Contacts of the strand formed by residues 191 - 200 (chain D) in PDB entry 3ARE
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 TYR 191 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152D GLY 3.0 24.6 + - - -
153D PHE* 2.7 47.6 + - + +
154D TYR* 3.6 20.9 - + - -
155D PRO* 5.2 0.2 - - + -
156D ASP* 3.7 46.0 + - + -
179D PRO* 4.3 13.0 - - + -
180D LEU* 3.3 19.7 - - - +
181D LYS* 4.2 13.9 - - + -
182D GLU* 3.6 2.2 - - - +
187D ASN 5.2 3.6 + - - -
189D SER* 3.6 17.9 - - - -
190D ARG* 1.3 74.1 - - - +
192D ALA* 1.3 60.9 + - - +
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Residues in contact with ALA 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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181C TRP* 3.7 30.5 - - + -
150D ALA 3.2 10.8 - - - +
151D THR* 3.9 2.7 - - + -
153D PHE* 3.7 2.7 - - - -
179D PRO* 3.5 3.3 - - - +
180D LEU* 2.8 45.4 + - + +
182D GLU* 3.9 18.6 - - + +
191D TYR* 1.3 74.5 - - - +
193D LEU* 1.3 61.3 + - - +
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Residues in contact with LEU 193 (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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181C TRP* 5.5 1.3 - - - -
148D CYS 3.9 0.3 - - - +
149D LEU* 3.6 4.3 - - - +
150D ALA* 2.8 37.6 + - + +
153D PHE* 3.8 14.3 - - + -
158D VAL* 4.1 21.3 - - + +
160D LEU* 4.0 21.5 - - + +
175D THR* 3.9 20.0 - - + -
176D ASP* 3.6 35.9 - - + +
177D PRO 5.1 0.9 - - - +
178D GLN 4.2 0.2 - - - -
179D PRO* 3.9 26.7 - - + -
180D LEU* 5.0 0.4 - - - -
192D ALA* 1.3 74.1 - - - +
194D SER* 1.3 65.4 + - - +
215D VAL* 6.3 0.4 - - + -
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Residues in contact with SER 194 (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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161C THR* 3.4 18.6 + - - +
179C VAL* 4.1 10.3 - - - +
181C TRP* 4.7 0.7 - - - -
147D VAL* 5.0 0.4 - - - -
148D CYS 3.3 5.2 - - - -
149D LEU* 3.6 22.2 - - - -
160D LEU* 4.9 0.2 - - - -
175D THR* 3.6 4.7 - - - +
176D ASP* 2.6 47.7 + - - +
193D LEU* 1.3 75.4 - - - +
195D SER* 1.3 63.1 + - - +
196D ARG* 3.0 16.7 + - - -
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Residues in contact with SER 195 (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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146D LEU 3.7 0.2 - - - +
147D VAL* 3.4 6.1 - - - +
148D CYS* 2.8 32.9 + - - +
160D LEU* 3.6 25.3 - - - +
162D TRP* 2.8 28.6 + - - -
174D CYS 3.5 7.3 + - - -
175D THR* 3.1 22.9 + - - -
194D SER* 1.3 78.1 + - - +
196D ARG* 1.3 68.0 + - - +
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Residues in contact with ARG 196 (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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140C LEU* 4.0 20.2 - - + -
161C THR* 3.8 6.3 + - - -
162C ASP 4.1 0.8 + - - -
164C CYS* 3.9 13.5 - - - +
166C LEU* 4.1 16.4 - - + -
177C SER* 2.7 55.3 + - - +
178C ALA* 3.7 9.5 - - - +
179C VAL* 3.9 6.1 - - + +
145D THR* 4.1 12.3 - - + -
146D LEU 3.3 2.2 - - - -
147D VAL* 4.1 7.0 - - + -
162D TRP* 3.6 8.7 + - - -
172D GLY 4.1 1.3 - - - -
173D VAL* 3.3 5.2 - - - -
174D CYS* 3.0 33.5 + - - +
176D ASP* 2.3 37.6 + - - +
194D SER* 3.0 21.8 + - - -
195D SER* 1.3 81.4 + - - +
197D LEU* 1.3 60.3 + - - +
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Residues in contact with LEU 197 (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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145D THR* 4.3 1.1 - - - -
146D LEU* 2.8 43.2 + - + +
162D TRP* 3.6 43.7 - - + -
164D VAL* 3.7 26.9 - - + -
169D VAL* 3.8 7.0 - - + -
171D SER 3.7 22.9 - - - +
172D GLY 3.5 2.0 - - - +
173D VAL* 3.8 12.8 - - + -
196D ARG* 1.3 73.9 - - - +
198D ARG* 1.3 63.6 + - - +
199D VAL* 4.4 16.2 - - + -
211D PHE* 4.1 16.2 - - + -
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Residues in contact with ARG 198 (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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126C TYR* 5.1 0.2 - - - -
142C THR* 3.7 10.1 + - - +
143C ASP* 2.7 42.0 + - - -
166C LEU* 3.7 27.6 - - + -
168C MET* 3.4 29.9 - - - +
173C PHE* 3.5 9.5 - - - -
175C SER* 3.3 18.7 + - - -
137D GLU* 3.1 27.8 + - - +
141D THR* 4.0 15.8 + - - +
143D LYS* 3.7 15.8 - - + +
144D ALA 3.3 9.6 - - - +
145D THR* 3.1 20.6 + - + +
171D SER 5.0 0.2 - - - +
172D GLY* 3.0 19.2 + - - -
197D LEU* 1.3 75.0 - - - +
199D VAL* 1.3 67.2 + - - +
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Residues in contact with VAL 199 (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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168C MET* 4.0 7.9 - - - -
143D LYS* 3.6 4.0 - - - +
144D ALA 2.7 43.0 + - - +
146D LEU* 4.1 15.9 - - + -
164D VAL* 5.6 2.0 - - + -
171D SER 6.0 0.2 - - - +
197D LEU* 4.4 17.9 - - + -
198D ARG* 1.3 79.3 - - - +
200D SER* 1.3 63.6 + - - +
203D PHE* 4.0 30.7 - - + -
204D TRP* 4.3 12.3 - - + -
211D PHE* 4.3 13.2 - - + -
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Residues in contact with SER 200 (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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168C MET* 4.2 6.5 - - - +
171C MET* 5.0 15.7 - - - -
142D GLN 3.8 8.5 - - - -
143D LYS* 4.4 2.5 - - - +
144D ALA 4.4 0.4 - - - -
199D VAL* 1.3 76.7 - - - +
201D ALA* 1.3 66.2 + - - +
202D THR* 3.5 15.5 + - - -
203D PHE* 3.0 27.6 + - - +
204D TRP* 3.1 12.0 + - - +
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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