Contacts of the strand formed by residues 515 - 520 (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 TYR 515 (chain q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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447q MET* 4.3 0.9 - - - -
448q LYS* 3.2 15.3 - - + +
450q ALA* 4.6 11.7 - - + +
512q LEU* 3.0 20.9 + - + +
513q ALA* 3.9 5.9 - - - +
514q SER* 1.3 80.1 - - - +
516q SER* 1.3 61.1 + - - +
517q VAL 3.8 15.9 - - - +
518q VAL* 5.3 4.5 - - + -
547q LEU* 4.8 9.2 - - - +
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Residues in contact with SER 516 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440q GLU* 5.7 6.7 - - - -
442q TYR* 5.1 11.7 - - - -
445q LYS* 5.8 4.0 - - - -
447q MET* 3.7 19.3 - - - +
448q LYS 3.0 7.6 + - - -
449q ILE* 6.3 0.2 - - - -
515q TYR* 1.3 73.8 - - - +
517q VAL* 1.3 61.4 + - - +
546q GLU* 3.6 12.5 - - - +
547q LEU* 3.4 6.2 - - - +
548q LYS* 3.0 25.3 + - - +
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Residues in contact with VAL 517 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436q TYR* 5.9 6.5 - - + -
440q GLU* 5.6 9.2 - - + -
448q LYS 3.9 2.4 + - - -
449q ILE* 3.2 16.9 - - + +
450q ALA 3.0 22.9 + - - -
515q TYR* 3.8 5.9 - - - +
516q SER* 1.3 82.5 - - - +
518q VAL* 1.3 63.4 + - - +
548q LYS* 3.2 16.4 - - + +
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Residues in contact with VAL 518 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450q ALA* 3.5 12.6 - - + +
515q TYR* 5.3 4.9 - - + -
517q VAL* 1.3 77.6 - - - +
519q MET* 1.3 61.1 + - - +
520q VAL 4.0 0.8 + - - -
548q LYS 2.9 9.8 + - - +
549q VAL* 3.3 10.0 - - + +
550q LEU 3.0 23.2 + - - +
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Residues in contact with MET 519 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434q PRO* 6.0 5.4 - - + -
450q ALA 2.7 16.4 + - - +
451q CYS* 3.3 9.6 - - + +
452q THR* 2.8 28.9 + - - -
517q VAL 4.2 0.2 - - - -
518q VAL* 1.3 75.0 - - - +
520q VAL* 1.3 61.9 + - - +
521q ASP* 3.4 4.8 + - + +
550q LEU* 3.3 18.4 - - + +
552q ALA* 6.2 2.7 - - + -
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Residues in contact with VAL 520 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452q THR* 4.3 11.2 - - - -
518q VAL* 4.0 1.8 + - - +
519q MET* 1.3 70.0 - - - +
521q ASP* 1.3 64.9 + - - +
523q ALA* 4.6 6.1 + - + +
530q THR* 5.9 7.6 - - - +
533q LEU* 5.8 9.0 - - + -
550q LEU 2.9 11.5 + - - +
551q VAL* 3.4 9.0 - - + +
552q ALA* 2.8 26.1 + - - +
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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