Contacts of the strand formed by residues 205 - 214 (chain B) in PDB entry 3QS1
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 LEU 205 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199B PHE* 3.0 32.3 + - - +
203B ASN* 1.4 86.2 - - + +
206B THR* 1.3 68.4 - - - +
226B GLU* 5.0 0.9 - - - +
227B PHE* 3.6 27.2 - - + -
230B LYS* 3.4 62.1 - - + +
231B PHE* 5.2 5.2 - - + +
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Residues in contact with THR 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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197B LEU 3.1 11.0 - - - -
198B HIS* 3.2 45.5 - - + +
203B ASN 4.3 2.2 + - - +
205B LEU* 1.3 83.2 - - - +
207B VAL* 1.3 65.6 + - - +
227B PHE* 4.4 3.0 - - - -
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Residues in contact with VAL 207 (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 LEU 4.2 1.0 - - - +
195B ASP* 3.5 2.8 - - - +
197B LEU* 3.1 39.8 + - + +
206B THR* 1.3 80.3 - - - +
208B GLU* 1.3 72.4 + - - +
210B ALA* 4.2 5.2 - - + -
227B PHE* 4.1 15.7 - - + -
297B ASN* 3.6 40.8 - - + +
299B PHE* 3.6 27.4 - - + -
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Residues in contact with GLU 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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195B ASP* 3.5 16.7 - - + +
207B VAL* 1.3 77.4 - - - +
209B LYS* 1.3 80.6 + - + +
210B ALA 3.6 0.2 + - - -
296B LYS* 4.3 5.5 + - - -
297B ASN* 5.1 0.2 - - - +
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Residues in contact with LYS 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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193B ASP* 3.5 32.0 - - - +
194B LEU* 3.4 7.6 - - - +
195B ASP* 2.5 47.8 + - - +
207B VAL 3.7 0.8 + - - -
208B GLU* 1.3 80.5 - - + +
210B ALA* 1.3 61.8 + - - +
211B THR* 4.2 1.2 + - - +
296B LYS* 3.4 15.9 + - - +
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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
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193B ASP* 3.5 2.2 - - - -
194B LEU* 2.4 52.9 + - - +
197B LEU* 3.0 30.1 - - + -
207B VAL* 4.2 5.4 - - + -
208B GLU 3.6 1.4 + - - -
209B LYS* 1.3 70.3 - - - +
211B THR* 1.3 62.0 + - - +
212B ALA 3.7 0.5 + - - -
296B LYS* 4.6 0.2 - - - +
297B ASN* 3.7 14.6 - - + +
299B PHE* 3.4 24.0 - - + -
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Residues in contact with THR 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ASN* 3.3 28.5 - - - +
191B GLN* 4.5 11.5 + - - +
192B VAL 3.2 10.3 - - - -
193B ASP* 4.3 3.8 - - - +
209B LYS 5.2 0.9 - - - +
210B ALA* 1.3 77.5 - - - +
212B ALA* 1.3 59.2 + - - +
213B ILE* 6.1 0.2 - - - -
296B LYS* 3.9 18.7 - - + +
297B ASN 3.2 3.8 + - - +
298B THR* 3.1 28.8 + - - +
299B PHE* 3.3 22.0 + - - +
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Residues in contact with ALA 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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190B TRP 3.6 1.6 - - - +
191B GLN* 3.3 2.4 - - - -
192B VAL* 3.0 35.3 + - + +
194B LEU* 4.1 29.2 - - + -
197B LEU* 5.5 4.0 - - + -
210B ALA 3.7 1.4 + - - -
211B THR* 1.3 73.2 - - - +
213B ILE* 1.3 63.5 + - - +
214B VAL* 3.6 2.4 + - + +
299B PHE* 3.3 10.1 - - + +
301B LEU* 4.2 22.7 - - + -
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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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34B GLY* 5.2 1.3 - - - -
189B TYR* 3.7 55.9 - - + -
190B TRP 3.9 3.4 - - - +
191B GLN* 4.4 10.1 - - + +
211B THR* 5.6 0.4 - - - +
212B ALA* 1.3 73.6 - - - +
214B VAL* 1.3 70.8 + - - +
215B ASP* 3.5 12.5 + - + +
291B LEU* 4.0 17.7 - - + -
298B THR* 3.9 25.4 - - + -
299B PHE 2.8 11.1 + - - -
300B ILE* 3.5 19.0 - - + +
301B LEU* 2.9 31.8 + - - +
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Residues in contact with VAL 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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33B THR* 2.8 21.8 + - - +
190B TRP* 3.1 24.0 + - + +
192B VAL* 5.8 4.3 - - + -
212B ALA* 4.8 3.6 - - + +
213B ILE* 1.3 74.6 - - - +
215B ASP* 1.3 60.3 + - - +
301B LEU* 3.6 17.9 - - + +
305B PHE* 5.2 1.6 - - + -
306B MET* 4.0 17.7 - - + -
311B THR* 4.6 7.4 - - + -
313B PHE* 3.4 33.2 - - + -
320B VAL* 4.7 6.3 - - + -
322B PHE* 4.2 26.9 - - + -
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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