Contacts of the strand formed by residues 448 - 453 (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 LYS 448 (chain q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442q TYR* 4.3 6.3 - - - -
447q MET* 1.3 75.3 - - - +
449q ILE* 1.3 66.9 + - - +
492q THR 4.2 10.1 - - - +
493q VAL 3.1 20.2 - - - +
495q ARG* 5.4 6.7 - - + +
514q SER* 3.0 12.7 + - - +
515q TYR* 3.2 6.2 - - + -
516q SER* 3.0 25.3 + - - -
517q VAL 3.9 0.5 + - - -
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Residues in contact with ILE 449 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434q PRO* 5.4 10.3 - - + +
436q TYR* 6.3 2.0 - - + -
437q LEU* 6.3 2.0 - - - +
442q TYR* 4.7 6.0 - - + +
448q LYS* 1.3 79.5 - - - +
450q ALA* 1.3 64.5 + - - +
451q CYS 4.1 0.2 + - - -
493q VAL 3.0 7.1 + - - +
494q LEU* 3.5 7.3 - - + +
495q ARG* 2.9 26.2 + - - +
515q TYR* 5.1 0.2 - - - -
517q VAL* 3.2 25.1 - - + +
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Residues in contact with ALA 450 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449q ILE* 1.3 75.6 - - - +
451q CYS* 1.3 58.3 + - - +
452q THR* 4.2 1.3 - - - -
495q ARG* 3.3 12.6 - - + +
497q MET* 6.1 3.1 - - + -
502q LEU* 5.7 9.6 - - + -
515q TYR* 4.6 9.9 - - + +
517q VAL 3.0 9.2 + - - +
518q VAL* 3.5 9.1 - - + -
519q MET* 2.7 33.5 + - - +
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Residues in contact with CYS 451 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430q THR* 5.6 3.8 - - - +
434q PRO* 4.8 17.9 - - + -
449q ILE 4.1 0.2 + - - -
450q ALA* 1.3 75.0 - - - +
452q THR* 1.3 62.5 + - - +
453q GLN* 4.0 0.5 + - - +
495q ARG 2.9 9.8 + - - +
496q TYR* 3.2 10.8 - - + +
497q MET* 2.9 25.6 + - - +
519q MET* 3.3 13.9 - - + +
521q ASP* 5.8 4.0 - - + -
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Residues in contact with THR 452 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450q ALA* 4.2 2.4 - - - -
451q CYS* 1.3 74.2 - - - +
453q GLN* 1.3 61.1 + - - +
497q MET* 3.1 7.9 - - - -
498q THR 4.7 1.1 - - - -
499q ASP* 4.2 22.7 - - - -
502q LEU* 5.2 9.0 - - - -
519q MET 2.8 15.2 + - - -
520q VAL* 4.3 11.4 - - - -
521q ASP* 3.2 31.9 + - - +
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Residues in contact with GLN 453 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451q CYS 5.3 0.7 - - - +
452q THR* 1.3 76.2 - - - +
454q PRO* 1.3 64.0 - - - +
455q ARG 3.3 19.8 + - - +
458q ALA* 4.2 9.4 - - + -
459q ALA* 4.1 16.4 - - + +
496q TYR* 6.3 0.4 - - + -
497q MET 2.7 13.4 + - - +
498q THR* 2.9 25.1 - - - -
499q ASP* 2.9 6.7 + - - -
521q ASP* 5.1 2.9 - - + -
522q GLU* 5.4 2.9 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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