Contacts of the strand formed by residues 375 - 382 (chain X) in PDB entry 2XB2
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 GLY 375 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250X GLY 3.2 10.3 + - - +
251X ILE* 3.2 9.5 - - - +
252X LYS* 2.9 24.8 + - - +
347X SER* 3.3 11.4 - - - -
368X SER* 4.0 11.2 - - - -
369X GLY* 4.2 4.9 - - - -
373X ARG 3.7 2.2 + - - -
374X LYS* 1.3 74.1 - - - +
376X VAL* 1.3 68.6 + - - +
410X LEU* 5.5 0.6 - - - +
411X ILE* 5.6 0.7 - - - -
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Residues in contact with VAL 376 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251X ILE* 4.4 1.8 - - - -
252X LYS* 3.4 3.6 - - + -
254X PHE* 3.8 21.1 - - + -
347X SER 2.9 7.1 + - - +
348X LEU* 3.1 38.9 - - + +
349X ILE* 2.9 25.5 + - - +
368X SER* 4.3 0.9 + - - -
375X GLY* 1.3 81.0 - - - +
377X ALA* 1.3 63.3 + - - +
378X ILE* 4.1 4.0 - - + -
407X VAL* 3.8 21.3 - - + +
410X LEU* 3.7 30.1 - - + -
411X ILE* 3.8 10.1 - - + +
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Residues in contact with ALA 377 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251X ILE* 4.2 7.4 - - + -
252X LYS 2.9 12.4 + - - +
253X GLN* 3.5 8.3 - - + -
254X PHE 2.9 27.9 + - - +
349X ILE* 3.3 12.1 - - + +
365X ILE* 3.5 38.1 - - + -
376X VAL* 1.3 74.9 - - - +
378X ILE* 1.3 61.7 + - - +
379X ASN* 4.0 4.5 + - - +
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Residues in contact with ILE 378 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254X PHE* 3.6 10.8 - - + +
255X PHE* 4.9 0.7 - - - -
256X VAL* 3.9 20.6 - - + +
271X LEU* 3.6 22.2 - - + -
348X LEU* 3.7 18.2 - - + -
349X ILE 2.9 6.9 + - - +
350X ILE* 3.4 18.2 - - + +
351X ASN* 3.0 26.2 + - - +
376X VAL* 4.1 8.5 - - + -
377X ALA* 1.3 75.7 - - - +
379X ASN* 1.3 62.9 + - - +
380X PHE* 3.5 27.9 + - + -
403X MET* 3.4 24.0 - - - -
407X VAL* 4.1 7.4 - - + -
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Residues in contact with ASN 379 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253X GLN* 5.0 0.2 - - - +
254X PHE 2.9 26.3 + - - +
255X PHE* 3.0 9.4 - - + +
256X VAL 2.8 23.9 + - - -
351X ASN* 3.0 30.5 - - - +
354X LEU* 4.0 6.6 - - + +
361X TYR* 3.1 31.6 + - - -
365X ILE* 5.2 0.6 - - - +
377X ALA* 4.0 9.3 + - - +
378X ILE* 1.3 73.9 - - - +
380X PHE* 1.3 64.8 + - - +
381X VAL* 3.5 1.6 + - + +
389X LEU* 3.4 29.3 - - + +
400X ILE* 4.1 5.1 - - - +
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Residues in contact with PHE 380 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256X VAL* 3.9 14.4 - - + +
258X VAL* 5.5 1.8 - - + -
264X LYS* 3.6 50.0 + - + -
267X THR* 3.8 27.4 - - + -
268X LEU* 4.1 10.1 - - + -
271X LEU* 4.0 11.4 - - + -
350X ILE* 3.8 20.4 - - + -
351X ASN 3.2 19.1 + - - +
352X TYR* 3.8 38.4 - + - +
354X LEU* 4.3 10.1 + - - +
378X ILE* 3.5 26.2 - - + -
379X ASN* 1.3 73.7 - - - +
381X VAL* 1.3 63.8 + - - +
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Residues in contact with VAL 381 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255X PHE* 3.9 27.4 - - + -
256X VAL 3.4 4.2 + - - +
257X ALA* 3.3 11.3 - - + +
258X VAL* 2.9 27.0 + - - +
354X LEU* 3.7 35.2 - - + -
379X ASN 4.2 5.6 - - - +
380X PHE* 1.3 79.0 - - - +
382X LYS* 1.3 61.6 + - - +
383X ASN 3.9 1.0 + - - +
385X ASP* 4.0 15.0 - - + +
386X ILE* 4.1 18.4 - - + +
389X LEU* 4.3 13.0 - - + -
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Residues in contact with LYS 382 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171S ASP* 3.5 17.7 + - - +
173S ASP* 2.9 42.5 + - - -
174S GLU* 4.2 17.2 + - - -
258X VAL* 3.1 18.8 - - + +
259X GLU 3.5 14.1 + - - +
260X ARG* 4.2 1.1 - - - +
261X GLU* 3.6 13.9 - - - +
264X LYS* 4.8 11.4 - - - +
380X PHE 4.3 0.4 + - - -
381X VAL* 1.3 72.5 - - - +
383X ASN* 1.3 89.9 + - - +
384X ASP 3.3 0.2 + - - -
385X ASP* 3.0 28.9 + - - +
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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