Contacts of the helix formed by residues 875 - 884 (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 GLU 875 (chain r).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843r GLU* 5.6 10.1 - - + -
871r THR* 5.1 9.4 - - - -
872r SER* 2.9 15.9 + - - +
874r GLY* 1.3 74.7 - - - +
876r LEU* 1.3 64.0 + - - +
877r GLN 3.2 2.9 - - - -
878r TYR* 2.9 27.9 + - + +
879r TYR* 3.3 9.2 + - - +
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Residues in contact with LEU 876 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443r GLU* 6.5 1.3 - - + -
689r TYR* 5.6 10.9 - - + +
691r GLY* 4.4 12.8 - - - +
871r THR* 5.5 4.0 - - - -
872r SER 3.2 4.8 + - - +
873r HIS* 3.0 28.0 + - - +
875r GLU* 1.3 80.0 - - - +
877r GLN* 1.3 61.6 + - - +
879r TYR* 3.8 5.9 + - - +
880r LEU* 3.6 16.6 + - - +
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Residues in contact with GLN 877 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428r CYS* 5.0 10.4 - - + +
873r HIS 4.3 2.0 + - - -
874r GLY 4.4 6.5 + - - +
875r GLU 3.2 0.4 - - - -
876r LEU* 1.3 77.2 - - - +
878r TYR* 1.3 63.2 + - - +
880r LEU* 3.0 17.9 + - - +
881r SER* 3.2 12.6 + - - -
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Residues in contact with TYR 878 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421r HIS* 5.2 8.1 - - + +
423r MET* 4.8 19.3 - - + -
874r GLY 5.2 0.2 + - - -
875r GLU* 2.9 20.4 + - + +
877r GLN* 1.3 79.2 - - - +
879r TYR* 1.3 58.7 + - - +
881r SER* 2.9 27.0 + - - +
882r LEU* 3.4 9.5 + - - +
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Residues in contact with TYR 879 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869r LEU* 5.5 10.8 - - + -
871r THR* 6.0 6.1 - - - -
875r GLU 3.3 9.7 + - - +
876r LEU* 4.3 5.6 - - - +
877r GLN 3.4 0.2 - - - -
878r TYR* 1.3 79.8 - - - +
880r LEU* 1.3 58.4 + - - +
882r LEU* 4.1 7.7 - - - +
883r LEU* 3.7 21.7 + - - +
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Residues in contact with LEU 880 (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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428r CYS* 5.3 8.5 - - + -
429r GLN 5.5 5.8 - - - +
876r LEU 3.6 10.8 + - - +
877r GLN* 3.0 12.5 + - - +
879r TYR* 1.3 75.8 - - - +
881r SER* 1.3 58.2 + - - +
882r LEU 3.0 9.6 + - - -
883r LEU* 5.6 0.7 - - - -
884r ASN* 3.3 27.4 + - - +
886r GLN* 5.1 0.3 - - - +
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Residues in contact with SER 881 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423r MET* 5.7 8.3 - - - -
425r ASN* 6.2 2.0 - - - -
427r ARG 5.9 0.9 - - - -
428r CYS* 5.1 9.1 - - - +
877r GLN 3.2 8.9 + - - -
878r TYR* 2.9 13.2 + - - -
880r LEU* 1.3 75.5 - - - +
882r LEU* 1.3 56.2 + - - +
884r ASN 2.8 13.0 - - - +
885r GLN* 4.3 0.2 - - - -
886r GLN* 3.0 23.0 + - - -
887r LEU* 2.9 37.9 + - - +
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Residues in contact with LEU 882 (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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654r THR 4.4 8.1 - - - +
655r LEU* 6.1 0.2 - - - +
846r ALA* 6.3 3.6 - - + -
878r TYR 3.4 7.7 + - - +
879r TYR* 4.1 11.0 - - - +
880r LEU 3.0 1.0 - - - -
881r SER* 1.3 77.1 - - - +
883r LEU* 1.3 60.9 + - + +
884r ASN 2.9 18.4 + - - +
885r GLN* 4.2 2.9 + - - -
887r LEU* 4.5 8.1 - - + -
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Residues in contact with LEU 883 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678r ASN* 4.7 10.9 - - - +
879r TYR 3.7 12.6 + - - +
880r LEU* 3.7 2.1 + - - +
882r LEU* 1.3 77.4 - - + +
884r ASN* 1.3 57.8 + - - +
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Residues in contact with ASN 884 (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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429r GLN 5.6 5.6 - - - +
430r LEU 6.2 0.7 - - - +
431r PRO* 6.0 7.4 - - + -
654r THR 5.2 0.2 - - - -
678r ASN* 5.4 5.8 - - - -
880r LEU 3.3 13.4 + - - +
881r SER 2.8 16.6 - - - +
882r LEU 2.9 4.3 - - - +
883r LEU* 1.3 76.3 - - - +
885r GLN* 1.3 61.4 + - - +
886r GLN* 2.7 11.3 + - + -
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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