Contacts of the strand formed by residues 260 - 265 (chain A) in PDB entry 3FEO
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 LYS 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A GLY 4.2 2.9 + - - -
259A MET* 1.3 73.4 - - - +
261A LEU* 1.3 63.6 + - - +
275A ALA 3.3 7.4 - - - +
276A THR* 2.4 42.1 + - - +
278A ARG* 4.7 4.0 - - - +
291A ASP* 2.9 19.9 + - - +
314A VAL* 3.6 8.6 + - + +
337A TRP* 3.8 18.2 - - + -
340A TYR* 4.1 11.2 - - + -
341A LEU* 3.6 14.1 - - + -
344A THR* 3.7 15.0 + - - +
346A SER* 3.2 32.5 - - - +
347A ILE 3.0 10.1 + - - +
348A ALA* 3.5 3.3 - - - -
349A ALA* 2.8 28.9 + - - +
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Residues in contact with LEU 261 (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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255A PHE* 5.2 1.8 - - + -
259A MET 3.7 11.0 - - - +
260A LYS* 1.3 77.6 - - - +
262A GLU* 1.3 65.7 + - - +
263A ALA* 4.9 0.2 - - + -
275A ALA* 3.0 48.3 + - + +
276A THR 3.8 9.9 - - - +
277A ILE* 3.8 13.7 - - + +
288A ILE* 4.0 18.2 - - + -
311A ILE* 3.8 39.7 - - + -
312A PHE 3.4 11.0 - - - +
314A VAL* 4.1 9.4 - - - +
337A TRP* 3.8 8.1 - - - -
349A ALA* 4.6 2.0 - - + -
354A PHE* 4.0 15.0 - - + -
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Residues in contact with GLU 262 (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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261A LEU* 1.3 78.0 - - - +
263A ALA* 1.3 64.4 + - - +
272A ILE* 3.7 15.5 - - + -
273A CYS 3.3 4.3 - - - +
275A ALA* 4.8 0.2 - - - -
311A ILE* 3.2 5.5 - - - +
312A PHE* 2.8 40.4 + - + +
313A PRO 3.7 13.0 - - - +
314A VAL* 4.3 0.4 - - - -
315A GLY* 3.0 14.8 + - - -
316A PHE* 3.7 4.7 - - - +
317A CYS* 2.9 44.6 + - - +
318A GLU 5.2 0.3 + - - -
324A LEU* 3.8 13.5 - - + +
337A TRP* 2.7 38.6 + - + -
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Residues in contact with ALA 263 (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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261A LEU* 4.9 0.9 - - + -
262A GLU* 1.3 75.6 - - - +
264A ILE* 1.3 72.6 + - - +
265A ASP* 3.0 2.1 + - - -
272A ILE* 3.6 5.6 - - - +
273A CYS* 2.8 40.8 + - + +
275A ALA* 4.2 16.6 - - + -
288A ILE* 4.5 7.6 - - + -
290A ILE* 5.6 1.2 - - + +
302A PHE* 4.8 4.0 - - + -
304A TYR* 4.3 7.2 - - + -
310A SER 3.4 8.7 - - - +
311A ILE* 4.0 14.1 - - + -
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Residues in contact with ILE 264 (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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263A ALA* 1.3 71.4 - - - +
265A ASP* 1.3 63.1 + - - +
266A PRO* 3.2 3.5 - - - +
269A LEU* 3.6 42.2 - - + +
271A THR 3.4 9.6 - - - +
272A ILE* 3.9 19.6 - - + +
304A TYR* 2.7 33.0 + - - +
309A PRO 4.5 0.7 - - - +
310A SER* 2.9 42.1 + - - +
312A PHE* 4.0 12.3 - - + -
392A LEU* 4.4 7.2 - - + -
407A TRP* 4.1 25.8 - - + +
408A VAL* 5.2 2.0 - - - +
409A ASP 5.9 0.4 - - - +
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Residues in contact with ASP 265 (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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263A ALA 3.0 6.1 + - - -
264A ILE* 1.3 71.4 - - - +
266A PRO* 1.3 69.2 - - - +
267A LEU* 2.8 21.5 + - - +
268A ASN* 2.9 45.0 + - - +
269A LEU* 3.5 6.2 + - - +
271A THR* 3.1 27.3 + - - +
273A CYS* 3.7 14.3 - - - -
290A ILE* 3.2 22.0 - - + +
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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