Contacts of the strand formed by residues 203 - 213 (chain A) 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 HIS 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A PRO* 4.2 3.5 - - - +
198A SER* 3.3 34.9 + - - +
200A ALA* 3.3 19.6 + - + +
201A HIS 3.2 16.7 - - - -
202A GLY* 1.3 86.3 + - - +
204A ARG* 1.3 69.0 + - - +
252A ASP* 2.8 24.0 + - - +
253A VAL 3.6 7.5 + - - +
254A GLU* 3.7 32.1 + - + +
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Residues in contact with ARG 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A SER* 2.6 41.4 + - - -
196A VAL 3.3 25.4 + - - +
197A PRO* 3.5 28.3 - - - +
198A SER* 3.8 4.7 - - - +
203A HIS* 1.3 78.2 - - - +
205A GLN* 1.3 59.5 + - - +
206A LEU* 4.9 1.8 - - + -
252A ASP* 3.5 1.7 - - - -
253A VAL* 2.8 47.6 + - + +
255A ALA* 5.1 10.3 - - + +
258A GLU* 3.9 23.8 - - - +
279A TRP* 6.5 0.2 - - - -
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Residues in contact with GLN 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A SER* 3.3 2.6 - - - -
196A VAL* 2.7 58.4 + - + +
198A SER* 3.8 13.7 - - - +
204A ARG* 1.3 70.3 - - - +
206A LEU* 1.3 71.4 + - - +
207A VAL* 3.9 10.8 + - + +
248A GLN* 5.1 2.2 + - - -
250A THR* 3.8 29.9 + - - +
251A LEU 3.6 7.0 - - - +
252A ASP* 4.5 6.5 - - + +
99B MET* 5.6 9.7 - - - +
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Residues in contact with LEU 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A SER 3.5 4.3 - - - +
195A SER* 4.0 8.1 - - - -
204A ARG* 4.9 2.2 - - + -
205A GLN* 1.3 74.5 - - - +
207A VAL* 1.3 61.0 + - - +
222A TRP* 3.8 39.7 - - + -
250A THR* 3.2 9.4 - - - -
251A LEU* 2.8 33.8 + - + +
253A VAL* 3.7 20.4 - - + -
258A GLU* 3.8 28.9 - - + +
261A LEU* 3.9 24.2 - - + -
279A TRP* 3.8 26.7 - - + -
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Residues in contact with VAL 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LEU* 3.5 6.2 - - - +
194A SER* 2.7 42.9 + - - +
195A SER* 5.1 0.2 - - - -
196A VAL* 5.2 2.2 - - + -
205A GLN* 4.1 20.0 - - + +
206A LEU* 1.3 80.3 - - - +
208A CYS* 1.3 61.1 + - - +
209A HIS* 3.3 36.4 + - + +
222A TRP* 4.0 3.8 - - - -
248A GLN* 3.6 24.7 - - + +
249A ALA 3.9 2.0 - - - -
250A THR* 3.9 12.3 - - + -
98B ASP 3.8 14.8 - - - +
99B MET* 4.2 7.0 - - - -
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Residues in contact with CYS 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ALA* 4.5 8.3 - - - -
192A TRP 4.0 2.0 - - - -
193A LEU* 3.8 9.2 - - - -
207A VAL* 1.3 70.5 - - - +
209A HIS* 1.3 68.0 + - - +
210A VAL* 3.7 15.5 + - - +
222A TRP* 3.9 8.7 - - + +
247A LEU 3.9 0.2 - - - +
248A GLN* 3.1 8.3 - - - -
249A ALA* 2.8 42.8 + - + +
263A CYS* 2.0 52.7 - - + -
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Residues in contact with HIS 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A VAL 4.3 0.4 - - - -
191A ALA* 3.0 29.3 - - - +
192A TRP* 2.9 64.9 + + + +
194A SER* 3.3 27.5 - - - -
207A VAL* 3.3 14.2 - - + +
208A CYS* 1.3 71.9 - - - +
210A VAL* 1.3 58.9 + - - +
211A SER 4.2 0.7 - - - -
246A TYR* 2.7 25.1 + - + +
247A LEU 4.0 2.2 - - - -
248A GLN* 3.8 3.3 + - - -
97B ARG 3.7 13.5 + - - -
99B MET 3.3 26.2 - - - -
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Residues in contact with VAL 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A PRO* 3.8 25.6 - - + -
190A VAL 3.4 5.4 - - - +
191A ALA* 4.3 2.0 - - + -
208A CYS* 4.1 8.5 - - - +
209A HIS* 1.3 78.5 - - - +
211A SER* 1.3 61.9 + - - +
213A PHE* 3.5 16.4 - - + -
218A VAL* 4.9 1.1 - - + -
220A VAL* 3.8 36.3 - - + -
246A TYR* 3.4 3.6 - - - -
247A LEU* 2.8 45.2 + - + +
265A VAL* 3.9 23.8 - - + -
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Residues in contact with SER 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A PRO* 4.5 0.9 - - - -
190A VAL* 2.9 36.9 + - - +
192A TRP* 3.7 16.4 - - - -
210A VAL* 1.3 75.4 - - - +
212A GLY* 1.3 61.5 + - - +
213A PHE 3.5 2.2 - - - -
240A ASN* 3.5 14.0 + - - -
245A TRP 3.6 3.1 - - - -
246A TYR* 3.5 21.5 - - - +
12B ARG* 3.0 33.1 + - - -
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Residues in contact with GLY 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A GLU* 3.5 11.8 - - - +
188A LYS 3.7 10.5 - - - +
211A SER* 1.3 77.6 + - - +
213A PHE* 1.3 60.1 + - - +
240A ASN* 3.8 1.0 - - - +
244A THR* 3.2 26.2 - - - +
245A TRP 2.9 9.4 + - - -
12B ARG* 3.1 26.8 + - - -
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Residues in contact with PHE 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A GLU 3.5 6.1 - - - -
189A PRO* 3.6 20.1 - - + +
210A VAL* 3.5 38.4 - - + -
211A SER 3.5 1.0 + - - -
212A GLY* 1.3 77.6 - - - +
214A TYR* 1.3 59.3 + - - +
215A PRO 3.3 13.1 - - - +
216A LYS 3.1 22.7 - - - -
218A VAL* 3.6 21.3 - - + -
237A PHE* 3.8 11.0 - + - -
244A THR* 3.8 0.4 - - - -
245A TRP* 3.0 61.6 + - + +
247A LEU* 4.1 10.3 - - + -
267A HIS* 3.5 23.1 - + + +
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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