Contacts of the strand formed by residues 342 - 349 (chain A) in PDB entry 3I5Y
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 342 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A THR* 4.8 0.2 - - - +
339A HIS* 3.2 31.7 + - + +
340A GLU 3.2 8.4 - - - +
341A ARG* 1.3 75.8 - - - +
343A ASP* 1.3 61.3 + - - +
344A GLN* 3.3 21.9 + - + +
464A ILE* 3.1 46.0 - - + +
465A GLY* 4.1 3.1 - - - +
467A THR* 4.0 7.0 - - + +
468A ALA* 3.4 21.3 - - + -
474A GLY 3.4 10.3 - - - +
475A SER 4.3 2.2 - - - -
476A SER* 3.8 32.5 - - - +
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Residues in contact with ASP 343 (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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341A ARG 3.3 4.7 + - - +
342A ILE* 1.3 67.9 - - - +
344A GLN* 1.3 61.0 + - - +
345A SER* 5.2 1.0 - - - -
474A GLY 3.0 16.1 + - - +
475A SER* 3.4 15.4 + - - +
476A SER 3.0 23.0 + - - +
501A LYS* 3.4 37.9 + - - +
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Residues in contact with GLN 344 (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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338A ALA* 4.0 20.0 - - - +
339A HIS 4.6 5.1 + - - -
340A GLU* 6.1 0.4 - - - +
342A ILE* 3.3 21.7 + - + +
343A ASP* 1.3 74.7 + - - +
345A SER* 1.3 64.2 + - - +
460A TYR* 2.5 36.3 + - - +
464A ILE* 3.8 9.5 - - + +
476A SER* 3.5 20.0 - - - +
497A ILE* 3.7 12.6 - - - +
498A VAL 5.8 1.4 + - - -
499A ILE* 4.0 17.8 - - + +
500A ALA* 4.7 3.0 + - - +
501A LYS* 3.7 20.4 + - - +
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Residues in contact with SER 345 (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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343A ASP* 5.2 1.6 - - - -
344A GLN* 1.3 76.8 - - - +
346A VAL* 1.3 61.1 + - - +
347A VAL* 5.1 2.2 - - - +
460A TYR* 5.4 1.4 + - - -
476A SER* 2.9 7.0 + - - +
477A VAL* 3.2 30.1 - - - +
478A LEU* 2.9 23.8 + - - +
499A ILE* 3.6 7.1 - - - +
501A LYS* 3.1 32.3 - - - -
503A GLU* 6.4 2.7 - - - -
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Residues in contact with VAL 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A SER* 1.3 74.7 - - - +
347A VAL* 1.3 66.3 + - - +
348A ILE* 4.0 9.3 + - + +
478A LEU* 3.2 26.2 - - + +
480A ILE* 3.7 32.5 - - + -
485A LEU* 6.2 0.2 - - + -
488A VAL* 4.6 3.8 - - + -
499A ILE* 3.9 15.5 - - + -
501A LYS 2.8 10.6 + - - +
502A GLN* 3.3 41.6 - - + +
503A GLU* 3.2 22.0 + - - +
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Residues in contact with VAL 347 (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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345A SER* 5.1 2.9 - - - +
346A VAL* 1.3 75.5 - - - +
348A ILE* 1.3 61.3 + - - +
349A SER* 3.7 2.1 + - - +
355A SER* 5.1 0.2 + - - -
358A ALA* 4.4 3.1 - - + -
362A HIS* 6.1 0.9 - - - +
477A VAL* 3.6 22.4 - - + -
478A LEU 2.8 8.3 + - - +
479A PHE* 3.6 28.1 - - + +
480A ILE 3.2 24.9 + - - +
503A GLU* 3.4 33.7 - - + +
504A LYS 4.7 0.4 - - - +
505A TYR* 3.6 31.0 - - + -
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Residues in contact with ILE 348 (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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346A VAL* 4.1 12.6 - - + +
347A VAL* 1.3 72.1 - - - +
349A SER* 1.3 71.5 + - - +
480A ILE* 3.4 5.8 - - + +
481A CYS 4.3 2.0 - - - -
482A LYS* 3.9 26.0 - - + +
485A LEU* 3.8 32.1 - - + -
502A GLN* 3.8 32.1 - - + +
503A GLU 2.8 19.0 + - - +
504A LYS* 3.4 12.4 - - + +
505A TYR* 3.2 19.7 + - - +
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Residues in contact with SER 349 (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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347A VAL 3.7 1.8 + - - -
348A ILE* 1.3 75.7 - - - +
350A GLU* 1.3 61.1 + - - +
351A LYS 3.4 19.3 - - - -
354A ASN* 3.4 17.4 - - - +
355A SER* 3.8 7.2 + - - -
358A ALA* 4.5 1.7 - - - +
480A ILE 2.7 14.6 + - - -
481A CYS* 4.0 1.3 - - - -
482A LYS* 2.8 29.6 + - - +
505A TYR* 3.3 36.3 - - - +
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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