Contacts of the strand formed by residues 207 - 218 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68E ARG* 2.8 46.1 + - - +
202E TYR* 3.8 0.3 - - - +
203E VAL* 3.4 6.2 - - - +
204E VAL* 3.0 35.7 + - + +
205E ASN* 2.9 16.4 + - + +
206E SER* 1.3 79.7 - - - +
208E LEU* 1.3 61.7 + - - +
209E SER* 4.0 2.6 + - - +
244E LYS* 3.2 34.6 + - - +
245E PRO 4.9 1.3 - - - +
246E GLY* 4.3 8.3 - - - -
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Residues in contact with LEU 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168E ILE* 4.2 5.8 - - + -
201E PHE* 4.1 18.4 - - + -
202E TYR 3.2 15.9 - - - +
203E VAL* 3.6 14.4 - - + -
206E SER 4.0 0.4 + - - -
207E GLU* 1.3 71.6 - - - +
209E SER* 1.3 69.0 - - - +
234E THR* 3.6 23.1 - - + +
237E ILE* 3.9 19.5 - - + +
238E ALA* 3.7 35.4 - - + +
241E THR* 4.4 4.5 - - - +
243E LEU* 4.0 18.4 - - + -
244E LYS 2.8 11.1 + - - +
245E PRO 3.9 0.3 - - - -
246E GLY 3.0 21.0 + - - -
247E ASP 4.3 0.2 + - - -
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Residues in contact with SER 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D PHE* 3.9 21.7 - - - +
68E ARG* 4.7 2.8 + - - -
201E PHE* 3.5 4.0 - - - -
202E TYR* 2.8 42.3 + - - +
204E VAL* 5.8 1.6 - - - +
207E GLU* 4.0 3.1 + - - +
208E LEU* 1.3 79.7 - - - +
210E CYS* 1.3 65.5 + - - +
234E THR* 4.6 0.7 - - - -
246E GLY* 4.1 2.3 - - - -
247E ASP* 3.1 36.3 + - - +
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Residues in contact with CYS 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D PHE* 3.9 4.5 - - - -
199E CYS* 4.2 10.8 - - - -
200E GLN 3.2 10.5 - - - -
201E PHE* 3.5 29.4 - - + -
209E SER* 1.3 76.3 - - - +
211E GLN* 1.3 70.1 + - - +
230E TYR* 4.8 7.9 - - - -
233E LEU* 5.9 0.2 - - - -
234E THR* 3.3 25.1 - - + +
247E ASP 3.0 7.0 + - - +
248E PHE* 3.2 20.9 - - + -
249E ILE 2.8 22.9 + - - -
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Residues in contact with GLN 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D PHE* 3.6 17.0 - - + -
60D GLY* 4.0 4.0 - - - -
213D TYR* 3.1 25.8 + - + +
251D THR* 3.2 16.6 - - - +
252D LEU 3.3 16.3 - - - +
253D GLY* 3.6 4.9 - - - -
62E GLN* 3.0 13.6 - - - +
199E CYS* 3.0 5.4 - - - +
200E GLN* 2.9 32.4 + - - +
210E CYS* 1.3 76.3 - - - +
212E LEU* 1.3 68.1 + - - +
249E ILE* 3.2 24.9 - - + +
251E THR* 2.6 29.8 + - - +
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Residues in contact with LEU 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D TYR* 5.7 0.2 - - - -
196E HIS* 3.8 36.6 - - + +
198E LEU 3.7 11.4 - - - +
199E CYS* 4.1 4.9 - - + -
211E GLN* 1.3 78.2 - - - +
213E TYR* 1.3 72.8 + - - +
214E GLN* 4.2 5.4 - - + +
226E ASN* 5.0 4.9 - - + +
230E TYR* 3.7 40.4 - - + -
248E PHE* 3.7 21.1 - - + -
249E ILE 2.9 6.7 + - - -
250E HIS* 4.1 21.3 - - + +
251E THR* 3.0 31.2 + - - +
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Residues in contact with TYR 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D ILE* 5.1 0.7 - - + -
198D LEU* 3.7 24.5 - - + -
200D GLN* 2.7 44.9 + - + +
211D GLN* 2.9 43.1 + - + +
213D TYR* 4.3 27.8 - + + -
251D THR* 5.3 0.2 - - + -
196E HIS 3.7 0.7 - - - -
197E ALA* 3.0 38.1 + - + +
198E LEU* 2.8 23.8 + - + +
212E LEU* 1.3 76.7 - - - +
214E GLN* 1.3 58.2 + - - +
215E ARG* 4.1 12.6 - - + -
251E THR* 3.4 21.8 - - + -
253E GLY* 3.5 7.1 - - - -
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Residues in contact with GLN 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E CYS* 2.8 16.5 - - - +
196E HIS* 3.6 23.7 - - - +
212E LEU* 4.0 4.6 - - + -
213E TYR* 1.3 76.5 - - - +
215E ARG* 1.3 61.8 + - - +
216E SER 2.8 19.4 + - - +
217E GLY* 4.2 1.8 - - - -
223E VAL* 4.5 1.4 - - - +
226E ASN* 3.2 29.4 + - - +
250E HIS* 2.5 37.2 + - + +
251E THR 3.1 6.2 + - - +
252E LEU* 3.4 20.8 - - + +
253E GLY 2.9 22.1 + - - -
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Residues in contact with ARG 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D ARG 3.6 9.3 + - - +
176D ARG* 3.5 11.7 - - - +
178D ILE* 3.6 29.6 - - + -
200D GLN* 3.2 27.7 + - - +
616D PO4 2.6 39.2 + - - -
182E TRP* 4.1 5.6 - - + -
193E PRO* 3.0 50.9 + - - +
194E PRO 3.1 15.6 + - - +
195E CYS* 2.8 26.5 + - - +
197E ALA* 4.7 2.4 - - + +
213E TYR* 4.0 8.4 + - + -
214E GLN* 1.3 73.2 - - - +
216E SER* 1.3 78.7 + - - +
254E ASP* 2.7 31.2 + - - +
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Residues in contact with SER 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D ARG* 3.1 31.4 + - - -
616D PO4 3.9 4.6 + - - -
195E CYS* 4.1 11.2 + - - +
214E GLN* 2.8 26.9 + - - +
215E ARG* 1.3 113.1 - - - +
217E GLY* 1.3 60.0 + - - +
218E ASP 4.4 0.2 - - - -
252E LEU* 4.6 0.7 - - - -
254E ASP 3.8 3.8 + - - -
256E HIS* 3.3 10.9 - - - -
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Residues in contact with GLY 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214E GLN* 4.2 2.7 - - - -
216E SER* 1.3 78.4 + - - +
218E ASP* 1.3 60.9 + - - -
219E MET* 3.1 10.8 + - - +
223E VAL* 3.8 6.5 - - - -
226E ASN* 5.4 0.4 - - - -
252E LEU* 3.6 22.0 - - - +
254E ASP 3.2 11.7 + - - -
255E ALA* 4.0 2.6 - - - -
256E HIS* 3.2 28.0 + - - -
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Residues in contact with ASP 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216E SER 4.4 0.4 - - - -
217E GLY* 1.3 68.2 - - - -
219E MET* 1.3 62.9 + - - +
220E GLY* 3.1 6.2 + - - -
221E LEU* 2.9 42.4 + - - +
222E GLY* 4.7 2.0 - - - -
223E VAL* 3.2 20.6 + - - +
226E ASN* 5.6 0.4 + - - -
256E HIS* 3.8 14.3 - - + +
258E TYR* 3.3 30.8 + - + -
261E HIS* 4.0 12.6 + - - -
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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