Contacts of the strand formed by residues 787 - 793 (chain B) 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 VAL 787 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665B THR* 5.0 2.0 - - - -
666B VAL* 4.4 20.9 - - + +
689B ALA* 5.6 6.3 - - + -
690B GLU 3.9 8.7 - - - +
691B PRO* 4.4 1.3 - - + -
692B LEU* 5.2 1.7 - - - +
742B PRO 3.5 3.3 + - - +
743B ASN* 3.3 25.1 - - - +
784B ILE* 5.8 4.5 - - + -
785B ARG* 3.3 8.2 - - - +
786B ASN* 1.3 81.7 - - - +
788B LYS* 1.3 62.8 + - - +
789B PHE 4.3 0.3 + - - -
820B PHE* 6.4 2.0 - - + -
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Residues in contact with LYS 788 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689B ALA* 3.4 5.4 - - - +
690B GLU 3.1 34.8 + - - +
691B PRO 5.0 4.0 - - - +
692B LEU* 5.8 5.1 - - + +
744B ILE* 3.3 28.0 - - + +
745B LEU* 5.4 0.7 - - - -
746B VAL 6.0 0.2 - - - +
787B VAL* 1.3 72.5 - - - +
789B PHE* 1.3 61.9 + - - +
790B LYS* 5.5 1.0 - - - +
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Residues in contact with PHE 789 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687B MET* 6.3 1.3 - - + -
688B ILE 3.7 9.2 - - - +
689B ALA* 4.4 6.1 - - + +
743B ASN 5.3 0.8 + - - +
744B ILE 3.2 7.2 + - - +
745B LEU* 3.3 28.8 - - + +
746B VAL 3.6 1.6 + - - -
787B VAL 4.3 0.2 + - - -
788B LYS* 1.3 73.7 - - - +
790B LYS* 1.3 59.8 + - - +
791B ILE 4.4 0.5 + - - -
816B VAL* 5.5 14.6 - - + +
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Residues in contact with LYS 790 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687B MET* 3.3 3.2 - - - +
688B ILE* 3.0 35.9 + - + +
689B ALA* 6.0 0.4 - - - -
746B VAL* 3.3 24.9 - - + +
749B THR* 5.1 11.4 - - - -
788B LYS 4.2 1.7 + - - +
789B PHE* 1.3 74.8 - - - +
791B ILE* 1.3 64.6 + - - +
792B LEU 3.5 0.2 + - - -
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Residues in contact with ILE 791 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685B ILE* 6.3 1.3 - - + -
686B THR 4.5 2.7 - - - +
687B MET* 3.7 11.4 - - + -
746B VAL 3.6 8.4 + - - +
747B ASP* 4.0 23.2 - - + +
749B THR* 4.9 8.7 + - - -
750B LEU 5.1 0.9 + - - -
789B PHE 4.3 0.4 + - - -
790B LYS* 1.3 74.2 - - - +
792B LEU* 1.3 63.1 + - - +
793B ASP* 4.7 9.2 - - - +
794B ALA* 5.5 5.6 - - + -
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Residues in contact with LEU 792 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686B THR* 2.8 27.0 + - - +
687B MET* 3.5 6.5 - - - +
688B ILE* 5.1 2.7 - - + +
749B THR* 6.1 1.3 - - - -
750B LEU* 3.5 31.4 - - + +
790B LYS 3.5 4.0 + - - -
791B ILE* 1.3 73.1 - - - +
793B ASP* 1.3 62.3 + - + +
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Residues in contact with ASP 793 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684B LYS 4.3 2.5 - - - +
685B ILE* 3.3 2.3 - - - +
686B THR* 2.9 35.0 + - - +
791B ILE* 4.7 4.5 - - - +
792B LEU* 1.3 79.5 - - + +
794B ALA* 1.3 65.1 + - - +
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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