Contacts of the strand formed by residues 209 - 221 (chain D) in PDB entry 6D6U
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 209 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163D THR* 3.6 6.4 - - - -
164D ARG* 2.8 69.4 + - + +
202D ILE* 4.4 15.9 - - + +
203D VAL 4.1 4.3 - - - -
204D GLN* 4.0 33.9 + - + +
208D GLY* 1.3 73.2 - - - -
210D TYR* 1.3 55.6 + - - +
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Residues in contact with TYR 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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159D SER* 3.8 9.4 - - - +
161D ALA 4.0 4.3 - - - -
162D TYR 3.3 41.5 - - - -
163D THR* 4.1 5.2 - - + -
164D ARG* 4.4 4.0 - - - +
202D ILE* 3.8 3.5 - - - +
203D VAL* 3.0 37.0 + - - +
205D SER* 5.0 2.9 - - - -
207D THR* 3.2 17.3 - - + +
208D GLY* 3.6 29.4 - - - -
209D GLU* 1.3 75.2 - - - +
211D VAL* 1.3 65.2 + - - +
212D VAL* 3.9 0.7 + - + +
410D FYP 3.2 60.8 - + - -
130E MET* 4.3 5.5 - - - -
132E ARG* 3.2 23.7 + - - -
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Residues in contact with VAL 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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158D GLY* 3.6 13.2 - - - -
159D SER* 3.7 13.1 + - - +
162D TYR 5.6 1.0 + - - +
163D THR 5.5 0.4 - - - -
164D ARG* 4.6 16.1 - - + +
167D VAL 3.6 23.6 - - - +
168D VAL* 4.8 7.2 - - + -
169D TYR* 4.0 32.5 - - + +
201D GLY 3.8 14.4 - - - +
202D ILE* 4.8 5.6 - - + +
209D GLU 4.4 0.2 + - - -
210D TYR* 1.3 73.9 - - - +
212D VAL* 1.3 69.5 + - - +
213D MET* 4.0 20.0 - - + -
102K ARG* 5.4 4.9 - - - +
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Residues in contact with VAL 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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102D HIS* 3.4 35.0 - - + +
156D LYS* 4.4 19.5 - - + -
157D PHE 4.2 4.9 - - - +
201D GLY* 3.5 28.7 + - - +
203D VAL* 4.3 24.2 - - + -
210D TYR 3.9 8.3 + - - +
211D VAL* 1.3 88.4 - - - +
213D MET* 1.3 73.2 + - - +
214D THR* 3.8 12.0 + - - +
410D FYP 4.5 3.6 - - - -
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Residues in contact with MET 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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43D THR* 5.4 2.2 - - - +
156D LYS* 3.5 1.6 - - - -
157D PHE* 3.2 64.1 + - + +
158D GLY* 4.7 0.2 - - - -
169D TYR* 3.5 44.4 - - + +
170D GLU* 4.9 1.3 - - - +
171D TRP* 3.3 35.4 - - + +
199D ASP 4.4 1.1 - - - -
200D SER* 3.3 31.4 - - - +
201D GLY 4.5 0.2 - - - +
211D VAL* 4.0 18.8 - - + -
212D VAL* 1.3 79.3 - - - +
214D THR* 1.3 61.0 + - - +
102K ARG* 6.0 0.7 - - - +
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Residues in contact with THR 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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154D PRO* 5.3 1.1 - - + -
155D LEU 3.8 4.7 - - - +
156D LYS* 3.8 24.5 - - + +
157D PHE* 5.6 0.4 - - - -
171D TRP* 3.9 3.0 - - - -
198D VAL* 3.4 6.6 - - - +
199D ASP* 3.2 45.4 + - + +
200D SER 5.2 0.5 + - - -
201D GLY* 5.9 0.2 - - - -
212D VAL* 3.8 9.2 + - - +
213D MET* 1.3 78.0 + - - +
215D THR* 1.3 72.7 + - - +
216D HIS* 3.4 31.9 - - + +
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Residues in contact with THR 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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45D ILE* 4.8 2.6 - - + +
153D CYS 4.2 0.2 - - - +
154D PRO* 3.4 3.8 - - - +
155D LEU* 2.8 47.5 + - - +
157D PHE* 4.5 5.5 - - - -
171D TRP* 3.6 20.8 - - - -
179D VAL* 3.9 21.0 - - + +
196D GLN* 5.1 0.4 - - + -
197D THR 3.3 9.6 - - - +
198D VAL* 4.0 2.2 - - + +
214D THR* 1.3 78.7 + - - +
216D HIS* 1.3 68.9 + - - +
217D PHE* 3.9 30.8 + - + -
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Residues in contact with HIS 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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152D ALA* 4.9 13.2 - - + -
153D CYS 3.9 2.2 - - - +
154D PRO* 4.1 24.8 - - + +
196D GLN* 3.5 6.9 - - - +
197D THR* 2.7 56.3 + - + +
199D ASP* 5.5 6.7 - - + +
214D THR* 3.4 29.1 - - + +
215D THR* 1.3 73.6 - - - +
217D PHE* 1.3 63.4 + - - +
218D HIS* 4.1 13.3 + + + +
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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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45D ILE* 6.0 1.3 - - + -
47D VAL* 4.2 9.6 - - + -
50D PHE* 4.1 30.7 - + + -
60D TYR* 4.4 8.1 - + - -
62D ILE* 3.6 29.8 - - + -
152D ALA* 3.4 2.9 - - - -
153D CYS* 3.0 43.0 + - + +
155D LEU* 4.4 16.6 - - + -
179D VAL* 4.0 12.1 - - + -
181D VAL* 5.9 1.3 - - + -
193D LEU* 4.7 10.5 - - + -
195D GLY 4.0 4.0 - - - +
196D GLN* 3.8 36.3 - - + -
215D THR* 3.9 23.1 - - + -
216D HIS* 1.3 73.5 - - - +
218D HIS* 1.3 61.8 + - - +
219D LEU* 4.6 3.4 - - + +
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Residues in contact with HIS 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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151D HIS 4.3 2.2 - - - -
152D ALA* 3.7 21.6 - - + +
193D LEU* 3.5 13.3 - - - +
194D LEU* 3.6 28.2 + - + -
195D GLY* 3.8 18.4 + - - +
196D GLN 4.8 0.7 - - - -
197D THR* 3.2 28.0 + - + -
216D HIS* 4.4 13.9 + + + -
217D PHE* 1.3 73.2 - - - +
219D LEU* 1.3 72.2 + - - +
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Residues in contact with LEU 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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50D PHE* 4.3 18.8 - - + -
53D VAL* 4.0 17.3 - - + -
150D ALA* 3.3 6.8 - - - +
151D HIS* 3.1 43.9 + - + +
153D CYS* 4.2 23.8 - - + -
188D LEU* 4.6 4.3 - - + -
191D TYR* 3.7 38.1 - - + -
192D ASP 3.7 12.8 - - - +
193D LEU* 4.1 15.5 - - + -
194D LEU* 4.8 1.8 - - - -
217D PHE 4.6 4.5 - - - +
218D HIS* 1.3 84.9 - - - +
220D LYS* 1.3 61.6 + - - +
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Residues in contact with LYS 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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148D MET* 4.3 16.2 + - - +
149D ASP 4.0 8.1 - - - +
150D ALA* 4.4 13.4 - - + +
191D TYR* 4.5 2.5 - - - -
192D ASP* 3.1 34.5 + - + +
194D LEU* 4.2 18.6 - - + -
219D LEU* 1.3 75.7 - - - +
221D ARG* 1.3 74.3 + - - +
222D LYS* 3.6 0.3 + - - +
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Residues in contact with ARG 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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55D ASP* 2.9 24.7 + - - -
143D LEU* 4.5 4.0 - - - +
146D PHE* 3.8 24.0 - - - -
147D PRO* 3.2 39.7 - - - +
148D MET* 5.4 2.3 - - - -
149D ASP* 3.4 36.8 + - - +
151D HIS* 6.1 0.8 + - - -
190D GLN* 3.6 15.5 + - + +
191D TYR* 2.5 54.4 + - + -
220D LYS* 1.3 85.3 + - - +
222D LYS* 1.3 70.8 - - - +
223D ILE* 3.9 2.4 + - - +
226D PHE* 4.2 15.5 - - + -
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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