Contacts of the helix formed by residues 200 - 214 (chain B) in PDB entry 6Y2G
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 ILE 200 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B GLY* 3.9 30.1 - - - +
129B ALA* 4.5 8.3 - - + -
130B MET 4.5 4.0 - - - +
131B ARG* 4.0 15.5 - - - +
132B PRO* 3.7 30.3 - - + -
199B THR* 1.3 69.1 - - - +
201B THR* 1.3 65.1 + - - +
202B VAL* 4.2 11.9 - - + -
203B ASN* 3.0 33.8 + - - +
204B VAL* 3.2 14.2 + - - +
240B GLU* 4.5 6.5 - - + -
289B ASP* 2.8 36.6 + - - +
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Residues in contact with THR 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B THR 3.2 1.2 + - - -
200B ILE* 1.3 72.2 - - - +
202B VAL* 1.3 62.9 + - - +
204B VAL* 3.2 5.1 + - - +
205B LEU* 3.2 25.1 + - + +
230B PHE* 3.7 37.0 - - + -
239B TYR* 3.6 23.4 - - + +
240B GLU* 2.7 41.5 + - - +
241B PRO 4.8 2.7 - - - -
242B LEU* 4.2 14.1 - - + -
246B HIS* 6.0 0.4 - - - -
268B LEU* 4.7 2.6 - - + +
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Residues in contact with VAL 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B GLY* 6.2 0.4 - - - -
200B ILE* 4.2 11.2 - - + -
201B THR* 1.3 80.1 - - - +
203B ASN* 1.3 71.8 + - - +
205B LEU* 3.6 5.5 + - - +
206B ALA* 3.1 24.8 + - - +
242B LEU* 4.3 6.7 - - - +
246B HIS* 3.8 54.2 + - + +
249B ILE* 5.4 2.5 - - + -
250B LEU* 3.9 22.5 - - + +
293B PRO* 4.3 13.3 - - + +
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Residues in contact with ASN 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B GLY* 3.2 21.8 + - - +
111B THR* 5.0 1.2 - - - +
129B ALA* 5.2 0.2 - - - +
200B ILE* 3.0 21.7 + - - +
202B VAL* 1.3 86.1 - - - +
204B VAL* 1.3 65.4 + - - +
206B ALA* 3.2 2.6 + - - -
207B TRP* 3.1 21.3 + - - +
288B GLU 4.1 2.3 - - - +
289B ASP* 3.0 31.1 + - - +
290B GLU* 4.2 2.6 - - - +
291B PHE 3.1 33.8 + - - +
292B THR* 3.4 16.5 - - - +
293B PRO* 3.8 3.8 - - - +
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Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B THR* 3.8 17.0 - - + -
200B ILE 3.2 7.1 + - - +
201B THR 3.2 6.6 + - - +
203B ASN* 1.3 76.1 - - - +
205B LEU* 1.3 61.7 + - - +
207B TRP* 3.1 7.4 + - + +
208B LEU* 3.0 29.6 + - + +
239B TYR* 4.2 10.3 - - + +
268B LEU* 3.8 31.0 - - + -
287B LEU* 4.1 17.9 - - + +
288B GLU 3.5 14.8 - - - +
289B ASP* 3.5 24.9 - - + -
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Residues in contact with LEU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B THR* 3.2 20.4 + - + +
202B VAL 3.8 2.9 - - - +
203B ASN 3.2 0.2 - - - -
204B VAL* 1.3 75.0 - - - +
206B ALA* 1.3 61.7 + - - +
208B LEU* 3.2 9.0 + - + +
209B TYR* 3.1 29.1 + - + -
230B PHE* 4.9 0.2 - - + -
242B LEU* 3.9 35.7 - - + -
250B LEU* 3.8 24.5 - - + -
261B VAL* 4.3 2.0 - - + +
264B MET* 3.6 41.0 - - + +
265B CYS* 4.1 11.4 - - - -
268B LEU* 4.0 21.1 - - + -
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Residues in contact with ALA 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B VAL 3.1 15.6 + - - +
203B ASN 3.2 8.5 + - - +
205B LEU* 1.3 74.0 - - - +
207B TRP* 1.3 56.2 + - - +
209B TYR* 3.2 10.6 + - - +
210B ALA 3.0 20.6 + - - -
250B LEU* 4.0 12.3 - - + +
253B LEU* 4.5 2.5 - - + -
291B PHE 4.2 0.4 - - - +
292B THR 4.1 2.5 - - - -
293B PRO* 3.8 32.8 - - + -
296B VAL* 3.6 20.0 - - + +
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Residues in contact with TRP 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B PHE* 4.3 5.5 - + - -
203B ASN 3.1 12.5 + - - +
204B VAL* 3.1 10.3 + - + +
206B ALA* 1.3 75.0 - - - +
208B LEU* 1.3 82.2 + - + +
210B ALA* 3.2 7.6 + - - +
211B ALA* 2.9 24.4 + - - +
281B ILE* 3.3 46.2 - - + -
282B LEU* 3.8 23.1 + - + +
284B SER* 4.1 2.5 - - - -
286B LEU 3.5 19.1 - - - -
287B LEU* 3.9 13.5 - - + -
288B GLU* 3.6 49.1 - - + +
291B PHE* 3.9 32.6 - + + -
296B VAL* 4.4 3.6 - - - +
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Residues in contact with LEU 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B VAL* 3.0 26.4 + - + +
205B LEU* 3.6 10.3 - - + +
207B TRP* 1.3 94.9 - - + +
209B TYR* 1.3 64.8 + - - +
211B ALA* 3.2 6.8 + - - +
212B VAL* 3.0 27.4 + - - +
219B PHE* 3.8 17.9 - - + -
264B MET* 3.8 34.3 - - + +
267B SER* 5.4 1.1 - - - -
268B LEU* 4.3 27.4 - - + +
271B LEU* 4.5 10.1 - - + -
281B ILE* 4.1 16.8 - - + -
287B LEU* 4.7 2.0 - - + -
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Residues in contact with TYR 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B LEU* 3.1 22.0 + - + -
206B ALA* 3.2 8.0 + - - +
208B LEU* 1.3 75.5 - - - +
210B ALA* 1.3 60.5 + - - +
212B VAL* 3.2 3.4 + - + +
213B ILE* 2.8 37.3 + - + +
250B LEU* 4.3 22.0 - - + -
253B LEU* 3.6 40.6 - - + -
254B SER* 3.9 7.9 - - - -
257B THR* 3.6 32.1 - - + -
259B ILE* 3.1 20.7 + - + -
260B ALA 3.8 1.9 + - - -
261B VAL* 3.5 26.7 + - + +
264B MET* 3.1 32.5 - - + +
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Residues in contact with ALA 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B PHE* 3.9 34.1 - - + -
206B ALA 3.0 8.4 + - - +
207B TRP* 3.2 9.4 + - - +
209B TYR* 1.3 76.1 - - - +
211B ALA* 1.3 63.8 + - - +
213B ILE* 3.4 6.3 + - - +
214B ASN* 2.9 31.3 + - - +
282B LEU* 3.9 2.9 - - + -
296B VAL* 3.7 25.7 - - + +
300B CYS* 5.3 1.3 - - - -
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Residues in contact with ALA 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B TRP 2.9 12.1 + - - +
208B LEU 3.4 9.2 - - - +
209B TYR 3.1 0.2 - - - -
210B ALA* 1.3 78.3 - - - +
212B VAL* 1.3 60.0 + - - +
214B ASN* 3.2 8.5 + - - +
216B ASP* 2.8 31.4 + - + +
219B PHE* 3.8 9.9 - - + -
281B ILE* 3.4 33.0 - - + -
282B LEU* 3.5 17.6 - - + +
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Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B LEU 3.0 17.7 + - - +
209B TYR* 3.2 7.2 + - + +
211B ALA* 1.3 75.8 - - - +
213B ILE* 1.3 57.8 + - - +
215B GLY* 2.8 23.6 + - - -
216B ASP 3.1 14.5 + - - +
217B ARG* 3.9 32.2 + - + +
219B PHE* 3.9 16.4 - - + -
220B LEU* 4.1 21.5 - - + -
257B THR* 3.3 28.3 - - + +
259B ILE* 5.0 1.1 - - + -
264B MET* 4.2 8.3 - - + -
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Residues in contact with ILE 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B TYR* 2.8 28.0 + - + +
210B ALA* 3.7 8.5 - - - +
212B VAL* 1.3 72.8 - - - +
214B ASN* 1.3 66.0 + - - +
215B GLY 3.4 1.5 + - - -
253B LEU* 4.6 17.5 - - + +
256B GLN* 3.6 42.0 - - + +
257B THR* 4.2 11.9 - - - +
296B VAL* 5.0 7.0 - - + -
300B CYS* 4.5 20.2 - - + -
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Residues in contact with ASN 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B SER* 3.9 9.3 + - - -
2B GLY* 3.2 36.4 + - - +
3B PHE* 4.2 19.6 - - - +
210B ALA* 2.9 28.1 + - - +
211B ALA 3.2 3.6 + - - +
212B VAL 2.8 1.6 + - - -
213B ILE* 1.3 85.4 - - - +
215B GLY* 1.3 59.6 + - - +
216B ASP* 3.5 3.8 + - + +
282B LEU* 4.3 13.5 - - + -
300B CYS* 4.7 5.5 - - - -
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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