Contacts of the strand formed by residues 327 - 331 (chain A) in PDB entry 3V3K
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 ILE 327 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A PHE* 3.9 10.5 - - - +
262A VAL* 3.4 42.4 - - + +
265A PHE 5.1 3.6 - - - +
266A ASN* 5.4 4.3 - - + -
278A LYS* 3.9 26.2 - - + -
280A PHE* 4.4 8.3 - - + -
324A PRO* 3.6 24.7 - - + +
325A SER 3.3 2.6 - - - +
326A ASP* 1.3 77.3 - - - +
328A PHE* 1.3 64.4 + - - +
329A VAL* 3.8 17.0 - - + +
390A PHE 4.4 0.4 - - - -
393A PHE* 2.9 41.8 + - + +
394A LEU* 3.8 1.0 + - - +
334C PHE* 4.6 6.1 - - + -
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Residues in contact with PHE 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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278A LYS 3.2 6.6 + - - -
279A LEU* 3.7 22.0 - - + -
280A PHE* 2.8 33.2 + - - +
281A PHE* 4.6 2.9 - + - -
327A ILE* 1.3 77.7 - - - +
329A VAL* 1.3 54.9 + - - +
330A SER* 4.0 11.9 - - - -
366A LEU* 3.8 27.6 - - + -
367A GLN* 4.2 8.5 - - + -
370A LEU* 3.4 34.8 - - + -
389A CYS* 3.6 25.8 - - + -
390A PHE 3.7 2.9 - - - -
392A ASN* 3.4 39.0 - - + -
394A LEU* 3.7 17.9 - - + -
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Residues in contact with VAL 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A PHE* 3.9 11.0 - - + +
258A VAL* 3.8 3.6 - - + -
262A VAL* 3.4 30.3 - - + -
280A PHE* 3.5 11.0 - - + -
282A ILE* 3.5 29.6 - - + -
327A ILE* 3.8 13.7 - - + -
328A PHE* 1.3 72.4 - - - +
330A SER* 1.3 58.5 + - - +
331A TYR* 3.3 32.7 - - + +
389A CYS* 3.3 3.3 - - - -
390A PHE* 2.8 38.6 + - + -
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Residues in contact with SER 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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280A PHE 2.7 15.0 + - - -
281A PHE* 3.7 8.5 - - - -
282A ILE* 3.0 27.2 + - - +
328A PHE* 3.8 5.8 + - - -
329A VAL* 1.3 70.5 - - - +
331A TYR* 1.3 58.9 + - - +
349A TYR* 2.6 29.8 + - - -
370A LEU* 3.2 31.8 - - - +
388A GLY 3.3 12.4 + - - -
389A CYS* 3.8 2.7 - - - -
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Residues in contact with TYR 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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240A PRO* 2.7 60.2 + - + +
241A GLY* 4.8 3.1 - - - -
258A VAL* 3.6 20.7 - - + +
282A ILE* 4.1 11.7 - - + -
286A GLY* 6.5 1.3 - - - -
329A VAL* 3.3 36.3 - - + +
330A SER* 1.3 73.8 - - - +
332A SER* 1.3 60.1 + - - +
333A THR 3.6 19.3 - - - +
335A PRO* 5.1 6.3 - - + -
349A TYR* 4.0 4.7 - - - -
387A PRO* 3.5 4.2 - - - +
388A GLY 2.9 36.7 + - - +
389A CYS* 4.8 0.9 - - - -
390A PHE* 4.4 12.1 - - + -
390C PHE* 4.4 17.7 - + - -
393C PHE* 5.1 4.5 - - + -
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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