Contacts of the strand formed by residues 479 - 483 (chain A) in PDB entry 3V9G
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 THR 479 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319A ASN* 2.8 38.7 + - - +
320A PHE* 3.7 7.3 + - - -
349A SER* 2.9 46.8 + - - -
478A LEU* 1.3 82.6 + - + +
480A GLY* 1.3 60.1 + - - +
500A ALA 4.5 1.7 - - - +
501A ALA* 3.6 5.2 - - - +
503A ASN* 3.2 16.6 - - + -
505A TYR* 4.3 1.6 - - + -
510A SER* 3.3 15.3 + - - +
520A PHE* 3.7 19.5 - - + -
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Residues in contact with GLY 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A PHE* 3.3 34.1 - - - -
479A THR* 1.3 78.6 + - - +
481A ALA* 1.3 61.4 + - - -
501A ALA* 3.6 2.0 - - - +
503A ASN 3.1 4.6 + - - -
504A PHE* 3.4 6.7 - - - -
505A TYR* 2.9 27.0 + - - -
510A SER* 4.2 3.7 - - - -
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Residues in contact with ALA 481 (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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320A PHE* 2.9 14.3 + - - -
321A HIS* 3.7 23.1 - - + +
322A PHE* 2.7 32.0 + - - -
480A GLY* 1.3 74.3 - - - +
482A VAL* 1.3 61.2 + - - +
483A PHE* 4.1 7.0 - - + -
504A PHE* 4.8 0.7 - - - -
505A TYR* 3.2 11.0 - - + +
508A ASP 3.3 26.5 - - - +
510A SER* 4.5 2.0 - - - -
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Residues in contact with VAL 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A PHE* 3.4 19.7 - - + +
324A HIS* 5.8 0.2 - - + -
481A ALA* 1.3 78.1 - - - +
483A PHE* 1.3 59.8 + - - +
484A SER* 4.0 20.4 + - - -
489A VAL* 5.4 2.0 - - + -
490A VAL* 4.6 12.6 - - + -
493A ALA* 3.9 24.7 - - + -
497A LEU* 4.0 10.1 - - + -
504A PHE* 3.5 31.4 - - + -
505A TYR 2.9 8.1 + - - +
506A ILE* 3.6 7.1 - - + +
507A ASN* 2.8 32.6 + - - +
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Residues in contact with PHE 483 (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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321A HIS* 3.5 38.6 - + + -
322A PHE 2.9 17.6 + - - +
323A VAL* 4.4 5.4 - - + -
324A HIS* 2.9 28.9 + - - +
327A ALA* 3.4 10.8 - - + +
328A ASP 5.1 1.3 - - - +
331A SER* 3.9 29.2 - - - -
332A VAL* 3.7 36.6 - - + -
335A GLY* 4.9 1.8 - - - -
336A THR* 4.9 0.2 - - - -
481A ALA* 4.1 4.3 - - + -
482A VAL* 1.3 73.1 - - - +
484A SER* 1.3 61.7 + - - +
507A ASN* 3.3 20.0 - - + +
508A ASP 3.5 39.0 - - - -
509A LYS* 4.3 1.1 - - - -
554B LEU* 4.1 6.7 - - + -
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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