Contacts of the helix formed by residues 209 - 224 (chain B) in PDB entry 6TOS
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 ASP 209 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208B ASP* 1.3 74.3 - - - +
210B LEU* 1.3 59.3 - - - +
212B PRO* 3.6 11.8 - - - +
213B LYS* 3.3 35.0 - - - +
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Residues in contact with LEU 210 (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 ASP* 3.0 9.0 + - + +
209B ASP* 1.3 77.3 - - - +
211B ALA* 1.4 65.0 + - - +
213B LYS* 3.0 29.7 + - + +
214B ILE* 3.1 37.3 + - + +
409B SOG 5.8 7.0 - - + -
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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
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206B TRP* 3.7 13.0 - - + -
208B ASP* 2.8 20.4 + - - +
210B LEU* 1.4 70.8 - - - +
212B PRO* 1.4 67.2 - - + +
213B LYS 3.3 0.2 + - - -
214B ILE* 3.3 7.3 + - - +
215B TYR* 3.0 24.8 + - - +
405B PGW 3.6 38.7 - - + +
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Residues in contact with PRO 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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206B TRP* 3.6 46.0 - - + +
208B ASP 3.1 26.9 - - - +
209B ASP* 3.6 13.9 - - - +
210B LEU 3.6 2.2 - - - -
211B ALA* 1.4 84.8 - - + +
213B LYS* 1.4 56.8 + - - +
216B HIS* 3.0 40.9 + - + +
322B ARG* 4.2 16.9 - - - +
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Residues in contact with LYS 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 ASP* 3.3 29.9 - - - +
210B LEU* 3.0 19.8 + - + +
212B PRO* 1.4 74.1 - - + +
214B ILE* 1.4 60.2 + - + +
217B SER* 2.7 34.2 + - - -
322B ARG 3.6 17.7 - - - +
323B VAL* 3.5 20.2 - - + +
325B GLY* 5.9 1.1 - - - +
409B SOG 3.1 62.6 + - + +
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Residues in contact with ILE 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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225A LEU* 3.7 29.8 - - + -
210B LEU* 3.1 41.9 + - + +
211B ALA* 3.3 6.5 + - - +
213B LYS* 1.4 70.7 - - + +
215B TYR* 1.3 65.6 + - - +
217B SER* 3.3 6.5 + - - -
218B CYS* 3.0 23.6 + - - -
405B PGW 3.7 30.7 - - + -
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Residues in contact with TYR 215 (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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175B ILE 5.3 0.7 + - - -
176B MET* 4.7 2.3 - - - -
178B PRO* 4.3 15.5 - - + -
179B GLN* 2.7 46.8 + - - +
182B VAL* 5.6 0.4 - - + -
204B GLU* 5.3 0.2 - - - -
206B TRP* 3.6 27.8 - + + -
211B ALA 3.0 17.3 + - - +
212B PRO 4.0 0.9 - - - +
214B ILE* 1.3 77.1 - - - +
216B HIS* 1.3 81.1 + + - +
218B CYS* 3.3 5.6 + - - +
219B PHE* 2.8 50.0 + + - +
405B PGW 3.8 57.4 - - + +
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Residues in contact with HIS 216 (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 GLU* 2.7 41.3 + - - -
212B PRO* 3.0 31.8 + - + +
215B TYR* 1.3 87.1 - + - +
217B SER* 1.3 58.9 + - - +
219B PHE* 3.9 6.3 - - - +
220B PHE* 3.2 27.0 + - - +
318B ASN* 4.6 14.0 - - - +
319B VAL* 3.9 5.9 - - - +
322B ARG* 3.4 40.1 - - + +
323B VAL* 3.9 10.1 - - + -
401B NRE 3.5 27.5 - - + +
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Residues in contact with SER 217 (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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221A ILE* 4.5 11.9 - - - -
213B LYS 2.7 23.1 + - - -
214B ILE* 3.6 6.2 - - - -
216B HIS* 1.3 73.7 - - - +
218B CYS* 1.4 63.0 - - - +
220B PHE* 3.4 6.1 + - - +
221B ILE* 3.1 34.6 + - - +
319B VAL* 5.2 1.6 - - - -
323B VAL* 3.4 22.5 - - - +
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Residues in contact with CYS 218 (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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221A ILE* 3.8 24.7 - - + -
225A LEU* 3.8 25.1 - - - -
226A ALA* 4.4 5.2 - - + -
214B ILE 3.0 18.3 + - - +
215B TYR 3.7 6.1 - - - +
217B SER* 1.4 73.7 - - - +
219B PHE* 1.4 59.8 + - - +
221B ILE* 3.3 0.9 + - - -
222B VAL* 2.8 36.9 + - - +
405B PGW 3.7 44.2 - - + -
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Residues in contact with PHE 219 (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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127B ALA* 4.6 2.5 - - + -
130B VAL* 4.9 11.7 - - + -
176B MET* 3.7 28.0 - - + -
179B GLN* 4.4 0.2 - - - -
215B TYR* 2.8 43.0 + - + +
216B HIS* 3.9 11.7 - - - +
218B CYS* 1.4 73.4 - - - +
220B PHE* 1.3 57.1 + - + +
223B THR* 2.7 59.2 + - + -
315B SER* 6.2 0.2 - - - -
318B ASN* 5.5 3.8 - - + -
401B NRE 3.5 51.6 - - + -
405B PGW 3.9 18.8 - - + +
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Residues in contact with PHE 220 (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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407A SOG 4.3 10.3 - - + -
216B HIS 3.2 8.3 + - - +
217B SER* 3.8 3.8 - - - +
218B CYS 3.3 0.2 - - - -
219B PHE* 1.3 82.0 - - + +
221B ILE* 1.3 67.8 + - + +
223B THR* 4.5 1.1 - - - -
224B TYR* 3.0 39.6 + + + +
225B LEU* 3.0 57.9 + - + -
312B LEU* 5.9 1.1 - - + -
315B SER* 3.7 36.1 - - - +
316B VAL* 4.7 12.6 - - + -
319B VAL* 3.4 31.6 - - + -
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Residues in contact with ILE 221 (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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217A SER* 5.0 5.6 - - - +
218A CYS* 4.0 28.9 - - - -
221A ILE* 3.3 43.1 - - + -
222A VAL* 4.0 17.3 - - + -
407A SOG 3.9 29.4 - - + -
217B SER* 3.1 24.8 + - - +
218B CYS 4.0 2.0 - - - +
220B PHE* 1.3 81.6 - - + +
222B VAL* 1.3 64.2 + - - +
225B LEU* 4.1 7.2 - - + -
226B ALA* 2.9 31.1 + - + +
227B PRO* 3.4 1.2 - - - +
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Residues in contact with VAL 222 (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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221A ILE* 4.2 8.3 - - + -
222A VAL* 4.7 3.1 - - + -
226A ALA* 3.8 27.8 - - + -
230A LEU* 6.3 0.2 - - + -
134B VAL* 4.6 2.4 - - - +
135B LEU* 5.9 1.6 - - - +
175B ILE* 4.8 7.2 - - + -
218B CYS 2.8 22.4 + - - +
221B ILE* 1.3 77.6 - - - +
223B THR* 1.3 59.9 + - + +
227B PRO* 3.2 21.1 - - - +
404B PGW 3.8 23.1 - - + +
405B PGW 3.7 46.4 - - + -
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Residues in contact with THR 223 (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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130B VAL* 4.4 18.9 - - + +
131B SER* 5.1 5.4 - - - -
134B VAL* 3.5 29.2 - - + +
175B ILE* 5.8 0.9 - - + -
176B MET* 3.7 30.1 - - + -
219B PHE* 2.7 45.6 + - + +
220B PHE* 4.5 0.3 - - - -
222B VAL* 1.3 78.1 - - + +
224B TYR* 1.3 65.4 + - - +
227B PRO* 4.1 4.5 - - - -
307B PHE* 4.9 2.8 - - - -
315B SER* 5.6 0.5 + - - -
405B PGW 4.2 10.3 - - + -
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Residues in contact with TYR 224 (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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220B PHE* 3.0 36.1 + + + +
222B VAL 3.5 1.6 + - - -
223B THR* 1.3 85.0 - - - +
225B LEU* 1.3 76.9 + - + +
226B ALA 3.7 1.1 - - - -
227B PRO* 3.6 2.1 - - - +
228B LEU* 3.2 57.3 + - + +
307B PHE* 5.1 1.6 - + - -
308B ALA* 2.7 35.0 + - - +
311B TYR* 3.7 14.6 - - + -
312B LEU* 3.3 43.3 - - + +
315B SER* 3.5 22.0 - - - +
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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