - - -
209A LEU* 1.3 77.0 - - + +
211A GLY* 1.3 61.5 + - - +
253A ASP* 4.1 30.4 - - + +
254A THR* 3.7 17.3 - - - +
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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