Contacts of the strand formed by residues 220 - 230 (chain A) in PDB entry 1WXR
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 LYS 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A ALA* 3.6 25.5 - - - +
214A PHE* 3.7 10.5 - - - -
215A ASP* 2.9 33.1 + - - +
218A GLN* 3.1 44.3 + - + +
219A ASN* 1.3 79.2 - - - +
221A TRP* 1.3 71.8 + - - +
222A VAL* 4.5 5.6 - - + -
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Residues in contact with TRP 221 (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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45A ALA* 3.6 21.7 - - + +
46A ALA 2.9 21.5 + - - -
47A MET 5.2 0.2 - - - -
48A PRO* 3.6 39.6 - - + +
117A THR* 4.8 4.3 + - - -
118A ALA* 3.9 9.7 + - - +
137A VAL* 3.6 20.9 - - + -
139A TYR* 3.6 32.3 - + - -
212A PHE* 3.8 25.1 - - + -
213A ALA* 3.3 32.1 - - - -
214A PHE* 3.6 29.0 - + - -
220A LYS* 1.3 79.8 - - - +
222A VAL* 1.3 67.3 + - - +
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Residues in contact with VAL 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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117A THR* 4.8 0.4 - - - -
118A ALA* 3.6 11.9 - - + -
119A VAL 3.5 21.1 - - - +
120A THR* 3.5 25.8 - - - -
121A ALA 4.7 0.7 - - - +
135A TYR* 4.7 7.9 - - + -
212A PHE* 3.3 9.0 - - - -
213A ALA 2.9 36.9 + - - +
215A ASP* 4.5 10.5 - - + +
218A GLN* 3.8 22.0 - - - +
220A LYS* 4.3 9.0 - - + +
221A TRP* 1.3 80.6 - - - +
223A LEU* 1.3 61.9 + - - +
224A VAL* 4.3 7.6 - - + +
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Residues in contact with LEU 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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61A THR* 4.3 12.8 - - + +
63A ILE* 3.8 27.4 - - + -
69A ALA* 4.5 3.8 - - + -
117A THR* 3.9 8.7 - - + -
118A ALA 2.9 19.1 + - - +
119A VAL* 3.5 5.7 - - + +
120A THR 2.8 23.2 + - - -
210A PRO* 3.6 29.4 - - + -
211A LEU 3.5 16.2 - - - +
212A PHE* 4.0 13.6 - - + -
222A VAL* 1.3 70.5 - - - +
224A VAL* 1.3 59.8 + - - +
225A GLY 3.7 8.5 - - - +
226A VAL* 4.8 2.9 - - + -
243A ILE* 3.5 32.1 - - + +
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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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120A THR* 3.9 7.3 - - - +
129A TYR* 3.9 44.0 - - + -
138A PHE* 4.1 10.1 - - + -
182A ILE* 4.9 4.7 - - + -
211A LEU* 2.9 28.7 + - + +
212A PHE 4.3 0.7 - - - -
213A ALA* 3.5 32.8 - - + +
222A VAL* 4.3 4.5 - - + +
223A LEU* 1.3 73.8 - - - +
225A GLY* 1.3 59.4 + - - +
242A VAL* 3.3 13.3 - - + +
243A ILE* 2.9 26.5 + - - +
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Residues in contact with GLY 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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211A LEU* 2.7 34.8 + - - +
223A LEU* 3.7 4.2 - - - +
224A VAL* 1.3 83.9 - - - +
226A VAL* 1.3 65.6 + - - +
240A TRP* 4.2 8.7 - - - -
241A ALA 3.1 15.5 - - - -
242A VAL* 4.1 0.7 - - - -
243A ILE* 3.7 7.8 - - - +
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Residues in contact with VAL 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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61A THR* 5.4 1.6 - - - +
69A ALA* 4.2 20.9 - - + +
70A SER 3.6 24.5 - - - +
71A VAL* 4.0 9.2 - - + -
102A PHE* 3.8 15.7 - - + -
208A GLY* 3.4 23.6 - - - +
209A SER 3.3 4.3 - - - +
210A PRO* 4.5 4.9 - - + -
223A LEU* 4.8 5.2 - - + -
225A GLY* 1.3 78.8 - - - +
227A LEU* 1.3 64.1 + - - +
228A THR* 3.4 1.9 + - - +
240A TRP* 3.4 4.7 - - - -
241A ALA* 2.9 32.3 + - + +
243A ILE* 4.4 11.9 - - + -
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Residues in contact with LEU 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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71A VAL* 3.4 4.7 - - - +
140A ARG* 4.0 13.0 - - - +
202A GLY* 3.9 13.5 - - - +
203A GLU 5.0 2.5 - - - +
206A ASP* 3.3 36.6 - - + +
207A SER* 3.1 11.6 - - - +
208A GLY 2.8 24.9 + - - -
209A SER* 2.9 14.5 + - - +
226A VAL* 1.3 70.2 - - - +
228A THR* 1.3 61.3 + - - +
229A ALA* 4.0 19.3 - - - +
238A ASN* 3.8 27.8 - - - +
239A ASN 3.6 8.5 - - - +
240A TRP* 3.2 30.1 - - + +
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Residues in contact with THR 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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71A VAL* 3.8 15.7 - - + -
73A HIS* 3.4 20.8 - - - -
101A ASP* 3.6 33.3 - - + +
181A MET* 3.4 18.9 - - + +
207A SER* 3.6 7.0 + - - -
226A VAL 3.4 0.8 + - - +
227A LEU* 1.3 73.9 - - - +
229A ALA* 1.3 61.3 + - - +
239A ASN* 2.8 28.4 + - - +
241A ALA* 3.8 21.1 - - + +
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Residues in contact with ALA 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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207A SER* 5.1 0.9 - - - -
227A LEU* 3.9 8.4 - - - +
228A THR* 1.3 84.8 + - - +
230A GLY* 1.3 62.7 + - - +
238A ASN* 3.2 13.5 + - - +
239A ASN* 2.9 43.2 + - - +
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Residues in contact with GLY 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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201A TYR* 3.8 3.4 - - - -
202A GLY 4.7 2.2 + - - -
229A ALA* 1.3 79.7 - - - +
231A ASN* 1.3 63.6 + - - -
232A GLY 3.2 9.8 + - - -
237A GLY 3.3 13.5 - - - -
238A ASN* 3.5 11.2 - - - +
239A ASN* 5.0 1.3 - - - -
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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