Contacts of the strand formed by residues 219 - 225 (chain B) in PDB entry 2XXA
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 GLU 219 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B LEU* 3.6 20.5 - - + +
99B PHE* 4.0 7.1 - - + -
100B VAL 2.9 3.6 + - - +
101B ILE* 3.4 31.9 - - + -
102B LEU* 2.7 32.6 + - - +
217B PRO* 3.2 3.8 - - - +
218B HIS* 1.3 83.6 - - - +
220B VAL* 1.3 59.1 + - - +
221B MET* 3.8 9.5 - - + +
246B THR* 3.1 34.8 + - - +
247B GLY* 3.3 8.1 - - - -
274B ARG* 3.0 37.8 + - - +
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Residues in contact with VAL 220 (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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102B LEU* 3.5 9.4 - - + +
104B VAL* 4.0 16.2 - - + -
217B PRO* 3.9 21.8 - - + +
219B GLU* 1.3 75.6 - - - +
221B MET* 1.3 59.9 + - - +
222B LEU 3.6 0.7 + - - -
243B VAL* 3.7 30.5 - - + +
244B GLY 3.5 22.9 - - - +
245B LEU* 3.6 23.7 - - + +
246B THR* 2.8 28.2 + - + +
247B GLY 3.2 7.2 + - - +
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Residues in contact with MET 221 (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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91B LEU* 4.5 7.9 - - + -
101B ILE* 3.9 15.5 - - + -
102B LEU 2.8 8.2 + - - +
103B MET* 3.5 29.5 - - + +
104B VAL* 2.9 28.6 + - - +
118B LEU* 4.2 17.3 - - + -
219B GLU* 3.8 4.8 - - + +
220B VAL* 1.3 71.2 - - - +
222B LEU* 1.3 63.0 + - - +
223B THR 4.0 0.3 + - - -
247B GLY* 3.5 8.7 - - - -
248B ILE 3.7 19.3 - - - -
249B THR* 3.0 27.8 - - - +
274B ARG* 3.9 15.9 - - + -
275B TYR* 3.8 28.0 - - + -
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Residues in contact with LEU 222 (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 VAL* 3.3 7.0 - - + +
105B GLY* 3.8 18.2 - - - -
220B VAL 3.6 0.4 + - - -
221B MET* 1.3 72.5 - - - +
223B THR* 1.3 60.5 + - - +
224B ILE* 3.8 26.9 + - + -
235B GLN* 4.1 12.8 - - + +
236B ALA* 4.2 11.0 - - + -
239B PHE* 3.7 38.4 - - + -
245B LEU* 3.8 28.3 - - + -
247B GLY 2.8 15.9 + - - +
248B ILE* 3.3 17.0 - - + +
249B THR 3.0 23.5 + - - -
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Residues in contact with THR 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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103B MET* 3.3 25.6 - - - +
104B VAL 3.0 7.3 + - - -
105B GLY* 4.1 8.7 - - - -
106B VAL 4.7 0.7 + - - -
109B VAL* 3.4 34.8 - - - +
111B LYS* 3.6 16.5 - - - +
114B THR* 3.9 11.0 - - - +
221B MET* 5.0 0.7 - - - +
222B LEU* 1.3 73.8 - - - +
224B ILE* 1.3 65.0 + - - +
235B GLN* 4.9 0.7 - - - +
249B THR* 3.6 14.1 - - - +
251B THR* 3.5 33.4 - - + +
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Residues in contact with ILE 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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109B VAL* 4.5 1.8 - - - -
222B LEU* 3.8 23.8 - - + +
223B THR* 1.3 79.2 - - - +
225B ASP* 1.3 67.4 + - - +
228B THR* 4.8 3.1 - - - +
232B ALA* 5.1 14.6 - - + +
235B GLN* 3.8 24.5 - - + +
248B ILE* 3.8 32.1 - - + -
249B THR 3.0 6.7 + - - +
250B LEU* 3.5 24.5 - - + +
251B THR* 3.2 23.2 + - - -
261B VAL* 5.4 3.4 - - + -
262B ILE* 3.8 13.0 - - + -
265B VAL* 5.3 12.1 - - + -
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Residues in contact with ASP 225 (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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109A GLN 4.5 2.3 - - - +
110A GLY 5.5 0.2 - - - +
222A ASP* 5.5 1.9 - - - +
224A MET* 6.0 0.2 - - + -
108B GLY 4.0 5.2 - - - +
109B VAL* 3.7 19.4 - - + +
224B ILE* 1.3 73.5 - - - +
226B ALA* 1.3 70.1 + - - +
227B SER* 2.6 28.9 + - - -
228B THR* 2.6 44.9 + - + +
250B LEU* 4.2 3.5 - - - +
251B THR* 3.7 8.1 - - - -
252B LYS* 3.2 45.3 + - - +
261B VAL* 5.6 1.6 - - - +
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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