Contacts of the strand formed by residues 207 - 218 (chain B) in PDB entry 3HB8
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 GLU 207 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B ARG* 2.5 50.9 + - - +
202B TYR* 3.8 1.4 - - - +
203B VAL* 3.5 4.9 - - - -
204B VAL* 3.1 36.2 + - + +
205B ASN* 2.9 10.9 + - - +
206B SER* 1.3 78.0 - - - +
208B LEU* 1.3 59.7 + - - +
209B SER* 4.0 2.2 + - - +
244B LYS* 3.2 19.7 - - + +
245B PRO 4.0 7.9 - - - +
246B GLY* 4.3 4.3 - - - -
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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
----------------------------------------------------------
168B ILE* 3.6 25.1 - - + -
201B PHE* 3.9 10.3 - - + -
202B TYR 3.6 7.6 - - - +
203B VAL* 3.9 10.1 - - + +
206B SER 3.8 1.2 + - - -
207B GLU* 1.3 73.0 - - - +
209B SER* 1.3 73.8 + - - +
234B THR* 3.5 24.2 - - + +
237B ILE* 3.7 15.5 - - + +
238B ALA* 3.5 35.2 - - + +
241B THR* 4.7 2.0 - - - +
243B LEU* 4.1 16.2 - - + -
244B LYS 2.7 13.6 + - - +
245B PRO* 3.6 1.6 - - - +
246B GLY 2.6 30.6 + - - -
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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
----------------------------------------------------------
59A PHE* 4.0 20.3 - - - +
68B ARG* 4.8 1.7 + - - -
201B PHE* 3.3 8.8 - - - -
202B TYR* 2.7 45.3 + - - +
207B GLU* 4.0 1.8 + - - +
208B LEU* 1.3 74.5 - - - +
210B CYS* 1.3 62.0 + - - +
234B THR* 4.8 1.1 - - - -
246B GLY* 3.8 2.1 - - - -
247B ASP* 2.8 39.0 + - - +
249B ILE* 4.9 0.2 - - - -
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Residues in contact with CYS 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PHE* 3.8 3.8 - - - -
199B CYS* 4.1 10.1 - - - -
200B GLN 3.4 8.3 - - - -
201B PHE* 3.4 33.2 - - + -
209B SER* 1.3 74.3 - - - +
211B GLN* 1.3 69.0 + - - +
230B TYR* 4.6 13.9 - - - -
234B THR* 3.2 24.6 + - - +
247B ASP 2.9 6.9 + - - +
248B PHE* 3.2 15.2 - - + -
249B ILE* 2.8 31.2 + - - +
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Residues in contact with GLN 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PHE* 3.6 17.0 - - + -
60A GLY* 3.9 4.5 - - - -
213A TYR* 2.9 30.7 + - + +
251A THR* 3.6 8.5 - - - +
252A LEU 3.0 18.7 + - - +
253A GLY* 3.5 5.9 - - - -
62B GLN* 3.1 18.2 - - - +
199B CYS* 3.1 7.1 - - - +
200B GLN 2.9 30.2 + - - -
210B CYS* 1.3 78.1 - - - +
212B LEU* 1.3 61.9 + - - +
248B PHE* 4.9 0.2 - - - -
249B ILE* 3.1 26.8 - - + +
251B THR* 2.7 27.4 + - - +
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Residues in contact with LEU 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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213A TYR* 5.5 0.2 - - - -
196B HIS* 3.6 44.4 - - + +
198B LEU 3.5 13.2 - - - +
199B CYS* 4.4 0.7 - - + -
211B GLN* 1.3 77.0 - - - +
213B TYR* 1.3 71.6 + - - +
214B GLN* 3.6 16.6 - - + +
226B ASN* 4.8 2.7 - - + -
230B TYR* 3.7 36.8 - - + +
248B PHE* 4.0 20.1 - - + -
249B ILE 2.9 6.4 + - - +
250B HIS* 3.8 12.8 - - + -
251B THR* 2.9 33.1 + - - +
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Residues in contact with TYR 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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178A ILE* 5.4 0.9 - - + -
198A LEU* 3.9 21.8 - - + -
200A GLN* 2.8 40.5 + - + +
211A GLN* 3.4 46.4 + - + +
213A TYR* 3.7 33.2 - + + -
251A THR* 5.1 0.4 - - - -
196B HIS* 3.6 4.0 - - - -
197B ALA* 3.1 40.8 + - + -
198B LEU* 2.8 36.0 + - + +
211B GLN 4.3 0.2 - - - -
212B LEU* 1.3 72.7 - - - +
214B GLN* 1.3 59.7 + - - +
215B ARG* 4.1 12.1 - - + -
251B THR* 3.6 10.1 - - + -
252B LEU 5.2 0.2 - - - -
253B GLY* 4.0 3.5 - - - -
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Residues in contact with GLN 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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195B CYS* 3.3 16.0 - - - +
196B HIS* 3.5 19.5 - - + +
212B LEU* 3.6 7.1 + - + +
213B TYR* 1.3 74.7 - - - +
215B ARG* 1.3 61.8 + - - +
216B SER 3.0 24.9 + - - +
217B GLY* 3.5 14.1 - - - -
218B ASP 4.7 0.4 - - - +
223B VAL* 4.4 4.6 - - - +
226B ASN* 2.9 32.0 + - - +
250B HIS* 2.8 29.2 + - - +
251B THR 2.9 9.0 + - - +
252B LEU* 3.4 14.5 - - + +
253B GLY* 2.8 25.1 + - - -
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Residues in contact with ARG 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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175A ARG* 3.1 21.0 + - - +
176A ARG* 3.8 8.1 - - - +
178A ILE* 3.7 15.7 - - + -
200A GLN* 3.2 33.9 + - - +
182B TRP* 3.7 23.2 - - - -
192B LEU* 5.4 0.4 - - - +
193B PRO* 3.2 35.4 + - - +
194B PRO 2.9 21.4 + - - -
195B CYS* 3.0 28.7 + - - +
197B ALA* 4.8 2.2 - - + +
213B TYR* 4.0 8.0 + - + -
214B GLN* 1.3 71.5 - - - +
216B SER* 1.3 64.3 + - - +
254B ASP* 2.7 29.9 + - - +
615B PO4 2.6 36.3 + - - -
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Residues in contact with SER 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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175A ARG* 3.1 29.4 + - - -
195B CYS* 3.7 15.8 - - - -
214B GLN* 3.0 21.4 + - - +
215B ARG* 1.3 106.8 - - - +
217B GLY* 1.3 57.3 - - - +
252B LEU* 4.2 1.6 - - - -
254B ASP* 3.6 4.9 - - - -
256B HIS* 3.2 10.9 - - - -
615B PO4 3.6 10.5 + - - -
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Residues in contact with GLY 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B GLN* 3.5 14.4 - - - -
216B SER* 1.3 76.7 + - - +
218B ASP* 1.3 61.5 + - - -
219B MET* 3.3 5.2 + - - +
223B VAL* 3.9 4.9 - - - -
252B LEU* 3.8 13.7 - - - +
254B ASP 3.1 10.3 + - - -
255B ALA* 3.9 2.1 - - - -
256B HIS* 3.2 32.3 + - - -
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Residues in contact with ASP 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B GLN* 4.7 0.8 - - - +
217B GLY* 1.3 68.6 - - - -
219B MET* 1.3 65.2 + - - +
220B GLY* 3.1 14.7 + - - -
221B LEU* 3.4 29.9 + - - +
222B GLY* 3.4 7.7 + - - -
223B VAL* 3.0 24.0 + - - +
256B HIS* 4.0 13.5 + - - +
258B TYR* 4.0 31.0 + - + -
261B HIS* 4.2 7.4 + - - -
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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