Contacts of the helix formed by residues 204 - 221 (chain A) in PDB entry 4YAY
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 PHE 204 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A LEU* 5.6 5.4 - - + -
116A VAL* 5.7 0.7 - - + -
200A ASN* 3.4 21.4 + - - +
202A LEU 3.5 1.6 - - - -
203A GLY* 1.3 81.8 - - - +
205A LEU* 1.3 64.8 + - + +
206A PHE 3.6 0.7 - - - -
207A PRO* 3.5 6.1 - - - +
208A PHE* 3.1 35.4 - + + +
249A PHE* 5.5 0.9 - + - -
250A PHE* 3.5 49.1 - + + -
253A TRP* 3.7 21.8 - + + -
254A ILE* 5.1 6.7 - - + -
257A GLN* 3.3 42.6 - - + +
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Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ASN* 2.8 44.1 + - - +
201A ILE* 4.1 14.6 - - + -
204A PHE* 1.3 75.5 - - + +
206A PHE* 1.3 60.3 + - - +
208A PHE* 4.3 1.1 - - - +
209A LEU* 3.2 30.1 + - - +
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Residues in contact with PHE 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ILE 3.4 20.8 + - - +
202A LEU* 4.1 10.5 - - + +
205A LEU* 1.3 77.4 - - - +
207A PRO* 1.4 68.6 - - + +
209A LEU* 3.5 8.5 - - - +
210A ILE* 3.3 31.3 + - + +
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Residues in contact with PRO 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A VAL* 3.6 25.6 - - + -
117A PHE* 5.9 2.2 - - + -
120A THR* 3.5 22.2 - - + +
202A LEU 3.2 24.5 - - - +
203A GLY 4.5 0.2 - - - +
204A PHE* 3.5 16.4 - - - +
206A PHE* 1.4 85.9 - - + +
208A PHE* 1.4 55.2 + - - +
209A LEU 3.1 1.8 - - - -
210A ILE* 3.0 12.6 + - + +
211A ILE* 2.8 43.6 + - + +
250A PHE* 5.3 2.2 - - + -
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Residues in contact with PHE 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 PHE* 3.1 27.4 - + - +
205A LEU 4.5 0.9 - - - +
206A PHE 3.5 0.4 - - - -
207A PRO* 1.4 80.1 - - - +
209A LEU* 1.3 56.1 + - - +
211A ILE* 4.0 5.0 - - + +
212A LEU* 3.1 30.3 + - + +
250A PHE* 3.9 44.0 - + + -
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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 LEU* 3.2 21.0 + - + +
206A PHE* 3.5 9.2 - - - +
207A PRO 3.1 0.4 - - - -
208A PHE* 1.3 76.7 - - - +
210A ILE* 1.4 69.6 + - + +
212A LEU* 3.7 4.9 + - - +
213A THR* 3.1 34.4 + - - +
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Residues in contact with ILE 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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120A THR* 3.9 23.8 - - + -
124A ILE* 4.2 21.1 - - + -
206A PHE* 3.3 23.8 - - + +
207A PRO* 3.0 9.9 + - + +
209A LEU* 1.4 81.4 - - + +
211A ILE* 1.3 64.4 + - - +
213A THR* 3.4 6.9 + - - -
214A SER* 3.1 24.1 + - - +
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Residues in contact with ILE 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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116A VAL 4.5 1.3 - - - +
119A LEU* 3.9 10.3 - - + -
120A THR* 3.6 37.0 - - - +
123A SER* 3.4 20.9 - - - +
207A PRO* 2.8 23.3 + - + +
208A PHE* 4.0 5.6 - - + +
210A ILE* 1.3 70.0 - - - +
212A LEU* 1.4 59.9 + - - +
214A SER* 3.3 3.8 + - - -
215A TYR* 3.0 55.3 + - + -
246A VAL* 3.6 15.0 - - + -
250A PHE* 3.7 32.1 - - + -
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Residues in contact with LEU 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 PHE* 3.1 22.3 + - + +
209A LEU* 4.1 5.4 - - - +
211A ILE* 1.4 76.7 - - - +
213A THR* 1.4 55.7 + - - +
215A TYR* 3.3 5.4 + - + +
216A THR* 2.7 47.3 + - + -
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Residues in contact with THR 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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127A TYR* 4.8 2.6 - - + -
209A LEU* 3.1 24.9 + - - +
210A ILE* 3.7 6.7 - - - +
211A ILE 3.4 0.2 - - - -
212A LEU* 1.4 77.7 - - - +
214A SER* 1.3 63.6 + - - +
216A THR* 3.3 22.7 - - + +
217A LEU* 3.4 20.7 + - + +
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Residues in contact with SER 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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123A SER* 3.5 35.9 + - - -
124A ILE* 3.9 11.4 + - - +
127A TYR* 3.8 22.7 - - - +
210A ILE* 3.1 14.9 + - - +
211A ILE 3.5 8.7 - - - -
213A THR* 1.3 78.8 - - - +
215A TYR* 1.3 56.0 + - - +
217A LEU* 3.4 4.2 + - - +
218A ILE* 3.0 29.2 + - - +
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Residues in contact with TYR 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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119A LEU 4.0 0.2 + - - -
123A SER* 2.7 40.5 + - - -
126A ARG* 4.3 13.2 - - + -
211A ILE* 3.0 38.3 + - + +
212A LEU* 4.0 5.6 - - + +
214A SER* 1.3 70.7 - - - +
216A THR* 1.3 61.3 + - - +
217A LEU 3.2 2.0 - - - -
218A ILE* 3.1 16.6 - - + -
219A TRP* 3.0 32.6 + - - +
239A PHE* 3.9 14.4 - + - -
242A ILE* 2.9 33.1 - - + +
243A MET* 4.2 20.6 - - + +
246A VAL* 3.4 26.5 - - + +
247A LEU* 6.2 0.7 - - + -
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Residues in contact with THR 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 LEU* 2.7 30.3 + - + +
213A THR* 3.3 22.9 - - + +
215A TYR* 1.3 74.6 - - - +
217A LEU* 1.3 68.7 + - + +
219A TRP* 4.6 2.4 - - - +
220A LYS* 3.2 41.6 + - - +
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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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127A TYR* 3.6 31.4 - - + +
131A VAL* 3.7 18.9 - - + +
213A THR* 3.4 25.2 + - + +
214A SER 3.6 3.8 - - - +
216A THR* 1.3 90.1 - - + +
218A ILE* 1.3 61.5 + - - +
220A LYS* 4.0 19.7 - - - +
221A ALA* 3.4 21.8 + - - +
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Residues in contact with ILE 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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126A ARG* 3.4 37.5 - - + +
127A TYR* 4.5 1.6 - - - +
130A ILE* 3.5 30.5 - - + +
131A VAL* 4.0 10.5 - - + -
214A SER 3.0 20.3 + - - +
215A TYR* 3.1 29.8 - - + +
217A LEU* 1.3 75.3 - - - +
219A TRP* 1.3 65.9 + - - +
220A LYS 3.3 0.2 - - - -
221A ALA 3.1 3.6 + - - -
222A LEU* 3.1 21.7 + - + +
239A PHE* 3.3 32.1 - - + -
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Residues in contact with TRP 219 (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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215A TYR 3.0 18.6 + - - +
216A THR* 4.6 2.2 - - - +
218A ILE* 1.3 76.7 - - - +
220A LYS* 1.4 61.5 + - + +
222A LEU* 3.2 3.9 + - + +
223A LYS* 2.8 82.5 + - + +
239A PHE* 3.7 35.4 - + + -
243A MET* 4.3 20.2 - - + -
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Residues in contact with LYS 220 (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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216A THR* 3.2 35.9 + - - +
217A LEU* 4.0 23.2 - - - +
218A ILE 3.3 0.2 - - - -
219A TRP* 1.4 82.9 - - + +
221A ALA* 1.4 56.5 + - - +
222A LEU 3.3 0.9 + - - -
223A LYS* 3.6 31.8 + - + +
224A LYS* 5.3 0.9 + - - +
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Residues in contact with ALA 221 (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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130A ILE* 4.0 21.4 - - + +
131A VAL* 4.6 8.3 - - + -
217A LEU 3.4 15.6 + - - +
218A ILE 3.1 5.3 + - - +
220A LYS* 1.4 75.9 - - - +
222A LEU* 1.4 58.7 + - - +
224A LYS 5.4 1.3 - - - -
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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