Contacts of the strand formed by residues 865 - 872 (chain r) 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 865 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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683r VAL* 4.5 7.5 - - - +
684r PRO 2.8 16.2 + - - +
685r LEU* 3.2 3.6 - - - -
686r GLU* 2.9 23.3 + - - +
824r HIS 3.7 12.3 - - - -
856r ALA* 4.2 7.2 - - - -
857r GLY* 3.9 15.9 - - - -
864r LYS* 1.3 75.6 - - - +
866r GLU* 1.3 60.6 + - - +
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Residues in contact with GLU 866 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685r LEU* 5.7 1.6 - - - -
686r GLU* 3.2 21.5 - - + +
688r THR* 6.6 0.2 - - - -
824r HIS 3.6 5.3 + - - -
825r THR* 3.6 28.4 - - - -
826r VAL 3.6 0.3 + - - -
856r ALA* 3.4 19.1 - - - +
864r LYS 4.2 0.4 + - - -
865r GLY* 1.3 74.4 - - - +
867r GLY* 1.3 60.1 + - - +
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Residues in contact with GLY 867 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685r LEU* 5.9 0.8 - - - +
686r GLU 3.0 7.8 + - - +
687r GLN* 3.8 3.1 - - - +
688r THR* 2.9 29.2 + - - +
825r THR* 5.5 0.7 - - - -
826r VAL* 3.4 11.2 - - - -
853r LEU* 6.3 3.4 - - - -
856r ALA* 4.8 5.8 - - - -
866r GLU* 1.3 77.5 - - - +
868r ILE* 1.3 60.8 + - - -
869r LEU 4.2 0.2 - - - -
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Residues in contact with ILE 868 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688r THR* 3.3 15.9 - - - -
711r LYS* 5.7 8.3 - - + -
826r VAL 3.0 12.5 + - - +
827r ILE* 3.4 11.9 - - + +
828r ILE* 2.8 27.6 + - - +
867r GLY* 1.3 72.6 - - - +
869r LEU* 1.3 59.5 - - - +
870r ILE* 3.8 1.7 + - + +
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Residues in contact with LEU 869 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688r THR 2.9 12.6 + - - +
689r TYR* 3.5 8.1 - - + +
690r VAL* 2.9 24.9 + - - +
828r ILE* 4.1 13.2 - - + -
867r GLY 4.2 0.4 - - - -
868r ILE* 1.3 72.5 - - - +
870r ILE* 1.3 61.2 + - - +
871r THR* 3.6 6.9 + - - +
879r TYR* 5.5 11.0 - - + -
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Residues in contact with ILE 870 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690r VAL* 3.6 13.5 - - + +
704r MET* 5.7 9.9 - - + +
707r ILE* 5.9 7.4 - - + -
828r ILE 3.1 16.6 + - - +
829r LYS* 4.7 3.1 - - - -
830r GLY* 3.0 31.6 + - - +
831r THR* 4.1 1.2 + - - -
868r ILE* 3.8 2.2 + - + -
869r LEU* 1.3 71.5 - - - +
871r THR* 1.3 58.5 + - - +
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Residues in contact with THR 871 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690r VAL 2.9 12.6 + - - +
691r GLY* 4.0 1.8 - - - -
692r ILE* 2.9 24.6 + - - +
830r GLY* 4.4 6.7 - - - -
831r THR* 4.3 17.5 - - - -
869r LEU* 3.6 7.7 + - - -
870r ILE* 1.3 76.6 - - - +
872r SER* 1.3 68.3 + - - +
875r GLU* 5.1 9.2 - - - -
876r LEU* 5.4 5.4 - - - -
879r TYR* 6.0 6.3 - - - -
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Residues in contact with SER 872 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691r GLY* 4.0 0.4 - - - -
692r ILE* 4.0 8.3 - - - +
830r GLY 5.0 2.8 + - - -
871r THR* 1.3 77.2 - - - +
873r HIS* 1.3 66.6 + - - +
874r GLY* 3.1 4.0 - - - -
875r GLU* 2.9 24.0 + - - +
876r LEU* 3.2 7.1 + - - -
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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