Contacts of the strand formed by residues 204 - 216 (chain B) in PDB entry 3RT0
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 204 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199B ARG* 5.6 0.2 + - - -
202B MET* 3.8 29.3 - - + +
203B GLU* 1.3 82.3 - - - +
205B ALA* 1.3 61.6 + - - +
241B VAL* 5.7 0.2 - - - -
242B TYR 3.4 4.9 - - - +
243B ASP* 3.2 27.6 - - - +
252B ASP* 4.7 4.3 - - - +
255B ARG* 5.2 1.6 + - - -
431B SER* 2.8 25.7 + - - -
492B ASP* 5.2 0.9 - - - +
493B ASN* 3.4 25.1 + - - +
495B SER* 2.8 33.6 + - - +
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Residues in contact with ALA 205 (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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194B SER* 4.8 5.2 - - - -
204B ASP* 1.3 76.9 - - - +
206B PHE* 1.3 60.8 + - - +
241B VAL* 3.7 4.5 - - - +
242B TYR* 2.8 34.4 + - + +
251B ALA* 3.6 33.2 - - + +
252B ASP* 3.9 11.7 - - - +
255B ARG* 4.0 19.5 - - + +
495B SER* 4.9 0.7 + - - -
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Residues in contact with PHE 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B THR* 3.7 32.8 - - + -
194B SER* 3.6 33.0 - - - +
205B ALA* 1.3 77.4 - - - +
207B ALA* 1.3 67.2 + - - +
208B VAL* 4.1 19.1 - - + -
240B GLY 3.2 14.1 - - - +
241B VAL* 4.4 11.4 - - + -
242B TYR* 4.1 4.9 - - - -
255B ARG* 3.3 23.6 - - - +
495B SER* 5.2 3.4 - - - -
497B ILE* 4.6 2.2 - - + -
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Residues in contact with ALA 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B PHE* 1.3 76.6 - - - +
208B VAL* 1.3 65.5 + - - +
238B PHE* 3.8 19.7 - - + +
239B PHE* 3.4 2.8 - - - -
240B GLY 2.8 37.7 + - - +
242B TYR* 4.0 7.4 - - + -
255B ARG* 3.7 23.3 - - + +
259B HIS* 4.5 9.4 - - + +
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Residues in contact with VAL 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B TRP* 3.5 46.7 - - + +
192B THR* 4.1 7.0 - - - +
206B PHE* 4.1 13.3 - - + -
207B ALA* 1.3 80.9 - - - +
209B SER* 1.3 66.0 + - - +
210B PRO* 3.9 9.3 - - + +
238B PHE 3.2 3.1 - - - -
239B PHE* 3.7 30.1 - - + -
497B ILE* 3.9 15.5 - - + -
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Residues in contact with SER 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ALA 4.3 0.2 - - - -
208B VAL* 1.3 76.7 - - - +
210B PRO* 1.3 65.4 + - - +
212B PHE* 3.0 44.8 - - - +
237B HIS* 5.1 0.2 - - - -
238B PHE* 2.7 38.8 + - - -
259B HIS* 4.4 15.3 - - - -
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Residues in contact with PRO 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B PRO* 3.8 25.6 - - + -
190B TRP* 3.8 24.2 - - + -
208B VAL* 3.9 13.6 - - + +
209B SER* 1.3 85.5 + - - +
211B HIS* 1.3 77.4 + - + +
212B PHE* 3.0 5.3 + - - -
237B HIS* 3.7 10.1 - - + +
239B PHE* 6.0 0.7 - - + -
467B GLY 4.5 5.2 - - - +
468B LYS 5.3 3.8 - - - +
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Residues in contact with HIS 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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186B CYS 4.0 6.7 - - - -
187B ILE* 5.2 1.1 - - + -
188B PRO* 3.6 19.8 - - + +
210B PRO* 1.3 83.8 - - + +
212B PHE* 1.3 62.6 + - - +
213B LEU 3.5 3.3 + - - +
214B LYS* 5.9 2.3 + - - +
235B THR* 3.5 30.5 + - + +
236B GLY 3.9 0.7 - - - -
237B HIS* 2.9 31.0 + + - -
467B GLY* 4.3 9.1 + - - -
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Residues in contact with PHE 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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209B SER* 3.0 38.8 - - - +
210B PRO 3.0 2.0 + - - -
211B HIS* 1.3 80.3 - - - +
213B LEU* 1.3 91.0 + - + +
214B LYS* 4.3 0.7 + - - +
236B GLY 3.1 5.4 + - - +
238B PHE* 4.3 15.3 - + + -
259B HIS* 3.2 49.6 - + + -
260B PHE* 3.8 31.4 - + - -
262B LEU* 5.8 0.2 - - + -
263B ALA* 4.1 8.9 - - + +
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Residues in contact with LEU 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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211B HIS 4.8 0.4 - - - -
212B PHE* 1.3 110.9 - - + +
214B LYS* 1.3 64.5 + - - +
215B LEU* 4.0 20.2 - - + -
235B THR* 3.3 8.5 + - - -
236B GLY* 2.7 41.0 + - - +
238B PHE* 5.3 2.2 - - + -
262B LEU* 4.0 12.8 - - + -
263B ALA* 4.1 20.2 - - + +
266B ILE* 4.0 14.8 - - + -
333B LEU* 3.8 37.7 - - + -
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Residues in contact with LYS 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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211B HIS 5.9 1.9 + - - +
212B PHE 4.3 1.0 + - - +
213B LEU* 1.3 75.3 - - - +
215B LEU* 1.3 64.5 + - - +
216B PRO* 3.6 8.0 - - - +
233B HIS* 3.9 31.4 - - + -
234B LEU 3.7 4.0 - - - +
235B THR* 5.5 4.7 - - - +
266B ILE* 4.4 6.6 - - - +
270B LYS* 4.1 10.0 - - - +
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Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B LEU* 4.0 18.6 - - + -
214B LYS* 1.3 72.4 - - - +
216B PRO* 1.3 73.6 - - + +
217B ILE* 3.1 1.4 + - - -
220B LEU* 4.2 26.2 - - + +
233B HIS* 3.3 4.4 - - - -
234B LEU* 2.7 39.8 + - - +
236B GLY* 4.1 19.3 - - - -
266B ILE* 3.5 31.6 - - + -
286B TRP* 3.9 25.8 - - + -
333B LEU* 4.8 10.5 - - + -
334B VAL 5.7 0.2 - - - +
335B CYS* 4.4 11.7 - - + -
340B VAL* 6.5 0.4 - - + -
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Residues in contact with PRO 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LYS 3.6 8.3 - - - +
215B LEU* 1.3 85.4 - - + +
217B ILE* 1.3 65.8 + - - +
218B LYS* 3.1 4.3 - - + +
219B MET* 2.9 41.5 + - + +
220B LEU* 4.1 2.6 + - - +
232B THR 3.9 6.3 - - - +
233B HIS* 3.9 6.7 - - + +
266B ILE* 4.0 11.0 - - + +
269B ILE* 5.3 0.4 - - + -
270B LYS* 3.3 32.1 - - + +
272B GLU* 3.6 24.2 - - - +
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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