Contacts of the strand formed by residues 270 - 276 (chain B) in PDB entry 5X61
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 ALA 270 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B PRO* 3.6 33.0 - - + +
269B ASN* 1.3 77.8 - - - +
271B ALA* 1.3 69.9 + - - +
272B VAL 3.9 0.3 + - - -
301B ASN 4.5 13.5 - - - +
303B ILE* 4.6 6.1 - - + +
348B GLY 3.1 10.8 + - - +
349B GLY* 3.6 2.4 - - - -
350B ASP* 2.8 25.8 + - - +
353B ARG* 3.6 3.6 - - - +
802B SO4 4.8 7.0 - - - +
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Residues in contact with ALA 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ALA* 1.3 77.3 - - - +
272B VAL* 1.3 59.7 + - - +
302B VAL* 3.4 23.4 - - + +
303B ILE* 3.3 24.8 + - - +
353B ARG* 3.4 34.9 - - - +
637B ALA* 4.1 17.9 - - + +
638B LYS* 4.1 11.0 - - + -
802B SO4 4.2 3.0 + - - +
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Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ALA 4.1 2.2 - - - +
271B ALA* 1.3 78.4 - - - +
273B MET* 1.3 66.1 + - - +
274B LEU* 3.9 0.6 + - + -
303B ILE* 3.5 32.5 - - + -
305B VAL* 3.8 18.2 - - + -
340B VAL* 4.5 2.9 - - + -
344B ILE* 4.0 11.7 - - + -
349B GLY* 3.9 17.0 - - - -
350B ASP 4.1 11.9 - - - +
353B ARG 3.2 6.1 + - - +
354B VAL* 3.5 28.2 - - + -
355B THR* 2.8 31.9 + - - +
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Residues in contact with MET 273 (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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272B VAL* 1.3 73.2 - - - +
274B LEU* 1.3 59.7 + - - +
296B LEU* 4.2 22.4 - - + -
300B GLU* 6.2 0.2 - - - -
302B VAL* 3.8 21.9 - - + +
303B ILE 3.2 8.4 + - - +
304B VAL* 3.5 8.0 - - - +
305B VAL 2.9 26.7 + - - +
355B THR* 3.5 4.9 - - - +
357B PHE* 3.6 34.4 - - + -
383B ILE* 3.8 28.7 - - + -
633B TRP* 4.3 15.5 - - + +
634B SER* 4.3 14.6 - - - -
637B ALA* 3.8 25.8 - - + -
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Residues in contact with LEU 274 (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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272B VAL* 3.9 0.8 + - + -
273B MET* 1.3 70.7 - - - +
275B TRP* 1.3 67.9 + - - +
276B ILE* 3.8 2.5 + - + +
305B VAL* 3.3 28.0 - - + +
307B LEU* 3.6 31.2 - - + +
336B ALA* 6.0 0.2 - - + -
337B LEU* 3.5 26.5 - - + -
340B VAL* 3.7 25.8 - - + -
354B VAL* 4.0 18.8 - - + -
355B THR 3.0 9.7 + - - +
356B LEU* 3.5 19.2 - - + +
357B PHE* 2.9 29.6 + - - +
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Residues in contact with TRP 275 (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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274B LEU* 1.3 72.6 - - - +
276B ILE* 1.3 70.6 + - - +
277B PHE* 3.5 21.7 + + + +
278B GLY 5.1 0.7 - - - -
286B ALA* 5.4 2.5 - - - -
291B TYR* 3.4 51.1 - + + -
293B HIS* 4.9 2.2 - + + -
304B VAL* 5.4 0.4 - - + -
305B VAL 2.7 16.3 + - - +
306B SER* 3.6 27.4 - - - -
307B LEU 3.7 9.2 + - - +
357B PHE* 3.1 60.3 - + + -
358B GLY* 3.7 14.6 - - - -
359B GLU* 3.8 15.9 - - + -
385B GLN* 4.4 8.3 - - - -
604B ILE* 3.6 25.1 - - + -
607B VAL* 5.3 0.4 - - + -
608B PHE* 3.4 22.2 - + + -
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Residues in contact with ILE 276 (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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274B LEU* 4.8 5.2 - - + +
275B TRP* 1.3 76.9 - - - +
277B PHE* 1.3 73.7 + - - +
307B LEU* 4.0 22.7 - - + -
309B TYR* 3.8 6.5 - - + -
333B GLN* 3.5 40.8 - - + +
337B LEU* 5.1 1.1 - - + -
356B LEU* 4.5 11.4 - - + -
357B PHE 3.1 6.9 + - - -
358B GLY* 3.3 21.8 - - - -
359B GLU 3.9 1.0 + - - -
362B GLY* 3.4 19.0 - - - +
365B SER* 3.8 2.7 - - - -
366B VAL* 3.8 23.6 - - + -
369B HIS* 4.0 17.0 - - + +
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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