Contacts of the strand formed by residues 222 - 234 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A TYR* 3.5 32.0 + - - -
196A SER* 3.1 25.1 + - - +
197A SER 3.5 18.4 + - - +
198A SER* 3.6 20.8 - - - -
199A ARG* 3.9 4.9 - - - -
220A GLY 3.2 1.0 - - - -
221A LYS* 1.3 89.5 - - + +
223A ALA* 1.3 63.0 + - - +
224A GLN* 4.2 2.3 + - + +
247A GLN* 4.0 4.0 + - - +
248A ASN* 3.0 26.1 + - - +
415A CL 3.6 16.4 - - - +
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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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125A PHE* 3.6 34.3 - - + -
195A SER* 4.1 1.4 + - - +
196A SER* 3.6 3.8 + - - -
197A SER* 2.8 37.3 + - - +
199A ARG* 3.8 4.8 - - + +
222A ARG* 1.3 74.7 - - - +
224A GLN* 1.3 60.6 + - - +
247A GLN 3.3 4.3 - - - -
248A ASN 3.5 20.9 - - - +
249A THR* 3.6 8.5 - - - +
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Residues in contact with GLN 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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194A TYR* 3.2 30.2 + - + +
195A SER* 3.3 17.9 - - - +
196A SER* 4.6 4.6 + - - +
222A ARG* 5.4 1.6 - - + +
223A ALA* 1.3 75.6 - - - +
225A ALA* 1.3 59.9 + - - +
226A TRP* 3.7 26.7 - - - +
245A GLN 5.5 0.4 + - - -
246A THR* 3.3 2.1 - - - -
247A GLN* 2.7 63.7 + - + +
249A THR* 3.3 9.0 + - - -
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Residues in contact with ALA 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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101A VAL* 3.8 13.8 - - + +
119A MET* 4.2 1.1 - - + -
125A PHE* 6.4 0.7 - - + -
127A THR* 4.0 26.5 - - + -
194A TYR* 3.5 1.3 - - - -
195A SER* 2.8 46.4 + - - +
224A GLN* 1.3 76.3 - - - +
226A TRP* 1.3 62.9 + - - +
245A GLN 3.4 6.5 - - - -
246A THR* 4.2 11.7 - - + -
249A THR* 4.6 3.8 - - + +
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Residues in contact with TRP 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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101A VAL* 4.5 2.0 - - - -
119A MET* 3.8 5.3 - - - +
193A GLY 3.2 14.1 - - - +
194A TYR* 3.7 19.3 - + + -
224A GLN* 3.7 26.3 - - - +
225A ALA* 1.3 75.1 - - - +
227A ASN* 1.3 74.6 + - - +
228A VAL* 4.0 23.3 - - + -
243A TYR* 3.7 32.5 - + - -
244A GLY* 3.2 3.0 - - - -
245A GLN* 2.9 76.4 + - + +
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Residues in contact with ASN 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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101A VAL* 2.8 35.6 + - - +
104A THR* 3.7 11.7 - - - -
105A ASN* 3.9 8.1 - - - +
119A MET* 3.9 8.4 - - - -
192A GLY* 3.1 3.2 - - - -
193A GLY* 2.9 43.0 + - - +
226A TRP* 1.3 81.6 - - - +
228A VAL* 1.3 68.1 + - - +
242A MET* 3.6 25.3 - - + -
243A TYR 3.1 14.1 - - - +
244A GLY* 3.8 5.4 - - - -
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Residues in contact with VAL 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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104A THR* 4.0 4.5 - - - -
191A GLY 3.5 10.8 - - - +
192A GLY* 4.1 4.5 - - - -
226A TRP* 4.0 21.3 - - + -
227A ASN* 1.3 80.6 - - - +
229A GLY* 1.3 59.2 + - - +
242A MET* 3.3 3.3 - - - +
243A TYR* 2.8 50.3 + - + +
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Residues in contact with GLY 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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104A THR* 3.6 10.7 - - - +
107A TRP* 3.8 6.5 - - - -
190A LEU* 3.6 6.3 - - - +
191A GLY 2.9 31.6 + - - +
228A VAL* 1.3 77.4 - - - +
230A GLY* 1.3 58.4 + - - -
241A ALA 3.1 13.5 - - - -
242A MET* 4.1 0.9 - - - -
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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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107A TRP* 4.0 7.6 - - - +
189A THR 3.1 12.6 - - - -
190A LEU* 4.1 10.8 - - - -
229A GLY* 1.3 74.6 - - - -
231A LYS* 1.3 62.5 + - - +
240A ALA* 3.3 4.2 - - - +
241A ALA* 3.0 32.2 + - - +
406A LDA 4.6 10.3 - - - -
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Residues in contact with LYS 231 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A TRP* 3.4 42.9 - - + +
187A GLY 3.5 1.2 - - - +
188A VAL* 3.4 6.2 - - - +
189A THR* 3.0 54.7 + - - +
190A LEU* 5.3 0.2 - - - +
230A GLY* 1.3 76.7 - - - +
232A PHE* 1.3 60.1 + - - +
233A ASP* 5.0 13.4 + - + +
238A TYR* 3.6 28.2 + - + +
239A LEU 3.1 13.5 - - - +
240A ALA* 3.9 9.2 - - + +
406A LDA 4.8 7.0 - - - +
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Residues in contact with PHE 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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186A TRP 3.2 27.4 - - - -
187A GLY 3.3 4.5 - - - -
188A VAL* 4.0 3.8 - - + +
231A LYS* 1.3 72.2 - - - +
233A ASP* 1.3 66.1 + - - +
234A ALA* 3.9 14.1 - - + -
235A ASN* 4.0 11.0 - - - -
237A VAL* 3.5 21.0 - - + +
238A TYR* 3.2 7.4 - - - -
239A LEU* 2.8 62.8 + - + +
406A LDA 3.4 84.0 - - + +
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Residues in contact with ASP 233 (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 GLY* 2.8 21.2 + - - +
231A LYS* 5.0 14.5 + - + +
232A PHE* 1.3 76.6 - - - +
234A ALA* 1.3 63.1 + - - +
237A VAL 3.5 6.8 - - - +
238A TYR* 3.4 31.9 - - + +
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Residues in contact with ALA 234 (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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186A TRP 4.5 3.1 - - - +
187A GLY* 4.4 9.9 - - - -
232A PHE* 3.9 16.2 - - + -
233A ASP* 1.3 77.6 + - - +
235A ASN* 1.3 77.3 + - - +
236A ASN 3.2 3.1 - - - -
237A VAL* 2.8 33.9 + - - +
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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