Contacts of the strand formed by residues 687 - 692 (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 ILE 687 (chain q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611q ASP* 3.5 17.4 - - + +
612q ILE 5.1 0.7 - - - -
613q LEU* 4.6 19.1 - - + +
684q ILE* 3.6 16.2 + - + +
685q GLU 3.5 3.4 - - - -
686q GLY* 1.3 77.1 - - - +
688q ILE* 1.3 59.8 + - - +
689q TYR 4.8 2.7 - - - +
726q ARG* 3.8 20.5 - - + +
727q ALA* 3.5 11.9 - - - +
729q ARG* 5.5 1.0 - - - +
730q VAL* 5.0 10.9 + - - +
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Residues in contact with ILE 688 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609q PRO 4.9 3.8 - - - +
610q GLY* 4.1 19.3 - - - -
611q ASP 3.0 5.5 + - - -
686q GLY 3.3 3.8 + - - +
687q ILE* 1.3 74.7 - - - +
689q TYR* 1.3 61.4 + - + +
727q ALA* 3.3 15.9 - - - +
730q VAL* 6.5 0.4 - - + -
731q ALA* 5.6 2.2 - - + +
732q ALA 4.7 5.6 - - - +
733q GLY* 3.3 12.0 - - - -
734q LYS 3.1 21.8 + - - -
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Residues in contact with TYR 689 (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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603q ILE* 5.2 13.7 - - + -
610q GLY 5.9 0.9 - - - +
611q ASP 3.1 8.3 + - - +
612q ILE* 3.3 12.2 - - + +
613q LEU* 2.8 27.2 + - - +
687q ILE* 3.7 2.0 - - - +
688q ILE* 1.3 80.7 - - + +
690q VAL* 1.3 63.4 + - - +
727q ALA* 4.8 1.1 - - - -
734q LYS* 3.3 13.9 - - + +
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Residues in contact with VAL 690 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613q LEU* 3.3 13.0 - - + +
688q ILE 4.3 0.2 - - - -
689q TYR* 1.3 78.2 - - - +
691q LEU* 1.3 58.1 + - - +
692q ASP* 4.1 1.6 - - + -
723q ARG* 3.9 25.1 - - + +
726q ARG* 5.5 1.6 - - + -
727q ALA* 4.6 8.3 - - + +
734q LYS 3.0 10.4 + - - +
735q CYS* 3.3 12.4 - - + -
736q PHE* 2.8 33.6 + - - +
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Residues in contact with LEU 691 (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* 5.2 18.8 - - + +
599q SER* 5.2 8.7 - - - -
600q VAL* 5.8 4.3 - - + +
613q LEU 2.9 10.9 + - - +
614q VAL* 4.4 11.9 - - + -
615q PHE* 3.2 26.5 + - - +
690q VAL* 1.3 75.1 - - - +
692q ASP* 1.3 60.7 + - - +
693q PRO 3.9 1.7 - - - -
736q PHE* 3.5 11.7 - - + +
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Residues in contact with ASP 692 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615q PHE* 5.0 5.2 - - + -
690q VAL* 4.1 3.8 - - + -
691q LEU* 1.3 72.5 - - - +
693q PRO* 1.3 62.3 - - - +
694q GLY* 3.2 6.7 + - - +
720q ALA* 5.9 3.8 - - + +
723q ARG* 4.8 19.5 - - + -
735q CYS* 6.0 3.6 - - + -
736q PHE 2.7 15.1 + - - +
737q ARG* 3.5 8.6 - - + +
738q LEU* 2.8 26.3 + - - -
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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