Contacts of the strand formed by residues 324 - 332 (chain A) in PDB entry 4FOV
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 SER 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A SER* 2.7 32.6 + - - -
273A SER 3.4 17.6 + - - -
275A ILE* 3.5 23.1 - - - -
298A PHE* 3.6 5.9 - - - -
322A SER 4.8 0.5 + - - -
323A ALA* 1.3 77.2 - - - +
325A PHE* 1.3 62.8 + - - +
345A VAL* 3.8 1.2 - - - -
346A MET* 2.8 42.1 + - - +
350A ILE 4.4 1.0 + - - -
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Residues in contact with PHE 325 (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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275A ILE* 3.0 40.7 + - - +
277A ILE* 3.6 21.8 - - + +
296A MET* 3.6 44.4 - - + -
297A LYS* 3.3 25.1 - - - -
298A PHE* 3.3 30.3 - + - -
324A SER* 1.3 73.5 - - - +
326A ILE* 1.3 64.7 + - - +
343A ALA* 4.8 0.4 - - + -
344A ASP 3.3 14.4 - - - +
345A VAL* 3.8 24.5 - - + -
474A PHE* 3.4 34.5 - + - -
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Residues in contact with ILE 326 (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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262A ASP* 3.1 22.2 - - - +
264A ARG* 3.3 20.6 - - - +
270A ASP* 3.9 3.8 - - - -
271A SER* 3.6 40.2 - - - +
275A ILE* 3.9 4.0 - - + -
277A ILE* 4.0 4.0 - - - +
325A PHE* 1.3 78.2 - - - +
327A ASP* 1.3 78.8 + - - +
344A ASP* 2.9 42.0 + - + +
346A MET* 4.2 11.2 - - + -
701A CXS 3.5 31.0 - - + -
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Residues in contact with ASP 327 (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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246A ILE* 3.7 27.1 - - - +
262A ASP* 3.1 13.8 + - - -
264A ARG* 4.3 0.2 + - - -
326A ILE* 1.3 84.6 - - - +
328A SER* 1.3 59.7 - - - +
343A ALA* 3.2 14.1 - - - -
344A ASP* 3.5 11.8 + - - +
489A TYR* 5.7 0.3 - - - +
490A LEU* 3.3 25.0 - - - +
492A PRO* 4.2 17.4 - - + +
509A TYR* 4.8 2.1 + - - -
541A GLU* 4.7 1.5 - - - +
653A TYR* 5.3 0.2 - - - -
701A CXS 3.1 41.9 + - - +
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Residues in contact with SER 328 (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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246A ILE* 4.5 2.6 + - - +
248A THR* 3.3 11.6 - - - +
260A SER* 3.0 25.3 + - - -
261A ILE* 4.0 7.1 + - - -
262A ASP* 4.2 3.6 + - - -
277A ILE* 3.8 28.5 - - - +
327A ASP* 1.3 75.4 - - - +
329A SER* 1.3 61.8 + - - +
341A LEU* 4.1 4.5 - - - -
342A LEU 3.1 11.2 - - - -
343A ALA* 3.9 5.6 - - - -
490A LEU* 4.0 0.4 - - - -
492A PRO* 3.3 5.6 - - - +
493A GLY 3.0 19.2 + - - -
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Residues in contact with SER 329 (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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328A SER* 1.3 76.0 - - - +
330A ILE* 1.3 61.7 + - - +
341A LEU* 3.4 4.9 - - - +
342A LEU 2.8 30.1 + - - +
490A LEU* 3.6 13.5 - - - -
491A CYS 3.5 18.7 + - - -
493A GLY 3.2 17.2 + - - -
494A GLN 3.2 21.1 + - - -
495A GLY 3.4 1.7 + - - -
506A PHE* 3.5 17.9 - - - -
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Residues in contact with ILE 330 (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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248A THR* 3.4 11.4 - - - +
250A TYR* 3.4 32.4 - - + -
258A LEU* 3.9 28.0 - - + +
259A SER 4.2 1.1 - - - -
260A SER* 3.3 40.6 - - - +
329A SER* 1.3 77.4 + - - +
331A VAL* 1.3 67.3 + - - +
339A THR* 3.9 25.1 - - + -
340A ILE 3.4 5.6 - - - +
341A LEU* 4.2 11.4 - - + -
493A GLY 3.0 8.8 + - - +
494A GLN* 3.4 1.2 - - - -
495A GLY 2.8 23.6 + - - -
506A PHE* 3.9 1.3 - - - -
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Residues in contact with VAL 331 (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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250A TYR* 3.6 18.6 - - - +
330A ILE* 1.3 78.1 - - - +
332A GLU* 1.3 64.8 + - - +
339A THR* 3.7 5.0 - - - +
340A ILE* 2.8 44.0 + - + -
495A GLY* 3.7 23.6 - - - -
496A LEU 3.8 4.3 - - - +
497A ALA* 3.7 20.0 - - + +
504A LEU* 4.3 19.7 - - + -
505A ILE 6.0 0.2 - - - +
506A PHE* 3.4 31.0 - - + -
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Residues in contact with GLU 332 (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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250A TYR* 3.4 21.1 + - + +
251A THR 4.6 1.2 - - - +
252A LEU* 3.5 30.4 - - + +
253A SER* 2.8 42.5 + - - -
331A VAL* 1.3 77.6 - - - +
333A ASP* 1.3 70.4 + - - +
334A LYS* 3.7 4.5 + - + +
337A GLY* 4.2 12.1 - - - +
338A LYS 3.8 9.9 - - - +
339A THR* 4.3 5.8 + - - +
467A ARG* 4.6 9.5 + - - +
497A ALA* 3.5 24.1 - - - +
504A LEU* 4.0 4.1 - - - +
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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