Contacts of the strand formed by residues 189 - 201 (chain L) in PDB entry 5D4E
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 ARG 189 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6L LEU* 4.5 22.9 - - + +
29L GLU* 3.5 32.1 + - - -
185L ARG* 3.1 8.3 - - - +
186L LEU* 3.0 37.0 + - + +
188L GLN* 1.3 76.9 - - - +
190L THR* 1.3 60.1 + - - +
191L ASP* 3.6 7.0 - - - +
192L LEU* 4.0 31.5 - - + +
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Residues in contact with THR 190 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183L ASP* 4.9 6.8 - - - +
184L THR 3.5 13.7 + - - +
185L ARG* 4.0 19.7 - - + +
187L GLY 5.7 0.4 - - - +
188L GLN* 3.3 14.0 + - - +
189L ARG* 1.3 75.3 - - - +
191L ASP* 1.3 63.7 + - - +
192L LEU 3.5 2.2 - - - -
646N LYS* 5.8 0.4 - - + -
722N GLU* 3.3 44.9 - - + +
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Residues in contact with ASP 191 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L GLU* 4.5 4.8 - - - +
30L ARG* 3.9 41.9 + - - +
183L ASP* 4.6 10.1 - - - +
189L ARG* 4.6 7.1 - - - +
190L THR* 1.3 80.2 + - - +
192L LEU* 1.3 84.2 + - - +
193L ASP* 3.4 10.4 - - - +
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Residues in contact with LEU 192 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L LEU* 4.8 8.7 - - + -
27L PRO* 3.7 17.9 - - + -
28L LEU 3.4 13.5 - - - +
29L GLU* 3.9 20.2 - - - +
30L ARG 4.7 1.3 - - - +
183L ASP* 3.7 5.0 - - - -
184L THR* 2.9 44.0 + - + +
186L LEU* 3.6 38.4 - - + +
189L ARG* 4.0 28.5 - - + +
191L ASP* 1.3 96.1 - - - +
193L ASP* 1.3 61.4 + - - +
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Residues in contact with ASP 193 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25L LEU 4.2 0.2 - - - +
27L PRO* 3.5 7.8 - - - +
28L LEU* 2.7 53.2 + - + +
29L GLU 3.8 2.0 - - - -
30L ARG* 3.8 1.7 - - - +
31L GLY* 3.0 31.9 + - - -
33L GLY* 3.1 23.6 + - - +
34L VAL* 4.7 0.3 + - - +
181L VAL* 3.7 17.4 - - + +
182L GLU 3.7 3.0 - - - +
183L ASP* 5.3 2.3 - - - +
184L THR* 3.6 2.6 - - - +
191L ASP 3.4 9.7 - - - +
192L LEU* 1.3 80.3 - - - +
194L LYS* 1.3 59.2 + - - +
195L LEU 4.2 0.2 - - - -
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Residues in contact with LYS 194 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L VAL* 3.7 26.9 - - + +
25L LEU 3.8 3.1 - - - -
26L GLU* 3.3 35.3 + - + +
180L GLN 3.6 1.7 - - - +
181L VAL* 3.4 6.8 - - - -
182L GLU* 2.9 61.6 + - + +
184L THR* 4.1 11.7 - - + -
193L ASP* 1.3 75.3 - - - +
195L LEU* 1.3 61.4 + - - +
196L THR* 3.8 13.9 + - - +
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Residues in contact with LEU 195 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225K PHE* 4.8 14.1 - - + -
23L PHE 3.2 6.1 - - - +
24L VAL* 3.2 2.4 - - - -
25L LEU* 2.9 47.8 + - + +
28L LEU* 4.1 15.7 - - + -
33L GLY* 3.5 28.5 - - - +
36L LEU* 4.0 13.7 - - + -
37L GLY* 4.0 14.6 - - - +
40L LEU* 5.6 2.9 - - + -
179L PHE* 3.8 27.4 - - + -
180L GLN 3.9 4.7 - - - +
181L VAL* 4.0 4.0 - - + +
193L ASP 4.2 0.6 - - - -
194L LYS* 1.3 72.9 - - - +
196L THR* 1.3 68.4 + - - +
197L LEU* 5.0 8.7 - - + +
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Residues in contact with THR 196 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L GLU* 5.1 9.0 - - + +
23L PHE 3.6 4.7 - - - +
24L VAL* 3.9 19.7 - - + +
178L ALA 4.0 0.5 - - - +
179L PHE* 3.2 5.4 - - - +
180L GLN* 2.9 50.9 + - + +
182L GLU* 5.2 7.4 + - - -
194L LYS* 3.8 16.0 + - - +
195L LEU* 1.3 74.2 - - - +
197L LEU* 1.3 62.2 + - - +
198L ARG* 4.4 21.3 - - + -
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Residues in contact with LEU 197 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225K PHE* 5.6 3.8 - - + -
22L GLU* 3.4 2.9 - - - -
23L PHE* 2.9 51.5 + - + +
37L GLY* 5.6 3.8 - - - +
40L LEU* 4.2 17.0 - - + -
41L ARG* 5.6 1.8 - - + +
44L LEU* 4.5 8.1 - - + -
177L VAL* 3.6 27.4 - - + -
178L ALA 3.9 0.4 - - - +
179L PHE* 3.6 22.4 - - + -
195L LEU* 5.1 10.3 - - + -
196L THR* 1.3 75.5 - - - +
198L ARG* 1.3 66.1 + - - +
199L ILE* 4.3 10.3 - - + -
211L LEU* 3.8 32.1 - - + -
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Residues in contact with ARG 198 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L TYR* 3.2 24.8 + - - +
21L GLY 3.4 3.6 - - - -
22L GLU* 4.4 8.0 - - + -
176L ARG* 5.6 0.8 - - - +
177L VAL* 3.4 5.2 - - - +
178L ALA* 2.9 53.2 + - - +
180L GLN* 6.5 0.9 - - - -
196L THR* 4.4 18.2 - - + -
197L LEU* 1.3 75.0 - - - +
199L ILE* 1.3 64.2 + - - +
200L TRP* 3.4 39.6 - - + -
888N GLU* 4.0 17.4 + - - -
937N TYR* 5.5 5.1 + - - -
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Residues in contact with ILE 199 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L TYR* 3.2 6.3 - - - -
21L GLY 2.9 36.4 + - - +
23L PHE* 4.0 15.9 - - + -
44L LEU* 3.6 31.0 - - + -
174L VAL* 4.0 14.8 - - + -
176L ARG 3.5 7.4 - - - +
177L VAL* 4.6 3.1 - - + -
197L LEU* 4.3 13.7 - - + -
198L ARG* 1.3 79.4 - - - +
200L TRP* 1.3 65.0 + - - +
201L THR* 3.9 22.2 - - + -
207L PRO* 3.6 32.4 - - + +
210L ALA* 5.0 0.9 - - + -
211L LEU* 4.1 10.3 - - + -
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Residues in contact with TRP 200 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L GLU* 3.3 6.5 - - + -
20L TYR* 3.4 34.9 - + + -
174L VAL* 3.4 4.2 - - - +
175L ARG* 2.6 35.9 + - + -
176L ARG* 2.9 81.9 + - + +
178L ALA* 4.0 8.3 - - + -
198L ARG* 3.4 60.6 - - + -
199L ILE* 1.3 73.7 - - - +
201L THR* 1.3 57.3 + - - +
888N GLU* 5.5 0.4 - - - -
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Residues in contact with THR 201 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L ARG 3.0 21.0 + - - -
19L GLU* 2.7 28.5 + - - +
173L PRO 3.2 13.7 - - - +
174L VAL* 4.2 11.9 - - + -
175L ARG* 3.8 13.1 - - - +
199L ILE* 3.9 19.1 - - + -
200L TRP* 1.3 79.9 - - - +
202L ASP* 1.3 61.1 + - - +
203L GLY 3.4 1.8 + - - -
205L VAL* 2.9 29.9 + - + +
206L THR 4.3 0.7 - - - +
207L PRO* 3.9 13.9 - - + -
210L ALA* 4.7 2.2 - - + -
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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