Contacts of the strand formed by residues 244 - 258 (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 LYS 244 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67D LEU 5.9 0.2 - - - +
68D ARG* 3.3 41.8 - - - +
69D ASP* 4.7 10.0 + - - +
206D SER* 3.0 13.3 + - - +
207D GLU* 3.1 26.7 + - + +
208D LEU 3.0 19.5 + - - -
238D ALA* 4.4 0.2 - - - -
243D LEU* 1.3 71.8 - - - +
245D PRO* 1.3 75.5 - - + +
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Residues in contact with PRO 245 (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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67D LEU* 3.7 33.3 - - + +
68D ARG* 3.2 19.4 + - - -
207D GLU* 3.9 0.6 - - - +
208D LEU* 3.9 4.0 - - + +
234D THR* 4.7 3.4 - - + -
235D TYR* 3.8 33.4 - - + +
238D ALA* 3.7 19.7 - - + -
243D LEU 3.7 5.6 - - - +
244D LYS* 1.3 96.2 - - + +
246D GLY* 1.3 60.6 + - - +
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Residues in contact with GLY 246 (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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67D LEU* 3.0 28.1 + - - +
68D ARG* 3.4 18.7 + - - -
207D GLU* 4.1 12.3 - - - -
208D LEU 2.5 20.4 + - - -
209D SER* 4.1 2.5 - - - -
244D LYS 3.3 1.6 + - - -
245D PRO* 1.3 71.8 - - - +
247D ASP* 1.3 69.3 + - - +
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Residues in contact with ASP 247 (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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64D ARG* 3.5 31.5 - - + +
65D TYR 3.6 5.6 - - - +
66D SER* 3.8 17.7 + - - -
67D LEU* 4.0 6.7 - - - +
68D ARG* 3.1 23.0 + - - -
208D LEU 3.6 0.7 + - - +
209D SER* 2.9 18.8 + - - +
210D CYS 2.8 25.1 + - - -
246D GLY* 1.3 81.4 - - - +
248D PHE* 1.3 60.8 + - - +
249D ILE* 4.0 15.0 - - + -
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Residues in contact with PHE 248 (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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63D ALA 3.7 1.0 - - - +
64D ARG* 3.6 1.6 - - - -
65D TYR* 2.9 51.7 + + + +
67D LEU* 4.4 15.5 - - + -
72D PRO* 5.7 0.2 - - + -
210D CYS* 3.2 22.2 - - + -
212D LEU* 3.8 32.1 - - + -
227D ILE* 3.9 31.0 - - + -
230D TYR* 3.3 41.3 - - + -
231D ALA* 4.8 6.3 - - + -
234D THR* 4.6 1.3 - - - +
247D ASP* 1.3 74.4 - - - +
249D ILE* 1.3 63.0 + - - +
250D HIS* 3.7 25.6 - + + -
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Residues in contact with ILE 249 (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* 3.4 25.4 - - + +
63D ALA 3.2 5.6 - - - +
64D ARG* 3.1 43.1 - - + +
209D SER* 4.7 1.1 - - - -
210D CYS 2.7 10.5 + - - +
211D GLN* 3.0 40.9 - - + +
212D LEU 2.9 26.2 + - - -
247D ASP* 4.0 14.1 - - + +
248D PHE* 1.3 79.7 - - - +
250D HIS* 1.3 60.0 + - - +
251D THR* 3.9 0.2 - - - +
59E PHE* 3.7 27.8 - - + +
60E GLY* 4.0 4.3 - - - -
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Residues in contact with HIS 250 (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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36D GLN* 4.9 6.7 + - - -
61D MET 4.4 0.2 - - - -
62D GLN* 2.9 5.6 - - - -
63D ALA* 2.7 41.3 + - + +
65D TYR* 4.5 9.8 - - + -
212D LEU* 3.8 24.7 - - + +
214D GLN* 2.8 27.6 + - - +
223D VAL* 4.2 18.3 - - + +
226D ASN* 4.7 1.8 - - + +
227D ILE* 4.1 15.6 - - + +
248D PHE* 3.7 22.3 + + + -
249D ILE* 1.3 70.8 - - - +
251D THR* 1.3 64.9 + - - +
252D LEU* 3.5 35.8 + - + +
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Residues in contact with THR 251 (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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61D MET 3.4 2.9 - - - -
62D GLN* 2.9 13.3 + - - +
211D GLN* 2.7 29.0 + - - -
212D LEU 2.9 15.3 + - - +
213D TYR* 3.8 12.7 - - + -
214D GLN* 2.8 29.5 + - - +
249D ILE 4.0 0.2 + - - -
250D HIS* 1.3 73.3 - - - +
252D LEU* 1.3 63.8 + - - +
62E GLN* 3.7 10.5 - - - +
211E GLN* 3.2 31.2 - - - +
213E TYR* 5.6 0.2 - - - -
251E THR* 3.8 9.6 - - + -
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Residues in contact with LEU 252 (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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36D GLN* 4.5 8.7 - - - +
61D MET* 2.8 43.6 + - + +
213D TYR* 4.9 0.4 - - - -
214D GLN* 3.4 44.0 - - + +
217D GLY* 3.9 15.9 - - - +
219D MET* 3.7 35.0 - - + -
223D VAL* 4.5 1.6 - - + -
250D HIS* 3.5 27.6 + - + +
251D THR* 1.3 74.0 - - - +
253D GLY* 1.3 66.4 + - - +
254D ASP 5.0 0.4 - - - +
255D ALA* 4.3 10.1 - - + +
211E GLN* 3.3 11.5 - - - +
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Residues in contact with GLY 253 (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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59D PHE* 3.1 12.7 - - - -
60D GLY 2.8 28.1 + - - -
213D TYR* 3.6 7.5 + - - -
214D GLN 2.7 14.7 + - - -
215D ARG 3.2 8.3 - - - -
252D LEU* 1.3 71.8 - - - +
254D ASP* 1.3 58.2 + - - +
255D ALA* 3.6 1.2 + - - +
200E GLN* 3.5 18.4 - - - -
211E GLN* 3.6 5.4 - - - -
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Residues in contact with ASP 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D LYS* 2.9 31.0 + - - +
57D SER* 2.9 22.3 + - - -
58D VAL 3.8 3.1 - - - -
59D PHE* 3.6 5.4 - - + -
215D ARG 2.6 15.0 + - - +
216D SER* 4.5 0.2 - - - -
217D GLY 3.1 25.3 + - - -
252D LEU* 5.1 1.1 - - - -
253D GLY* 1.3 69.7 - - - +
255D ALA* 1.3 58.6 + - - +
256D HIS* 3.0 17.7 + - - +
175E ARG* 3.3 26.9 + - + -
200E GLN* 4.7 3.6 - - - +
202E TYR* 3.2 14.3 - - + -
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Residues in contact with ALA 255 (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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40D ILE* 3.8 5.6 - - + +
56D LEU 3.9 0.2 - - - +
57D SER* 3.2 2.9 + - - -
58D VAL 2.7 46.0 + - - +
61D MET* 3.5 27.4 - - + -
217D GLY 3.8 5.8 - - - -
219D MET* 3.4 21.5 - - + -
252D LEU* 4.3 11.7 - - + -
253D GLY 3.6 2.1 + - - +
254D ASP* 1.3 69.4 - - - +
256D HIS* 1.3 60.5 + - - +
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Residues in contact with HIS 256 (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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40D ILE* 4.5 2.7 - - - -
55D THR* 3.4 17.3 - - + +
56D LEU 3.1 13.9 - - - +
57D SER* 4.1 6.3 - - - -
216D SER* 3.3 26.0 - - - -
217D GLY 3.3 19.3 + - - -
218D ASP* 3.6 16.1 - - - -
219D MET* 2.9 28.0 + - - +
254D ASP* 3.0 24.3 + - - +
255D ALA* 1.3 74.5 - - - +
257D ILE* 1.3 68.4 + - - +
258D TYR* 5.0 3.6 - + - -
565D UMP 3.4 20.9 + - - -
175E ARG* 3.4 24.6 + - - +
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Residues in contact with ILE 257 (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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37D ILE* 4.5 4.5 - - + -
40D ILE* 3.6 28.3 - - + -
41D LEU* 3.5 36.1 - - + -
55D THR* 2.4 19.1 + - - -
56D LEU* 3.1 14.5 + - + +
218D ASP* 5.0 4.5 - - - -
219D MET* 3.3 28.0 - - + +
256D HIS* 1.3 83.8 - - - +
258D TYR* 1.3 67.4 + - - +
259D LEU* 4.3 0.3 - - - -
261D HIS* 5.7 0.4 - - + -
262D ILE* 4.8 5.2 - - + -
265D LEU* 3.6 31.0 - - + -
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Residues in contact with TYR 258 (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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169A LYS* 3.3 23.2 + - + -
170A THR* 3.8 25.1 - - + -
49D ASP* 3.1 28.4 + - + +
53D THR* 3.5 22.9 - - + -
54D GLY 3.9 0.9 - - - -
55D THR* 3.3 23.8 + - + +
218D ASP* 3.7 26.2 + - - -
256D HIS* 5.0 4.0 - + - -
257D ILE* 1.3 74.5 - - - +
259D LEU* 1.3 65.6 + - - +
260D ASN 4.4 1.1 - - - +
261D HIS* 3.1 46.0 + + + +
262D ILE* 3.6 6.8 + - - +
565D UMP 4.8 8.7 + - - -
175E ARG* 5.5 2.5 + - - -
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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