Contacts of the strand formed by residues 204 - 222 (chain D) in PDB entry 1UHG
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 204 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D ARG* 3.5 0.2 - - - -
200D VAL* 3.0 38.1 + - + +
201D THR* 2.9 43.1 + - + +
202D GLU 3.4 0.4 - - - -
203D GLN* 1.3 79.2 - - - +
205D SER* 1.3 74.3 + - - +
206D LYS* 5.7 2.9 - - - +
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Residues in contact with SER 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D PRO* 4.2 19.7 - - - +
198D PHE 3.2 12.6 - - - -
199D ARG* 3.5 17.8 - - - +
200D VAL* 4.4 1.1 - - - +
201D THR 4.9 0.3 + - - -
202D GLU 5.4 1.7 + - - -
203D GLN 5.4 0.2 - - - -
204D GLU* 1.3 86.2 + - - +
206D LYS* 1.3 61.2 + - - +
207D PRO* 4.7 1.4 - - - +
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Residues in contact with LYS 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D PRO* 4.2 2.7 - - - -
198D PHE* 2.7 38.7 + - + +
200D VAL* 5.1 10.1 - - + +
204D GLU* 5.7 3.4 - - - +
205D SER* 1.3 74.9 - - - +
207D PRO* 1.3 86.9 - - + +
208D VAL* 6.2 0.7 - - + -
384D SER* 5.4 7.6 - - - +
385D PRO* 6.1 4.0 - - + +
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Residues in contact with PRO 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D ALA* 4.8 14.1 - - + -
196D MET 3.6 8.1 - - - +
197D PRO* 4.3 5.2 - - + -
205D SER 4.7 1.3 - - - +
206D LYS* 1.3 113.6 - - + +
208D VAL* 1.3 59.8 + - - +
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Residues in contact with VAL 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D ALA* 3.2 3.9 - - - -
196D MET 2.9 40.1 + - - +
198D PHE* 3.7 25.8 - - + -
206D LYS* 6.2 0.7 - - + -
207D PRO* 1.3 74.8 - - - +
209D GLN* 1.3 68.5 + - - +
210D MET* 3.2 24.2 + - + -
283D PRO* 3.8 10.1 - - + -
284D ARG 4.4 4.3 - - - +
385D PRO* 3.6 35.0 - - + +
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Residues in contact with GLN 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D THR* 3.5 22.6 + - + +
194D GLN* 4.0 9.2 - - - +
195D ALA* 3.7 22.1 + - - +
208D VAL* 1.3 75.8 - - + +
210D MET* 1.3 59.3 + - - +
283D PRO* 3.4 2.9 - - - +
284D ARG* 3.0 56.6 + - + +
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Residues in contact with MET 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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192D ASP 4.2 1.4 - - - +
193D THR* 3.3 4.4 - - - -
194D GLN* 2.9 39.2 + - + +
196D MET* 3.7 38.8 - - + -
197D PRO 5.0 0.4 - - - +
198D PHE* 4.3 0.9 - - + -
208D VAL* 3.2 25.4 + - + +
209D GLN* 1.3 71.5 - - - +
211D MET* 1.3 67.8 + - - +
212D TYR* 4.0 1.2 + - - +
281D TYR* 3.7 13.2 - - + -
282D LEU 3.4 12.1 - - - -
283D PRO* 3.3 26.2 - - + -
360D ALA 3.5 19.1 - - - +
361D ASP* 3.9 21.1 - - + -
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Residues in contact with MET 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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184D TRP* 4.6 0.2 - - - +
188D PHE* 3.6 26.2 - - + -
193D THR* 3.7 17.7 - - - +
210D MET* 1.3 74.8 - - - +
212D TYR* 1.3 61.4 + - - +
281D TYR* 3.2 6.1 - - - -
282D LEU* 2.8 68.4 + - + +
283D PRO 3.8 13.9 - - - +
284D ARG* 3.6 20.0 - - + -
334D ILE* 4.2 7.2 - - + -
335D ASN* 3.2 41.5 - - - +
336D GLU* 3.3 14.6 - - + -
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Residues in contact with TYR 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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188D PHE* 3.5 10.5 - - - +
189D LYS 4.5 1.6 + - - -
192D ASP* 3.5 60.9 + - + +
193D THR* 4.7 0.6 + - - -
210D MET 4.0 1.9 + - - +
211D MET* 1.3 77.8 - - - +
213D GLN* 1.3 73.1 + - - +
214D ILE* 3.3 21.5 - - + +
279D LYS* 2.7 41.7 + - + -
280D VAL 3.2 11.9 - - - -
281D TYR* 3.4 49.8 - + + -
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Residues in contact with GLN 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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186D LYS* 3.1 36.3 + - - +
187D ALA 3.5 10.6 + - - +
188D PHE* 3.5 41.2 - - + -
189D LYS 5.4 0.7 - - - +
192D ASP* 5.2 2.2 - - - +
212D TYR* 1.3 83.2 - - - +
214D ILE* 1.3 68.3 + - - +
215D GLY* 4.6 0.5 - - - -
217D PHE* 3.5 34.4 - - + -
232D LEU* 5.7 0.2 - - - +
278D ILE 3.8 0.3 - - - +
279D LYS* 3.5 1.7 - - - -
280D VAL* 2.7 37.2 + - + +
342D VAL* 5.7 3.1 - - - +
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Residues in contact with ILE 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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212D TYR* 3.3 30.5 - - + +
213D GLN* 1.3 83.0 - - - +
215D GLY* 1.3 61.4 + - - +
277D LYS* 5.2 0.9 - - + -
278D ILE 3.4 9.0 - - - +
279D LYS* 3.6 22.0 - - + +
342D VAL* 4.4 11.1 - - - +
347D ALA 5.6 0.2 - - - +
350D ASP* 3.8 31.6 - - + +
351D ALA* 3.6 32.3 - - + +
354D VAL* 3.8 22.7 - - + -
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Residues in contact with GLY 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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186D LYS* 4.8 4.0 - - - -
213D GLN* 4.6 2.0 - - - -
214D ILE* 1.3 77.5 - - - +
216D LEU* 1.3 64.5 + - - -
217D PHE* 3.4 22.3 + - - -
276D ARG 3.4 0.3 - - - +
277D LYS* 4.0 7.9 - - - -
278D ILE 2.9 33.0 + - - +
342D VAL* 5.4 4.7 - - - -
350D ASP* 5.0 2.9 - - - -
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Residues in contact with LEU 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D LYS* 2.7 37.7 + - - +
215D GLY* 1.3 70.7 - - - -
217D PHE* 1.3 63.2 + - - +
275D GLU* 3.5 36.8 - - + +
276D ARG* 3.4 34.3 - - - +
277D LYS* 3.8 33.0 - - + +
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Residues in contact with PHE 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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186D LYS* 3.7 26.9 - - + -
213D GLN* 3.5 30.7 - - - -
215D GLY* 3.5 31.9 - - - -
216D LEU* 1.3 74.6 - - - +
218D ARG* 1.3 62.8 + - - +
219D VAL* 3.5 4.2 + - - +
230D LEU* 3.6 20.9 - - + -
231D GLU 3.6 8.7 - - - +
232D LEU* 3.4 25.8 - - + -
233D PRO* 4.2 15.0 - - + -
274D GLU 3.4 0.7 - - - +
275D GLU* 3.4 8.5 + - - -
276D ARG* 2.8 31.0 + - - +
278D ILE* 4.0 4.7 - - + -
280D VAL* 3.9 24.9 - - + -
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Residues in contact with ARG 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 PHE* 1.3 71.3 - - - +
219D VAL* 1.3 58.7 + - - +
230D LEU* 3.7 2.4 - - - +
231D GLU* 3.0 65.7 + - + +
268D THR* 3.2 28.1 + - - -
269D SER 3.7 9.5 + - - -
270D SER* 4.2 5.9 - - - +
273D MET* 3.2 45.4 + - + +
274D GLU* 3.4 8.0 - - - +
275D GLU* 3.5 31.2 + - + +
369D LYS* 5.7 2.8 - - - +
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Residues in contact with VAL 219 (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 PHE 3.9 7.6 - - - +
218D ARG* 1.3 76.4 - - - +
220D ALA* 1.3 79.8 + - - +
221D SER* 5.7 0.4 - - - -
228D LYS* 5.2 4.9 - - + -
229D ILE 3.2 16.8 - - - +
230D LEU* 4.5 9.4 - - + -
272D VAL 4.1 0.3 - - - +
273D MET* 3.4 5.9 - - - +
274D GLU* 3.0 35.2 + - - +
276D ARG* 3.9 30.0 + - + +
278D ILE* 4.3 23.6 - - + -
356D GLU* 4.3 11.7 - - - +
358D PHE* 4.9 7.4 - - + -
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Residues in contact with ALA 220 (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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219D VAL* 1.3 82.5 - - - +
221D SER* 1.3 61.1 + - - +
222D MET* 4.1 3.1 - - - +
228D LYS* 3.2 5.0 - - - +
229D ILE* 2.8 47.9 + - + +
272D VAL* 3.6 38.4 - - + +
273D MET* 3.8 5.8 - - + -
276D ARG* 6.2 1.1 - - - +
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Residues in contact with SER 221 (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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219D VAL* 5.7 0.4 - - - -
220D ALA* 1.3 74.6 - - - +
222D MET* 1.3 65.7 + - - +
223D ALA 3.9 1.4 + - - -
227D MET 3.6 5.4 + - - -
228D LYS* 3.6 28.1 - - - +
247D ASP* 5.5 0.7 + - - -
272D VAL* 6.0 0.3 - - - +
356D GLU* 5.1 10.1 - - - -
3401D SO4 4.0 5.5 + - - -
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Residues in contact with MET 222 (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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220D ALA* 4.5 8.1 - - - +
221D SER* 1.3 78.8 + - - +
223D ALA* 1.3 65.8 + - - +
225D GLU* 3.7 25.8 - - + +
226D LYS* 3.4 10.2 + - - -
227D MET* 2.7 41.5 + - + +
229D ILE* 5.2 1.6 - - + -
247D ASP* 4.6 2.4 - - - +
266D GLU* 5.5 3.4 - - + +
267D TRP* 3.4 35.4 - - + +
272D VAL* 3.7 34.5 - - + -
3401D SO4 3.5 22.2 - - - +
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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