Contacts of the strand formed by residues 479 - 483 (chain A) in PDB entry 6FP4
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 TYR 479 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321A LEU* 4.8 3.8 - - + -
324A PHE* 3.9 27.2 - + + +
325A ASP* 3.4 17.7 + - - +
328A MET* 3.4 36.3 - - + -
329A ALA 5.0 0.7 - - - -
332A VAL* 3.8 31.9 - - + -
471A THR* 4.2 0.9 - - - +
472A THR* 3.3 1.9 - - - -
473A VAL* 2.8 54.1 + - + +
475A THR* 4.8 0.2 - - - +
477A LEU 4.6 0.2 - - - +
478A GLU* 1.3 76.3 - - - +
480A GLY* 1.3 77.1 + - - +
481A ALA* 3.7 11.7 + - + +
538A HIS* 2.9 28.4 + - + -
539A VAL 3.3 9.2 - - - -
540A LEU* 4.3 2.5 - - + -
544A ALA* 4.0 1.6 - - - -
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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
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471A THR 3.3 9.9 - - - -
472A THR* 3.8 7.6 - - - -
479A TYR* 1.3 79.5 - - - +
481A ALA* 1.3 61.3 + - - -
537A LEU* 5.1 0.2 - - - -
538A HIS* 3.5 0.5 - - - -
539A VAL* 2.8 33.6 + - - +
544A ALA* 3.4 8.1 - - - +
548A THR* 3.4 21.3 - - - -
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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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324A PHE* 5.9 1.6 - - + -
469A VAL 4.6 0.2 - - - +
470A ALA* 3.3 3.5 - - - +
471A THR* 2.9 47.1 + - + +
479A TYR* 3.7 25.5 + - + +
480A GLY* 1.3 76.1 - - - +
482A CYS* 1.3 60.7 + - - +
483A GLY 5.4 2.5 - - - +
537A LEU 3.1 11.9 - - - +
538A HIS* 3.8 8.1 - - + +
548A THR* 3.8 5.3 - - - +
606A 250 5.9 2.5 - - - +
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Residues in contact with CYS 482 (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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468A ASN 3.3 25.6 - - - -
469A VAL 4.7 0.4 - - - -
470A ALA* 3.8 14.1 - - + +
481A ALA* 1.3 75.2 - - - +
483A GLY* 1.3 59.2 + - - +
536A GLY* 3.2 2.3 - - - -
537A LEU* 2.7 41.5 + - + +
538A HIS* 5.7 0.2 - - - -
548A THR* 4.2 8.7 - - + +
551A TYR* 6.0 0.2 - - + -
552A ALA* 3.9 22.4 - - + +
555A ILE* 3.7 36.5 - - + +
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Residues in contact with GLY 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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468A ASN* 3.7 25.7 - - - +
469A VAL 4.8 3.8 + - - -
481A ALA* 5.4 1.9 - - - +
482A CYS* 1.3 79.1 + - - +
484A LEU* 1.3 68.6 + - - -
485A SER 3.7 1.0 + - - -
535A LEU 3.3 10.1 - - - -
538A HIS* 4.8 4.6 - - - -
555A ILE* 5.6 0.7 - - - -
606A 250 5.1 17.0 + - - +
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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