Contacts of the strand formed by residues 221 - 232 (chain A) in PDB entry 1RX0
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 THR 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A PHE* 3.6 38.4 - - + +
170A ILE 3.6 3.4 - - - -
171A SER* 4.9 6.1 + - - -
210A LYS* 3.5 2.3 - - - +
211A GLU* 2.7 52.8 + - + +
213A LYS* 2.9 42.8 + - + +
219A GLN* 3.5 3.0 + - - +
220A PRO* 1.3 74.0 + - - +
222A ARG* 1.3 64.5 + - - +
399A FAD 4.7 5.4 - - + +
357C LEU* 5.2 0.7 - - + -
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Residues in contact with ARG 222 (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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169A PHE 4.7 3.1 - - - -
170A ILE* 3.3 30.6 + - - +
173A ALA* 2.9 43.3 + - + +
174A GLY* 4.2 7.9 - - - +
175A GLU* 5.7 3.0 + - - -
207A PHE* 3.9 13.9 + - + +
208A GLY 2.8 29.6 + - - +
209A LYS* 3.2 16.5 - - - +
210A LYS* 3.3 36.1 - - - +
211A GLU* 4.2 5.2 - - - -
220A PRO* 4.8 4.9 - - - +
221A THR* 1.3 79.2 - - - +
223A ALA* 1.3 70.2 + - - +
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Residues in contact with ALA 223 (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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166A SER* 5.6 2.2 - - - -
167A LYS 3.2 15.7 - - - +
168A ALA* 4.6 6.1 - - + +
169A PHE 4.9 0.4 - - - +
207A PHE* 3.3 8.7 - - - +
208A GLY* 2.9 36.8 + - - +
209A LYS 4.6 0.2 + - - -
211A GLU* 4.5 8.6 + - - +
222A ARG* 1.3 77.3 - - - +
224A VAL* 1.3 61.4 + - - +
225A ILE* 4.1 13.0 - - + -
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Residues in contact with VAL 224 (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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137A CYS* 4.2 10.5 - - - -
166A SER* 3.3 2.9 - - - -
167A LYS* 2.7 43.9 + - + +
170A ILE* 3.6 31.6 - - + -
173A ALA* 3.8 14.1 - - + -
179A TYR* 4.3 6.1 - - + -
205A LEU* 3.5 27.4 - - + -
206A SER 3.7 3.8 - - - +
207A PHE* 4.1 9.4 - - + -
223A ALA* 1.3 75.5 - - - +
225A ILE* 1.3 62.4 + - - +
226A PHE* 3.5 21.0 - - + -
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Residues in contact with ILE 225 (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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165A GLY 3.7 8.7 - - - +
166A SER* 4.2 14.1 - - - -
204A GLY 3.4 3.6 - - - +
205A LEU* 3.4 5.7 - - - +
206A SER* 2.8 54.6 + - - +
207A PHE 4.6 2.0 - - - +
208A GLY* 4.5 17.5 - - - +
223A ALA* 4.5 9.4 - - + -
224A VAL* 1.3 82.6 - - - +
226A PHE* 1.3 65.7 + - - +
227A GLU* 4.0 26.5 - - + +
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Residues in contact with PHE 226 (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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152A THR* 4.3 9.9 - - + -
163A LEU* 3.6 43.7 - - + +
164A ASN* 3.4 2.8 - - - +
165A GLY 2.8 47.0 + - - +
167A LYS* 4.1 13.9 - - + -
179A TYR* 5.7 0.7 - - + -
181A VAL* 3.8 34.8 - - + -
198A VAL* 4.2 14.8 - - + -
204A GLY 3.4 3.1 - - - -
205A LEU* 3.5 22.9 - - + -
224A VAL* 3.5 28.3 - - + -
225A ILE* 1.3 73.4 - - - +
227A GLU* 1.3 65.7 + - - +
229A CYS* 4.2 12.8 - - + -
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Residues in contact with GLU 227 (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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164A ASN* 3.5 4.9 - - - -
204A GLY* 3.0 25.0 + - - +
206A SER* 5.1 4.6 + - - +
225A ILE* 4.0 20.1 - - + +
226A PHE* 1.3 78.1 - - - +
228A ASP* 1.3 75.3 + - - +
229A CYS 3.1 1.1 + - - +
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Residues in contact with ASP 228 (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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162A ILE* 3.7 20.3 - - + +
163A LEU 3.2 3.7 + - - -
164A ASN* 2.7 34.0 + - - +
203A PRO 4.7 1.6 - - - +
204A GLY* 4.9 0.7 - - - -
227A GLU* 1.3 75.1 - - - +
229A CYS* 1.3 61.7 + - - +
230A ALA* 3.4 4.5 + - - +
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Residues in contact with CYS 229 (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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161A TYR 3.3 2.3 - - - +
162A ILE* 4.3 0.7 - - - -
163A LEU* 2.8 39.2 + - + +
198A VAL* 4.5 2.5 - - - -
202A THR* 3.7 19.3 - - - -
203A PRO 3.5 20.6 - - - -
204A GLY 3.8 23.6 - - - +
205A LEU* 4.2 5.6 - - - -
226A PHE* 4.2 20.6 - - + -
227A GLU 3.9 0.4 - - - -
228A ASP* 1.3 73.7 - - - +
230A ALA* 1.3 63.9 + - - +
231A VAL* 3.5 15.6 + - - +
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Residues in contact with ALA 230 (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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160A HIS* 4.4 16.3 - - + -
161A TYR 3.4 5.6 - - - -
162A ILE* 3.7 20.6 - - + -
202A THR* 3.6 19.2 - - - +
203A PRO 4.2 3.8 + - - -
228A ASP 3.4 5.5 + - - +
229A CYS* 1.3 70.2 - - - +
231A VAL* 1.3 59.6 + - - +
232A PRO* 4.4 2.6 - - - +
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Residues in contact with VAL 231 (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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160A HIS* 3.2 4.8 - - - -
161A TYR* 2.7 42.4 + - + +
163A LEU* 3.9 17.7 - - + -
196A ILE* 3.9 11.0 - - + -
197A VAL 3.6 24.7 - - - +
198A VAL* 4.0 17.9 - - + -
202A THR* 4.7 2.7 - - + -
229A CYS* 3.7 25.8 - - - +
230A ALA* 1.3 79.2 - - - +
232A PRO* 1.3 82.7 - - + +
235A ASN* 3.8 3.8 - - - +
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Residues in contact with PRO 232 (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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159A ASP 3.8 8.3 - - - +
160A HIS* 3.8 15.9 - - + +
161A TYR* 4.5 2.4 - - - -
196A ILE* 4.9 0.3 - - - +
202A THR* 6.1 2.0 - - + -
230A ALA 4.4 2.5 - - - +
231A VAL* 1.3 94.8 - - + +
233A VAL* 1.3 60.8 + - - +
234A ALA* 4.1 9.6 - - + +
235A ASN* 2.9 44.9 + - - +
236A ARG 4.3 0.7 + - - -
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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