Contacts of the strand formed by residues 611 - 615 (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 ASP 611 (chain q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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610q GLY* 1.3 74.6 - - - +
612q ILE* 1.3 63.9 + - - +
670q LYS* 3.5 30.5 - - + +
685q GLU 5.4 2.2 - - - +
686q GLY* 2.8 26.4 + - - +
687q ILE* 3.5 6.1 - - + +
688q ILE 3.0 19.6 + - - -
689q TYR* 3.1 10.0 + - - +
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Residues in contact with ILE 612 (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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600q VAL* 5.7 10.3 - - + +
603q ILE* 5.8 6.7 - - + -
610q GLY 5.4 0.4 - - - +
611q ASP* 1.3 76.2 - - - +
613q LEU* 1.3 62.8 + - - +
614q VAL* 4.1 1.3 - - + -
669q ARG* 5.8 0.8 - - + +
670q LYS 2.9 12.2 + - - +
671q VAL* 3.4 11.5 - - + +
672q VAL* 2.9 28.4 + - - +
687q ILE* 5.1 1.8 - - - -
689q TYR* 3.3 15.3 - - + +
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Residues in contact with LEU 613 (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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612q ILE* 1.3 75.5 - - - +
614q VAL* 1.3 61.7 + - - +
615q PHE 4.1 0.2 + - - -
672q VAL* 3.5 9.6 - - + +
674q ALA* 6.2 2.2 - - + -
678q ALA* 5.8 8.3 - - + -
687q ILE* 4.6 14.6 - - + +
689q TYR 2.8 12.4 + - - +
690q VAL* 3.3 9.3 - - + +
691q LEU* 2.9 25.7 + - - +
726q ARG* 5.6 8.5 - - + -
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Residues in contact with VAL 614 (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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596q CYS* 5.9 6.1 - - + -
600q VAL* 6.1 5.2 - - + -
612q ILE* 4.1 1.5 - - + -
613q LEU* 1.3 74.0 - - - +
615q PHE* 1.3 59.0 + - - +
616q LEU* 3.7 1.0 + - + +
671q VAL* 6.4 1.8 - - + -
672q VAL 2.9 12.9 + - - +
673q VAL* 3.4 10.6 - - + -
674q ALA* 2.7 35.1 + - - +
691q LEU* 3.8 15.3 - - + -
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Residues in contact with PHE 615 (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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613q LEU 4.1 0.4 - - - -
614q VAL* 1.3 73.1 - - - +
616q LEU* 1.3 63.0 + - - +
674q ALA* 3.1 7.6 - - - +
675q THR 5.3 5.4 - - - +
676q ASN* 6.0 1.3 - - - -
691q LEU 3.2 16.8 + - - +
692q ASP* 5.0 7.2 - - + -
693q PRO* 4.3 19.3 - - - +
694q GLY 6.2 0.9 - - - +
695q PHE 5.3 7.3 - - - +
723q ARG* 5.8 7.2 - - + -
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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