Contacts of the strand formed by residues 733 - 737 (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 GLY 733 (chain q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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579q PRO 3.1 8.7 + - - +
580q VAL* 3.2 7.4 - - - +
581q ASP* 2.9 23.0 + - - +
688q ILE* 3.3 17.5 - - - -
727q ALA* 3.7 12.6 + - - -
728q GLY* 4.8 0.2 - - - -
731q ALA 3.2 2.6 + - - -
732q ALA* 1.3 74.6 - - - +
734q LYS* 1.3 61.6 + - - +
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Residues in contact with LYS 734 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580q VAL* 5.1 0.7 - - - -
581q ASP* 3.4 11.9 - - + +
688q ILE 3.1 7.1 + - - +
689q TYR* 3.3 12.1 - - + +
690q VAL 3.0 22.9 + - - +
727q ALA* 3.6 5.7 - - - +
733q GLY* 1.3 75.6 - - - +
735q CYS* 1.3 62.0 + - - +
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Residues in contact with CYS 735 (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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580q VAL* 5.1 2.4 - - + +
581q ASP 2.9 10.7 + - - +
582q ILE* 3.5 6.8 - - + +
583q PHE* 2.9 28.7 + - - +
690q VAL* 3.3 13.7 - - + +
692q ASP* 6.0 3.6 - - + -
724q ALA* 4.0 35.4 - - + +
734q LYS* 1.3 76.4 - - - +
736q PHE* 1.3 62.6 + - - +
737q ARG* 3.7 1.4 + - + +
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Residues in contact with PHE 736 (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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583q PHE* 3.8 13.5 - - + -
599q SER* 5.0 13.9 - - - -
690q VAL 2.8 15.1 + - - +
691q LEU* 3.5 8.1 - - + +
692q ASP* 2.7 33.8 + - - +
735q CYS* 1.3 71.3 - - - +
737q ARG* 1.3 58.7 + - - +
738q LEU 3.8 0.3 + - - -
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Residues in contact with ARG 737 (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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582q ILE* 6.2 2.2 - - + -
583q PHE 2.8 22.9 + - - +
584q TYR* 3.7 2.7 - - + -
585q THR* 3.5 10.4 + - - -
692q ASP* 3.5 12.3 - - + +
735q CYS* 3.7 1.7 + - + +
736q PHE* 1.3 72.2 - - - +
738q LEU* 1.3 58.4 + - - +
739q TYR* 3.0 23.9 + - + +
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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
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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