Contacts of the helix formed by residues 200 - 211 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179C ASN* 4.7 0.2 + - - -
199C PHE* 1.3 78.1 - - - +
201C VAL* 1.3 58.9 + - - +
202C ASN* 3.6 7.3 + - - +
203C THR* 3.0 32.4 + - - +
204C MSE 2.9 30.5 + - - +
230C ILE* 3.9 19.1 - - + -
232C SER* 3.6 30.1 - - - +
236C ASP* 3.7 5.4 - - - -
302C MSE 5.1 6.7 - - + -
305C THR* 4.2 14.5 + - - +
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Residues in contact with VAL 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C PHE* 3.9 16.1 - - + -
200C THR* 1.3 73.2 - - - +
202C ASN* 1.3 62.4 + - - +
204C MSE 3.8 6.4 - - + +
205C LYS* 3.1 33.2 + - + +
229C PHE* 4.4 1.3 - - + -
235C ARG* 4.1 10.5 - - + +
236C ASP* 2.8 31.4 + - - +
239C MSE 3.8 39.5 - - + -
254C ASP* 3.3 31.6 - - - +
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Residues in contact with ASN 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C THR* 3.1 7.1 - - - +
201C VAL* 1.3 80.3 - - - +
203C THR* 1.3 61.0 + - - +
205C LYS* 4.0 1.2 - - - +
206C ASN* 2.9 58.2 + - - +
232C SER* 5.9 0.9 - - - +
233C ASP* 6.4 1.6 - - + -
235C ARG* 3.2 32.2 + - - +
236C ASP* 4.8 0.2 + - - -
299C ASP* 4.9 10.3 + - - -
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Residues in contact with THR 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C ASN* 3.4 40.5 + - + +
200C THR* 3.0 23.5 + - - +
202C ASN* 1.3 79.4 + - - +
204C MSE 1.3 57.1 + - - +
206C ASN* 3.8 8.5 + - + +
207C SER* 2.9 43.9 + - - +
305C THR* 5.3 1.8 + - - -
350C ASN* 5.9 0.7 + - - -
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Residues in contact with MSE 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C ASN* 5.6 0.9 - - - +
197C TYR* 4.2 10.3 - - - +
199C PHE* 4.1 23.7 - - + +
200C THR 2.9 18.9 + - - +
201C VAL* 3.8 13.7 - - + +
203C THR* 1.3 77.7 - - - +
205C LYS* 1.3 72.2 + - + +
207C SER* 3.3 6.2 + - - -
208C LEU* 3.1 26.9 + - + +
216C PHE* 4.3 1.0 - - + -
219C VAL* 3.7 32.8 - - + -
239C MSE 5.2 1.8 - - + -
262C TYR* 3.9 42.0 - - + -
263C PHE* 3.9 26.9 - - + -
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Residues in contact with LYS 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A SER* 6.3 0.6 - - - -
119A HIS* 6.2 3.8 - - - -
201C VAL* 3.1 25.1 + - + +
202C ASN 4.2 1.6 - - - +
204C MSE 1.3 83.4 - - + +
206C ASN* 1.3 67.6 + - - +
208C LEU* 3.5 8.9 + - + +
209C VAL* 3.2 28.8 + - + +
235C ARG* 3.9 8.8 - - - +
239C MSE 5.2 0.4 - - + -
253C LEU 5.1 1.4 + - - -
254C ASP* 2.6 35.2 + - - +
257C ASP* 2.8 25.4 + - - +
262C TYR* 3.7 21.5 - - + +
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Residues in contact with ASN 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C ASN* 2.9 48.4 + - - +
203C THR* 3.8 7.2 - - + +
205C LYS* 1.3 74.8 - - - +
207C SER* 1.3 59.9 + - - +
209C VAL* 3.3 7.4 + - - +
210C SER* 2.9 36.5 + - - +
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Residues in contact with SER 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C ASN* 4.1 1.6 - - - +
180C GLY* 3.8 16.7 + - - -
203C THR* 2.9 31.9 + - - +
204C MSE 3.5 5.2 - - - -
206C ASN* 1.3 74.3 - - - +
208C LEU* 1.3 59.7 + - - +
211C TYR* 2.9 58.5 + - - +
216C PHE* 3.8 21.3 - - - -
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Residues in contact with LEU 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A HIS* 3.5 12.9 + - + -
204C MSE 3.1 26.3 + - + +
205C LYS* 3.8 11.7 - - + +
206C ASN 3.3 0.2 - - - -
207C SER* 1.3 75.4 - - - +
209C VAL* 1.3 60.8 + - - +
212C TRP* 3.3 35.8 + - + +
216C PHE* 3.5 36.6 - - + +
217C THR* 3.8 21.5 - - - +
218C SER* 3.9 6.7 - - - +
219C VAL* 5.0 2.9 - - + -
262C TYR* 3.6 35.9 - - + +
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Residues in contact with VAL 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PRO* 3.6 20.2 - - + +
102A TRP* 3.4 37.2 - - + +
103A ASP* 6.1 0.2 - - - +
119A HIS* 3.6 35.8 - - + +
205C LYS* 3.2 16.2 + - + +
206C ASN* 3.6 9.6 - - - +
207C SER 3.1 0.6 - - - -
208C LEU* 1.3 79.4 - - - +
210C SER* 1.3 67.1 + - - +
211C TYR 3.6 0.3 + - - -
212C TRP* 3.9 4.9 + - - +
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Residues in contact with SER 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PRO* 3.7 18.4 - - - +
206C ASN* 2.9 19.3 + - - +
207C SER 3.2 0.2 + - - -
209C VAL* 1.3 81.3 - - - +
211C TYR* 1.3 86.9 + - - +
212C TRP 3.5 0.4 - - - -
213C ASN 5.2 0.2 + - - -
214C LEU* 4.7 4.7 - - - +
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Residues in contact with TYR 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C GLY* 4.5 8.3 - - - -
182C VAL* 4.8 0.2 - - + -
207C SER* 2.9 44.3 + - - +
210C SER* 1.3 95.1 - - - +
212C TRP* 1.3 65.2 + - - +
213C ASN 3.3 2.9 - - - -
214C LEU* 3.1 19.7 + - + +
215C GLY 3.1 7.4 + - - -
216C PHE* 2.9 29.8 + - + -
336C HIS* 3.2 30.8 - + - -
338C PHE* 3.5 39.3 - + + -
339C GLU* 4.7 4.0 - - - -
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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