Contacts of the strand formed by residues 478 - 482 (chain q) in PDB entry 6FF7
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 VAL 478 (chain q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463q ALA* 4.5 8.2 - - - +
466q VAL* 4.8 6.5 - - + +
467q ALA* 4.0 31.9 - - + +
470q MET* 5.7 4.0 - - + -
472q VAL* 4.8 2.6 - - + +
473q LYS 4.2 2.4 + - - -
474q LEU* 3.5 6.9 - - - -
475q GLY 2.8 22.3 + - - -
476q ASN 3.4 3.0 + - - -
477q GLU* 1.3 80.1 - - + +
479q GLY* 1.3 59.2 + - - +
494q LEU* 3.5 13.5 - - + +
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Residues in contact with GLY 479 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463q ALA* 3.9 12.7 - - - +
474q LEU* 5.5 0.4 - - - -
475q GLY* 4.0 5.8 - - - -
476q ASN 4.3 1.7 + - - -
477q GLU 4.1 0.2 - - - -
478q VAL* 1.3 75.5 - - - +
480q TYR* 1.3 62.7 + - - +
487q CYS 3.2 15.0 - - - -
488q THR* 4.8 4.5 - - - -
492q THR* 4.7 4.3 - - - -
494q LEU 3.1 10.8 + - - +
495q ARG* 4.4 4.3 - - - -
496q TYR 3.1 22.2 + - - -
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Residues in contact with TYR 480 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459q ALA* 4.1 15.5 - - + +
460q MET* 4.5 6.7 - - + -
463q ALA* 3.8 18.6 - - + +
479q GLY* 1.3 75.2 - - - +
481q SER* 1.3 63.8 + - - +
482q ILE* 4.3 1.8 - - + +
485q GLU 4.5 0.8 - - - +
487q CYS* 2.8 40.2 + - + +
488q THR* 4.1 3.4 + - - +
495q ARG* 5.2 1.6 - - - -
496q TYR 2.9 13.0 - - - +
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Residues in contact with SER 481 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459q ALA* 5.2 2.2 - - - +
480q TYR* 1.3 76.5 - - - +
482q ILE* 1.3 62.9 + - - +
485q GLU 4.0 2.5 - - - -
486q ASP* 4.6 8.3 - - - +
488q THR* 5.7 4.7 - - - -
495q ARG* 6.1 3.4 - - - -
496q TYR 3.0 6.7 + - - -
497q MET* 3.3 33.8 - - - +
498q THR 3.4 6.4 + - - -
501q MET* 4.0 11.5 - - - +
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Residues in contact with ILE 482 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456q ARG* 5.0 18.4 - - + +
459q ALA* 6.2 3.1 - - + -
460q MET* 6.5 0.9 - - + -
480q TYR* 4.3 0.9 - - + -
481q SER* 1.3 75.8 - - - +
483q ARG* 1.3 72.4 + - - +
484q PHE 5.1 0.4 - - - +
485q GLU* 2.8 35.7 + - + +
486q ASP* 4.6 1.7 - - - +
498q THR* 5.3 7.4 - - - +
501q MET* 5.1 6.1 - - - -
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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