Contacts of the strand formed by residues 222 - 234 (chain B) in PDB entry 5NXR
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 ARG 222 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174B ASP 4.0 0.4 + - - -
176B TYR* 3.8 11.5 + - - -
196B SER* 2.5 44.4 + - - +
197B SER* 3.5 11.0 + - - +
198B SER* 3.3 29.0 - - - +
199B ARG* 3.9 5.2 - - - -
220B GLY 3.2 1.2 - - - -
221B LYS* 1.3 91.3 - - + +
223B ALA* 1.3 63.7 + - - +
224B GLN* 5.5 7.1 + - - +
247B GLN* 4.0 4.5 - - - +
248B ASN* 3.0 26.0 + - - +
401B LDA 3.9 29.5 - - - -
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Residues in contact with ALA 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B PHE* 3.6 35.0 - - + -
195B SER* 4.1 0.7 + - - +
196B SER* 3.6 3.6 + - - -
197B SER* 2.8 37.3 + - - +
199B ARG* 3.8 4.6 - - + +
222B ARG* 1.3 73.3 - - - +
224B GLN* 1.3 62.3 + - - +
247B GLN 3.3 3.8 - - - -
248B ASN 3.5 21.1 - - - +
249B THR* 3.6 8.5 - - - +
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Residues in contact with GLN 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B TYR* 3.2 33.4 + - + +
195B SER* 3.4 17.0 - - - +
196B SER* 4.6 5.2 + - - -
222B ARG* 5.4 7.7 + - - +
223B ALA* 1.3 75.3 - - - +
225B ALA* 1.3 62.3 + - - +
226B TRP* 5.1 7.3 - - + -
245B GLN 4.7 0.2 - - - -
246B THR* 3.3 2.3 - - - -
247B GLN* 2.7 69.9 + - + +
249B THR* 3.3 7.1 + - - -
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Residues in contact with ALA 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B VAL* 3.8 14.1 - - + +
119B MET* 4.2 0.9 - - + -
125B PHE* 6.4 0.9 - - + -
127B THR* 4.1 25.6 - - + -
194B TYR* 3.5 1.3 - - - -
195B SER* 2.8 45.3 + - - +
224B GLN* 1.3 77.0 - - - +
226B TRP* 1.3 63.9 + - - +
245B GLN 3.4 9.6 - - - +
246B THR* 4.2 10.1 - - + -
249B THR* 4.6 4.3 - - + +
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Residues in contact with TRP 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B VAL* 4.5 2.0 - - - -
119B MET* 3.8 6.1 - - - +
193B GLY 3.2 15.0 - - - +
194B TYR* 3.7 25.4 - + + -
224B GLN* 5.1 6.5 - - + -
225B ALA* 1.3 78.0 - - - +
227B ASN* 1.3 75.1 + - - +
228B VAL* 4.0 23.6 - - + -
243B TYR* 3.7 26.5 - + - -
244B GLY* 3.2 3.0 - - - -
245B GLN* 2.9 78.1 + - + +
247B GLN* 6.1 0.6 - - - +
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Residues in contact with ASN 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B VAL* 2.7 36.3 + - - +
104B THR* 3.7 10.8 - - - -
105B ASN* 3.9 7.9 - - - +
119B MET* 3.9 8.2 - - - -
192B GLY* 3.1 2.6 - - - -
193B GLY* 2.9 44.0 + - - +
226B TRP* 1.3 84.9 - - - +
228B VAL* 1.3 60.9 + - - +
242B MET* 3.6 25.7 - - + -
243B TYR 3.1 13.9 - - - +
244B GLY* 3.8 5.4 - - - -
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Residues in contact with VAL 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B THR* 4.0 4.7 - - - -
191B GLY 3.5 14.8 - - - +
192B GLY* 4.1 2.0 - - - -
226B TRP* 4.0 17.7 - - + -
227B ASN* 1.3 73.9 - - - +
229B GLY* 1.3 65.2 + - - +
242B MET* 3.3 3.9 - - - +
243B TYR* 2.8 50.7 + - + +
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Residues in contact with GLY 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B THR* 3.6 11.1 - - - +
107B TRP* 3.8 6.7 - - - -
190B LEU* 3.6 6.2 - - - +
191B GLY 2.8 31.5 + - - +
228B VAL* 1.3 82.4 - - - +
230B GLY* 1.3 59.3 + - - -
241B ALA 3.1 13.5 - - - -
242B MET* 4.1 0.4 - - - -
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Residues in contact with GLY 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B TRP* 4.0 5.7 - - - +
189B THR 3.2 13.0 - - - -
190B LEU* 4.1 10.3 - - - -
229B GLY* 1.3 75.0 - - - -
231B LYS* 1.3 63.9 + - - +
240B ALA* 3.3 3.8 - - - +
241B ALA* 3.0 31.7 + - - +
403B LDA 4.4 11.7 - - - -
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Residues in contact with LYS 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B TRP* 3.4 42.1 - - + +
183B GLU* 6.0 0.4 + - - -
187B GLY 3.5 1.3 - - - +
188B VAL* 3.4 5.9 - - - +
189B THR* 3.0 54.5 + - - +
190B LEU* 5.3 0.2 - - - +
230B GLY* 1.3 75.9 - - - +
232B PHE* 1.3 59.5 + - - +
233B ASP* 5.0 13.1 + - + +
238B TYR* 3.6 28.3 + - + +
239B LEU 3.1 14.6 - - - +
240B ALA* 3.9 9.4 - - + +
403B LDA 4.4 7.8 - - - +
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Residues in contact with PHE 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B TRP 3.2 26.9 - - - -
187B GLY 3.3 7.4 - - - -
188B VAL* 4.0 11.0 - - + +
231B LYS* 1.3 71.3 - - - +
233B ASP* 1.3 61.6 + - - +
234B ALA* 3.9 11.2 - - + -
235B ASN* 4.0 10.8 - - - -
237B VAL* 3.5 37.0 - - + +
238B TYR* 3.2 7.8 - - - -
239B LEU* 2.8 44.4 + - + +
402B LDA 4.2 18.8 - - + -
403B LDA 3.7 66.7 - - + +
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Residues in contact with ASP 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B GLY* 2.7 22.1 + - - +
231B LYS* 5.0 14.5 + - + +
232B PHE* 1.3 74.6 - - - +
234B ALA* 1.3 63.6 + - - +
237B VAL 3.5 6.9 - - - +
238B TYR* 3.4 32.6 - - + +
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Residues in contact with ALA 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B TRP 4.9 0.2 - - - -
187B GLY* 4.3 8.1 - - - -
232B PHE* 3.9 9.7 - - + -
233B ASP* 1.3 78.2 + - - +
235B ASN* 1.3 77.7 + - - +
236B ASN 3.2 3.4 - - - -
237B VAL* 2.8 33.7 + - - +
403B LDA 3.9 15.7 - - - -
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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