Contacts of the helix formed by residues 200 - 211 (chain A) in PDB entry 6APL
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 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A ASN* 4.5 0.4 + - - -
199A PHE* 1.3 81.7 - - - +
201A VAL* 1.3 65.4 + - - +
202A ASN* 3.6 7.6 + - - +
203A THR* 2.7 39.5 + - + +
204A MSE 3.0 18.9 + - - -
230A ILE* 3.7 26.0 - - + +
232A SER* 3.3 32.5 - - - +
236A ASP* 3.7 5.2 - - - -
302A MSE 5.5 3.8 - - + -
305A THR* 4.7 8.6 + - - +
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Residues in contact with VAL 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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199A PHE* 4.0 7.6 - - + -
200A THR* 1.3 72.7 - - - +
202A ASN* 1.3 62.8 + - - +
204A MSE 3.4 4.8 + - + +
205A LYS* 3.1 33.6 + - + +
229A PHE* 4.2 9.4 - - + -
235A ARG* 3.9 12.1 - - + +
236A ASP* 2.7 32.0 + - - +
239A MSE 3.6 38.6 - - + -
254A ASP* 3.3 33.4 - - - +
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Residues in contact with ASN 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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200A THR* 3.1 7.9 + - - +
201A VAL* 1.3 79.4 - - - +
203A THR* 1.3 67.5 + - - +
205A LYS* 4.1 1.0 - - - +
206A ASN* 3.0 60.9 + - - +
232A SER* 5.6 2.0 - - - +
233A ASP* 6.4 2.2 - - + -
235A ARG* 3.3 30.7 + - - +
236A ASP* 4.6 0.2 + - - -
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Residues in contact with THR 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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179A ASN* 3.2 36.8 + - - +
200A THR* 2.7 35.1 + - + +
202A ASN* 1.3 83.2 - - - +
204A MSE 1.3 59.2 + - - +
206A ASN* 3.7 7.0 - - - +
207A SER* 2.8 35.7 + - - -
305A THR* 4.9 3.3 + - - +
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Residues in contact with MSE 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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179A ASN* 5.4 0.7 - - - +
197A TYR* 4.1 12.6 - - + +
199A PHE* 4.0 22.9 - - + +
200A THR 3.0 17.4 + - - +
201A VAL* 3.8 12.1 - - + +
203A THR* 1.3 77.1 + - - +
205A LYS* 1.3 68.3 + - + +
207A SER* 3.2 5.8 + - - -
208A LEU* 3.0 29.9 + - + +
216A PHE* 4.4 0.7 - - - -
219A VAL* 3.6 33.2 - - + -
239A MSE 5.1 2.0 - - + -
262A TYR* 3.7 44.0 - - + -
263A PHE* 3.8 27.4 - - + -
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Residues in contact with LYS 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 VAL* 3.1 22.0 + - + +
202A ASN 4.3 2.0 - - - +
204A MSE 1.3 82.7 - - + +
206A ASN* 1.3 68.6 + - - +
208A LEU* 3.3 9.0 + - + +
209A VAL* 3.1 30.6 + - + +
235A ARG* 3.9 12.5 - - - +
239A MSE 5.1 0.2 - - + -
253A LEU* 4.7 3.4 + - - +
254A ASP* 2.7 34.6 + - - +
257A ASP* 2.8 26.4 + - - +
262A TYR* 3.5 24.0 - - + +
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Residues in contact with ASN 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 ASN* 3.0 53.7 + - - +
203A THR* 3.8 7.6 - - - +
205A LYS* 1.3 76.7 - - - +
207A SER* 1.3 57.2 + - - +
209A VAL* 3.3 7.1 + - - +
210A SER* 2.9 36.6 + - - +
211A TYR* 5.6 0.2 - - - -
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Residues in contact with SER 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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179A ASN* 3.7 6.0 - - - +
180A GLY* 3.4 21.1 + - - -
203A THR* 2.8 27.2 + - - -
204A MSE 3.5 5.4 - - - -
205A LYS 3.2 0.2 - - - -
206A ASN* 1.3 70.1 - - - +
208A LEU* 1.3 59.5 + - - +
209A VAL 3.1 1.8 - - - -
211A TYR* 2.9 55.2 + - - +
216A PHE* 3.6 22.4 - - - -
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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 MSE 3.0 25.3 + - + +
205A LYS* 3.3 12.5 + - + +
207A SER* 1.3 76.3 - - - +
209A VAL* 1.3 60.0 + - + +
212A TRP* 3.2 40.9 - - + +
216A PHE* 3.7 34.8 - - + +
217A THR 3.8 6.1 - - - +
218A SER* 3.8 23.8 - - - +
219A VAL* 4.7 2.7 - - + -
262A TYR* 3.7 35.0 - - + -
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Residues in contact with VAL 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 LYS* 3.1 19.5 + - + +
206A ASN* 3.7 7.4 - - - +
207A SER 3.1 0.2 - - - -
208A LEU* 1.3 80.1 - - + +
210A SER* 1.3 67.9 + - - +
211A TYR 3.6 0.3 + - - -
212A TRP* 3.9 8.9 + - - +
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Residues in contact with SER 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 ASN* 2.9 19.6 + - - +
209A VAL* 1.3 80.7 - - - +
211A TYR* 1.3 86.9 + - - +
212A TRP 3.8 0.5 + - - -
213A ASN* 5.1 1.4 + - - +
214A LEU* 4.6 5.7 - - - +
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Residues in contact with TYR 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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180A GLY* 4.1 11.0 - - - -
182A VAL* 4.4 6.7 - - + -
207A SER* 2.9 42.8 + - - +
210A SER* 1.3 95.5 - - - +
212A TRP* 1.3 63.9 + - - +
213A ASN 3.3 2.9 - - - -
214A LEU* 3.0 30.6 + - + -
215A GLY 3.3 0.5 + - - -
216A PHE* 3.2 28.4 + + + -
336A HIS* 3.4 23.7 - + - -
338A PHE* 3.6 37.2 - + - -
339A GLU* 4.7 6.5 - - - -
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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