Contacts of the strand formed by residues 207 - 218 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68D ARG* 2.7 47.7 + - - -
203D VAL* 3.2 12.2 - - - +
204D VAL* 3.0 36.8 + - + +
205D ASN* 3.0 15.9 + - - +
206D SER* 1.3 81.6 - - - +
208D LEU* 1.3 61.6 + - - +
209D SER* 5.5 1.3 - - - +
243D LEU* 4.6 2.2 - - - -
244D LYS* 3.1 34.2 + - + +
245D PRO 3.9 0.2 - - - +
246D GLY* 4.1 7.5 - - - -
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Residues in contact with LEU 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D ILE* 4.1 14.8 - - + -
201D PHE* 4.1 12.1 - - + -
202D TYR 3.2 15.9 - - - +
203D VAL* 3.6 17.0 - - + -
207D GLU* 1.3 75.3 - - - +
209D SER* 1.3 69.3 + - - +
234D THR* 3.7 20.9 - - + +
237D ILE* 3.5 22.4 - - + -
238D ALA* 3.5 38.6 - - + +
241D THR* 4.8 2.2 - - - +
243D LEU* 4.6 7.0 - - + -
244D LYS 3.0 10.8 + - - +
245D PRO* 3.6 1.4 - - + +
246D GLY* 2.5 28.6 + - - -
247D ASP 3.6 0.7 + - - -
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Residues in contact with SER 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D PHE* 3.4 4.3 - - - -
202D TYR* 2.8 45.7 + - - +
204D VAL* 5.8 1.4 - - - +
207D GLU* 4.3 1.6 - - - +
208D LEU* 1.3 79.7 - - - +
210D CYS* 1.3 62.5 + - - +
234D THR* 5.0 0.7 - - - -
246D GLY* 4.0 2.6 - - - -
247D ASP* 2.9 36.0 + - - +
249D ILE* 4.7 0.9 - - - -
59E PHE* 4.0 19.9 - - - +
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Residues in contact with CYS 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D CYS* 4.1 10.3 - - - -
200D GLN 3.4 8.1 - - - -
201D PHE* 3.1 36.3 - - + -
209D SER* 1.3 74.9 - - - +
211D GLN* 1.3 66.8 + - - +
230D TYR* 4.8 7.6 - - - -
234D THR* 3.4 23.8 + - - +
247D ASP 2.8 6.9 + - - -
248D PHE* 3.2 18.8 - - + -
249D ILE* 2.7 30.3 + - - +
59E PHE* 3.7 3.6 - - - -
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Residues in contact with GLN 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D GLN* 2.7 20.6 - - - +
198D LEU* 4.2 0.3 - - - +
199D CYS* 3.0 6.1 - - - +
200D GLN* 2.8 31.3 + - - +
210D CYS* 1.3 75.4 - - - +
212D LEU* 1.3 68.2 + - - +
249D ILE* 3.0 20.2 - - + +
251D THR* 2.7 24.6 + - - -
59E PHE* 3.3 19.7 - - + -
60E GLY* 4.2 4.6 - - - -
213E TYR* 2.9 39.0 + - + +
251E THR* 3.6 6.5 - - - +
252E LEU 3.4 13.4 - - - +
253E GLY* 3.4 5.0 - - - -
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Residues in contact with LEU 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D HIS* 3.7 19.3 - - + +
198D LEU 3.8 9.4 - - - +
199D CYS* 4.2 1.1 - - + -
210D CYS* 5.4 0.2 - - - -
211D GLN* 1.3 77.2 - - - +
213D TYR* 1.3 80.2 + - - +
214D GLN* 4.2 8.3 - - - +
226D ASN* 4.7 4.0 - - + -
230D TYR* 3.2 51.8 - - + -
248D PHE* 3.8 21.0 - - + -
249D ILE 2.9 6.3 + - - -
250D HIS* 3.8 23.6 - - + +
251D THR* 2.9 31.0 + - - +
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Residues in contact with TYR 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D HIS* 3.5 5.7 - - - -
197D ALA* 2.9 50.5 + - + -
198D LEU* 2.9 26.8 + - + +
212D LEU* 1.3 76.6 - - - +
214D GLN* 1.3 59.4 + - - +
215D ARG* 3.7 12.3 - - + -
251D THR* 3.6 15.5 - - + -
253D GLY* 3.6 5.2 - - - -
178E ILE* 5.1 0.9 - - + -
198E LEU* 4.2 16.2 - - + -
200E GLN* 2.5 45.5 + - + +
211E GLN* 3.1 43.5 + - + +
213E TYR* 4.3 27.4 - + + -
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Residues in contact with GLN 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D CYS* 3.3 11.4 - - + +
196D HIS* 3.7 17.1 + - + +
212D LEU* 4.2 1.8 - - + +
213D TYR* 1.3 77.0 - - - +
215D ARG* 1.3 57.7 + - - +
216D SER 2.9 28.6 + - - +
217D GLY* 3.1 18.0 - - - -
223D VAL* 4.3 3.2 - - - +
226D ASN* 3.0 34.5 + - - +
250D HIS* 2.8 29.4 + - + +
251D THR 2.8 11.0 + - - +
252D LEU* 3.4 17.2 - - + +
253D GLY 2.7 30.5 + - - -
565D UMP 3.3 6.1 - - - -
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Residues in contact with ARG 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D TRP* 3.9 2.5 - - - -
192D LEU* 6.1 1.2 - - - +
193D PRO* 2.9 34.4 + - - +
194D PRO 2.7 28.9 + - - +
195D CYS* 2.9 32.3 + - - +
197D ALA* 4.8 1.5 - - + +
213D TYR* 3.7 7.4 - - + -
214D GLN* 1.3 70.8 - - - +
216D SER* 1.3 62.9 + - - +
253D GLY* 3.2 0.7 - - - -
254D ASP* 2.6 30.3 + - - +
565D UMP 2.7 44.2 + - - -
175E ARG 3.2 17.0 + - - +
176E ARG* 3.4 13.3 - - - +
178E ILE* 3.7 25.6 - - + -
200E GLN* 3.1 35.1 - - - +
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Residues in contact with SER 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D CYS* 3.8 4.9 - - - -
214D GLN* 2.9 22.1 + - - +
215D ARG* 1.3 91.8 - - - +
217D GLY* 1.3 59.8 + - - +
252D LEU* 4.4 1.6 - - - -
254D ASP 3.6 5.2 - - - -
256D HIS* 3.3 10.4 - - - -
565D UMP 3.4 36.3 + - - -
175E ARG* 3.3 30.7 + - - -
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Residues in contact with GLY 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D GLN* 3.1 18.2 - - - -
216D SER* 1.3 78.3 + - - +
218D ASP* 1.3 62.7 + - - -
219D MET* 3.4 3.6 + - - +
223D VAL* 3.8 4.7 - - - -
252D LEU* 3.9 9.7 - - - +
254D ASP 3.1 9.7 + - - +
255D ALA* 3.8 2.9 - - - -
256D HIS* 3.3 28.8 + - - -
565D UMP 4.3 2.5 - - - -
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Residues in contact with ASP 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D GLY* 1.3 69.3 - - - -
219D MET* 1.3 64.6 + - - +
220D GLY 2.8 10.9 + - - -
221D LEU* 3.0 32.3 + - - +
223D VAL* 3.1 18.7 + - - +
256D HIS* 3.6 17.7 - - - +
257D ILE* 5.0 3.5 - - - -
258D TYR* 3.7 28.2 + - - -
261D HIS* 5.2 6.3 + - - -
565D UMP 3.4 38.9 + - + +
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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