Contacts of the helix formed by residues 203 - 218 (chain A) in PDB entry 4N9W
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 GLY 203 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A GLU 4.2 0.2 + - - -
200A PRO 2.9 15.8 + - - -
201A ARG 3.2 1.2 - - - -
202A LYS* 1.3 78.8 - - - +
204A MET* 1.3 65.8 + - - +
205A ALA* 3.0 4.9 - - - -
206A VAL* 3.0 16.8 + - - +
207A LEU 3.5 2.1 + - - -
269A PRO* 3.2 31.4 - - - +
271A LEU* 4.3 10.5 - - - -
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Residues in contact with MET 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A PHE* 3.5 47.1 - - + -
197A TYR* 3.8 32.7 + - + +
199A GLU 5.3 0.6 + - - -
200A PRO* 4.8 0.6 + - - +
202A LYS* 3.4 4.9 + - - +
203A GLY* 1.3 75.8 - - - +
205A ALA* 1.3 57.7 + - - +
207A LEU* 3.2 19.0 + - + +
208A LEU* 2.9 36.0 + - + +
223A ILE* 5.5 1.6 - - - -
225A ILE* 3.8 26.5 - - + -
234A LEU* 3.7 33.9 - - + -
245A LEU* 6.2 0.7 - - - -
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Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A PRO* 6.0 1.1 - - + +
203A GLY* 3.0 2.6 - - - -
204A MET* 1.3 81.3 - - - +
206A VAL* 1.3 57.9 + - + +
208A LEU* 3.9 6.9 - - - +
209A ALA* 3.1 28.8 + - - +
237A GLN* 5.5 7.9 - - - +
271A LEU* 6.2 2.9 - - + -
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Residues in contact with VAL 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A GLY* 3.0 12.4 + - - +
205A ALA* 1.3 76.7 - - + +
207A LEU* 1.3 65.3 + - - +
209A ALA* 3.4 6.7 + - - +
210A ALA* 3.1 21.1 + - - +
269A PRO* 4.3 12.3 - - + +
271A LEU* 3.8 22.9 - - + -
314A ASP* 3.5 29.8 - - - +
315A ASP 4.2 5.8 - - - +
316A ALA* 4.0 25.3 - - + +
319A MET* 4.1 21.1 - - + -
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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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191A VAL* 4.5 9.2 - - + -
193A PHE* 4.0 27.8 - - + -
203A GLY 3.5 5.9 + - - +
204A MET* 3.2 15.8 + - - +
206A VAL* 1.3 79.3 - - - +
208A LEU* 1.3 64.2 + - - +
210A ALA* 3.2 5.7 + - + +
211A LEU* 3.1 21.0 + - + +
214A LEU* 5.4 1.6 - - + -
223A ILE* 3.8 36.3 - - + -
267A CYS* 4.0 16.6 - - + -
269A PRO* 4.4 9.8 - - + +
319A MET* 5.0 2.7 - - - -
323A LEU* 3.7 30.5 - - + -
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Residues in contact with LEU 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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204A MET* 2.9 25.1 + - + +
205A ALA* 3.9 8.3 - - - +
206A VAL 3.3 0.2 - - - -
207A LEU* 1.3 79.0 - - - +
209A ALA* 1.3 61.4 + - - +
211A LEU* 3.1 32.7 + - + +
212A PRO* 3.5 5.4 - - - +
234A LEU* 4.4 17.5 - - + -
237A GLN* 3.8 48.5 - - + +
238A ALA* 3.9 22.2 - - + -
241A LEU* 5.5 0.5 - - - +
245A LEU* 4.6 10.5 - - + -
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Residues in contact with ALA 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 ALA 3.1 18.1 + - - +
206A VAL* 3.8 1.1 - - - +
207A LEU 3.3 0.2 - - - -
208A LEU* 1.3 76.4 - - - +
210A ALA* 1.3 59.5 + - - +
212A PRO* 3.4 11.9 - - - +
213A LYS* 5.4 2.3 + - - +
316A ALA* 3.7 25.1 - - + +
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Residues in contact with ALA 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 VAL 3.1 12.2 + - - +
207A LEU* 3.6 9.4 - - + +
208A LEU 3.1 0.6 - - - -
209A ALA* 1.3 75.1 - - - +
211A LEU* 1.3 65.8 + - - +
212A PRO* 3.3 2.5 - - - -
213A LYS* 3.3 5.3 + - - -
214A LEU* 3.2 19.9 + - + +
316A ALA* 3.6 22.2 - - - +
319A MET* 4.4 8.7 - - + -
320A ALA* 3.7 26.9 - - + +
323A LEU* 5.0 6.5 - - + -
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Residues in contact with LEU 211 (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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207A LEU* 3.1 11.0 + - + +
208A LEU* 3.1 29.8 + - + +
210A ALA* 1.3 78.0 - - - +
212A PRO* 1.4 65.1 - - + +
214A LEU* 4.3 10.8 - - + -
215A VAL* 2.9 49.1 + - + +
221A VAL* 4.7 2.2 - - + -
223A ILE* 3.8 29.4 - - + -
238A ALA* 4.9 1.3 - - + -
241A LEU* 3.9 34.8 - - + +
244A HIS* 4.8 3.1 - - + -
245A LEU* 4.1 20.6 - - + -
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Residues in contact with PRO 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 LEU 3.5 9.2 - - - +
209A ALA* 3.4 17.7 - - - +
210A ALA 3.4 0.4 - - - -
211A LEU* 1.4 92.2 - - + +
213A LYS* 1.3 59.0 + - + +
215A VAL* 3.6 3.1 + - + +
216A ALA* 3.0 27.9 + - - +
241A LEU* 3.8 23.6 - - + -
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Residues in contact with LYS 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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209A ALA 5.9 1.8 - - - +
210A ALA* 3.3 9.5 + - - +
212A PRO* 1.3 79.0 - - + +
214A LEU* 1.3 64.4 + - - +
216A ALA* 3.4 8.1 + - - +
217A ARG* 3.3 18.5 + - - +
317A ASP* 2.6 40.2 + - - +
320A ALA* 3.9 21.5 - - + -
324A ILE* 3.6 18.0 - - + +
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Residues in contact with LEU 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A VAL* 4.0 15.9 - - + -
207A LEU* 5.4 1.6 - - + -
210A ALA 3.2 14.0 + - - +
211A LEU* 3.6 13.0 - - + +
213A LYS* 1.3 76.2 - - - +
215A VAL* 1.3 51.6 + - - +
217A ARG* 3.2 3.5 + - - +
218A PHE* 2.8 41.2 + - + +
221A VAL* 4.1 16.6 - - + -
223A ILE* 4.0 27.1 - - + -
320A ALA* 4.9 2.2 - - + +
323A LEU* 4.0 26.2 - - + -
324A ILE* 3.8 25.5 - - + +
327A LEU* 4.0 22.7 - - + -
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Residues in contact with VAL 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 LEU* 2.9 44.3 + - + +
212A PRO 4.0 2.9 - - - +
214A LEU* 1.3 71.5 - - - +
216A ALA* 1.3 65.9 + - - +
218A PHE 3.6 6.3 - - - -
219A PRO* 3.3 26.2 - - + +
221A VAL* 3.9 12.1 - - + -
241A LEU* 4.1 16.6 - - + -
244A HIS* 3.7 36.3 - - + +
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Residues in contact with ALA 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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212A PRO 3.0 18.4 + - - +
213A LYS* 3.7 8.5 - - - +
214A LEU 3.3 0.4 - - - -
215A VAL* 1.3 78.7 - - - +
217A ARG* 1.3 63.3 - - + +
219A PRO* 4.4 7.4 - - - +
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Residues in contact with ARG 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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213A LYS 3.3 11.8 + - - +
214A LEU 3.2 5.3 + - - +
216A ALA* 1.3 81.5 - - + +
218A PHE* 1.3 84.5 + - + +
219A PRO* 3.5 7.2 - - - +
324A ILE* 3.7 27.7 - - + +
328A GLU* 2.8 41.0 + - - +
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Residues in contact with PHE 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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188A GLY 4.3 5.6 - - - +
189A ARG* 4.0 26.2 - - + -
214A LEU* 2.8 21.2 + - + +
215A VAL* 3.3 6.9 - - - +
217A ARG* 1.3 90.9 - - + +
219A PRO* 1.3 59.7 - - - +
220A ASP 3.0 11.4 + - - -
221A VAL* 3.1 34.8 + - + +
324A ILE* 4.1 8.3 - - - -
327A LEU* 3.5 45.1 - - + -
328A GLU* 3.5 33.4 - - + -
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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