Contacts of the strand formed by residues 182 - 192 (chain D) in PDB entry 4BEI
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 GLY 182 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177D VAL* 3.8 20.3 - - - +
181D GLY* 1.3 75.6 - - - -
183D PHE* 1.3 57.3 + - - -
237D ASN* 3.5 6.9 + - - +
238D PHE* 2.7 43.5 + - - +
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Residues in contact with PHE 183 (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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100C GLN* 4.7 11.2 - - + -
174D ILE* 4.5 9.4 - - - +
177D VAL* 4.4 1.5 - - - +
182D GLY* 1.3 73.4 - - - -
184D VAL* 1.3 63.3 + - - +
185D PRO* 3.9 31.3 - - + +
235D GLY* 3.6 33.2 - - - -
236D ILE 3.5 14.6 - - - -
237D ASN* 3.9 18.6 - - + +
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Residues in contact with VAL 184 (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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170D ASN* 3.8 21.1 - - - +
174D ILE* 4.0 18.8 - - + +
177D VAL* 3.8 23.8 - - + -
183D PHE* 1.3 78.3 - - - +
185D PRO* 1.3 70.0 - - + +
186D PHE* 3.5 33.3 - - + -
235D GLY* 3.4 1.8 - - - -
236D ILE 2.9 29.8 + - - -
238D PHE* 4.0 19.1 - - + -
268D VAL* 4.4 8.5 - - + -
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Residues in contact with PRO 185 (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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170D ASN* 4.2 0.8 + - - +
171D GLN* 3.2 43.3 + - - +
172D PHE* 3.7 25.1 - - + -
174D ILE* 4.5 7.2 - - + -
183D PHE* 3.9 26.2 - - + +
184D VAL* 1.3 92.6 - - + +
186D PHE* 1.3 63.9 + - - +
233D VAL* 4.0 11.7 - - + -
235D GLY* 3.7 8.1 - - - -
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Residues in contact with PHE 186 (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* 4.7 2.5 - - + -
169D LYS 3.3 8.3 - - - +
170D ASN* 3.6 33.9 - - + -
184D VAL* 3.5 35.7 - - + -
185D PRO* 1.3 76.1 - - - +
187D THR* 1.3 67.6 + - - +
188D VAL* 4.2 2.9 - - + +
204D MET* 4.5 17.0 - - + -
216D VAL* 5.6 1.1 - - + -
233D VAL* 3.4 4.6 - - - -
234D ARG 2.8 47.3 + - - +
235D GLY 5.1 0.2 - - - -
236D ILE* 3.7 19.1 - - + -
249D ILE* 3.7 29.2 - - + -
266D MET* 4.0 27.6 - - + -
268D VAL* 4.1 7.2 - - + -
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Residues in contact with THR 187 (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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167D ASP 3.5 2.1 + - - +
168D ILE* 3.3 7.3 - - - +
169D LYS* 2.9 52.2 + - - +
171D GLN* 3.7 36.9 - - + +
186D PHE* 1.3 74.7 - - - +
188D VAL* 1.3 60.1 + - - +
189D ASP* 4.4 10.9 + - - -
232D LYS 3.7 4.9 - - - +
233D VAL* 4.4 9.6 - - + +
1273D PEG 4.7 13.0 - - - +
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Residues in contact with VAL 188 (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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167D ASP 3.6 2.0 - - - -
168D ILE* 4.1 16.2 - - + -
186D PHE 4.2 9.0 - - - +
187D THR* 1.3 77.9 - - - +
189D ASP* 1.3 67.3 + - - +
190D LEU* 3.7 23.6 - - + -
202D PHE* 4.0 20.6 - - + -
204D MET* 4.2 20.9 - - + -
230D TYR* 3.7 9.8 - - + +
231D SER* 3.3 4.0 - - - -
232D LYS* 2.8 49.7 + - + +
234D ARG* 4.4 10.8 - - + -
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Residues in contact with ASP 189 (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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165D THR* 3.8 2.1 - - - +
166D ILE* 3.6 1.2 - - - -
167D ASP* 2.7 59.0 + - + +
169D LYS* 5.5 2.8 + - - -
187D THR* 4.4 9.5 - - - -
188D VAL* 1.3 80.7 + - - +
190D LEU* 1.3 62.1 + - - +
191D ASN* 3.9 3.1 + - + +
229D THR* 4.2 8.9 - - + +
230D TYR 3.5 1.8 - - - -
231D SER* 2.6 30.2 + - - -
232D LYS 5.3 0.4 - - - +
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Residues in contact with LEU 190 (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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164D LEU* 4.4 5.8 - - + -
165D THR 3.4 5.4 - - - +
166D ILE* 4.2 29.6 - - + -
168D ILE* 4.7 2.9 - - + -
188D VAL* 3.7 21.3 - - + -
189D ASP* 1.3 77.1 - - - +
191D ASN* 1.3 60.5 + - - +
192D ASN 3.9 1.2 + - - -
200D VAL* 4.6 9.9 - - + -
202D PHE* 4.3 24.2 - - + -
222D TRP* 5.9 1.3 - - + -
224D ILE* 4.2 16.9 - - + +
228D ASP 4.1 0.2 - - - +
229D THR* 3.5 4.2 - - - +
230D TYR* 2.9 60.0 + - + +
253D VAL* 4.4 11.0 - - + -
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Residues in contact with ASN 191 (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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163D GLY 3.5 0.7 - - - +
164D LEU* 3.5 2.7 - - - -
165D THR* 2.8 55.1 + - + +
189D ASP* 3.9 3.3 - - + +
190D LEU* 1.3 71.7 - - - +
192D ASN* 1.3 60.7 + - - +
193D GLY* 3.2 5.6 + - - +
228D ASP 4.0 4.0 - - - +
229D THR* 4.2 14.6 - - + +
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Residues in contact with ASN 192 (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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164D LEU* 3.5 12.2 - - + +
190D LEU 3.9 1.2 + - - -
191D ASN* 1.3 67.2 - - - +
193D GLY* 1.3 59.8 + - - +
194D ARG* 3.0 29.7 + - - +
196D GLY 3.2 18.7 + - - -
198D ALA* 3.4 15.5 - - - +
224D ILE* 2.8 45.6 + - + -
225D ALA 3.2 11.8 + - - +
226D SER* 4.4 1.3 - - - -
227D GLY* 3.0 29.0 + - - -
228D ASP 3.1 9.6 + - - +
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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