Contacts of the strand formed by residues 322 - 328 (chain B) in PDB entry 1XAI
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 GLN 322 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236B LYS* 4.8 5.0 - - - +
243B THR* 3.6 16.1 + - - +
315B LYS* 3.6 37.1 + - + +
316B ASN* 3.3 19.2 + - - +
317B ASP* 3.6 21.1 - - - +
320B GLY 4.2 3.4 - - - +
321B VAL* 1.3 82.8 - - - +
323B MET* 1.3 64.0 + - - +
334B VAL* 3.2 30.1 - - - +
335B GLN* 3.6 20.3 - - - +
336B HIS* 3.8 11.2 + - + +
337B VAL 4.8 0.2 - - - +
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Residues in contact with MET 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B GLY* 6.1 2.2 - - - +
243B THR* 3.6 33.4 - - + +
244B PHE 5.5 0.9 - - - +
263B GLY 5.5 0.7 - - - +
266B TYR* 3.8 36.8 - - + -
267B GLN* 4.1 16.2 - - + -
270B VAL* 4.3 3.1 - - + -
310B MET* 5.0 0.2 - - - -
315B LYS* 4.4 0.7 - - - +
321B VAL* 4.6 2.7 - - + -
322B GLN* 1.3 76.6 - - - +
324B VAL* 1.3 65.2 + - - +
325B LEU* 3.6 26.6 + - + +
333B VAL 3.6 0.3 - - - +
334B VAL* 3.2 8.3 - - - +
335B GLN 3.2 29.3 + - - +
337B VAL* 3.8 22.9 - - + +
342B LEU* 3.9 18.4 - - - -
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Residues in contact with VAL 324 (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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236B LYS 3.0 24.7 - - - +
237B PHE* 3.7 19.5 - - + -
239B ASN* 4.0 7.8 + - + +
240B LEU* 3.3 25.5 - - + +
241B GLY 4.5 3.4 + - - +
243B THR* 4.5 2.2 + - - -
267B GLN* 3.2 19.6 - - - +
315B LYS* 3.8 24.6 - - + +
323B MET* 1.3 74.6 - - - +
325B LEU* 1.3 60.2 + - - +
332B ILE* 3.3 27.6 - - + -
333B VAL 3.7 2.5 - - - -
334B VAL* 4.0 9.6 - - + -
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Residues in contact with LEU 325 (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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267B GLN* 3.5 12.6 - - - +
270B VAL* 3.3 31.6 - - + -
271B ALA* 4.2 2.2 - - + +
274B LEU* 3.4 21.5 - - + -
275B PHE* 3.3 35.9 - - + -
323B MET* 3.8 26.7 - - + +
324B VAL* 1.3 75.2 - - - +
326B MET* 1.3 60.4 + - - +
327B ARG 4.1 0.2 - - - -
332B ILE* 3.1 6.9 - - - +
333B VAL* 2.8 39.6 + - - +
335B GLN* 4.1 17.3 - - + -
337B VAL* 4.2 7.2 - - + -
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Residues in contact with MET 326 (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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184B LEU* 2.8 39.0 - - + +
185B LEU* 4.5 3.1 - - + +
240B LEU* 4.9 5.8 - - + -
267B GLN* 2.6 22.3 + - - +
268B PHE* 4.1 22.9 - - + -
271B ALA* 2.8 31.3 - - - +
275B PHE* 4.1 0.7 - - - -
279B HIS* 3.0 10.8 + - + -
325B LEU* 1.3 73.4 - - - +
327B ARG* 1.3 57.1 - - - +
328B GLN* 3.9 14.6 - - - +
329B PHE* 3.9 33.7 - - + -
330B GLY 4.4 0.2 - - - +
331B ASP 4.0 2.2 - - - -
332B ILE* 3.9 30.7 - - + +
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Residues in contact with ARG 327 (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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275B PHE* 3.2 49.8 - - + +
277B SER* 2.7 38.5 + - - +
279B HIS* 4.6 1.3 - - - -
325B LEU 4.0 0.4 + - - -
326B MET* 1.3 73.2 - - - +
328B GLN* 1.3 64.0 + - + +
331B ASP* 3.0 41.6 + - - +
333B VAL* 3.7 30.2 - - + +
335B GLN* 3.9 9.5 + - - -
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Residues in contact with GLN 328 (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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279B HIS* 5.4 2.5 - - - -
326B MET* 3.5 9.6 - - - +
327B ARG* 1.3 83.7 - - + +
329B PHE* 1.3 67.8 + - + +
330B GLY 2.7 3.6 + - - -
331B ASP* 2.4 50.5 + - + +
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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