Contacts of the helix formed by residues 833 - 845 (chain B) in PDB entry 6QVC
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 THR 833 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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599B SER* 5.9 3.6 - - - -
603B ILE* 3.4 26.9 - - + +
604B PHE* 4.7 8.3 - - + -
831B GLN 4.5 5.6 - - - +
832B THR* 1.3 74.9 - - - +
834B LEU* 1.3 53.7 + - - +
835B HIS* 4.4 6.5 + - - +
836B LYS* 2.9 38.3 + - + +
837B THR* 2.7 33.3 + - - -
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Residues in contact with LEU 834 (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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603B ILE* 3.6 31.2 - - + +
605B VAL* 5.1 12.1 - - + +
608B ILE* 6.2 1.6 - - + -
832B THR 3.7 2.1 + - - -
833B THR* 1.3 71.2 - - - +
835B HIS* 1.3 65.7 + - + +
837B THR* 3.9 8.5 - - + -
838B HIS* 2.9 30.7 + - + +
861B LEU* 6.4 0.7 - - + -
866B LEU* 4.2 27.8 - - + +
869B ALA* 3.6 36.1 - - + +
870B ILE* 3.7 32.8 - - + +
872B GLY 5.7 2.5 - - - -
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Residues in contact with HIS 835 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595B TRP* 3.0 55.1 + + + +
598B LEU* 2.5 34.4 + - + -
599B SER* 3.9 18.6 - - - -
603B ILE* 3.9 25.0 - - + +
833B THR* 3.3 6.5 - - - +
834B LEU* 1.3 82.1 - - + +
836B LYS* 1.3 54.6 + - + +
838B HIS* 3.5 3.8 + - - +
839B THR* 2.5 38.0 + - - -
870B ILE* 4.8 15.8 - - + +
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Residues in contact with LYS 836 (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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822A ASP* 5.1 10.5 + - - -
832B THR* 4.1 12.8 - - + -
833B THR* 2.9 29.1 + - + +
835B HIS* 1.3 75.1 - - + +
837B THR* 1.3 60.2 + - - +
839B THR* 3.4 10.3 - - - +
840B LEU* 2.8 27.5 + - - +
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Residues in contact with THR 837 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B VAL* 4.2 4.6 - - + +
828B LEU* 4.8 12.6 - - + -
832B THR* 3.3 26.5 + - - +
833B THR 2.7 22.9 + - - -
834B LEU* 3.7 12.6 - - + -
836B LYS* 1.3 69.5 - - - +
838B HIS* 1.3 60.3 + - - +
840B LEU* 3.1 10.7 + - + +
841B PHE* 3.0 39.8 + - + -
861B LEU* 4.4 30.5 - - + -
866B LEU* 4.5 5.6 - - + -
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Residues in contact with HIS 838 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B LEU* 3.6 33.7 - - + +
591B PRO* 3.1 28.5 + - + -
595B TRP* 3.6 33.5 - + + +
834B LEU* 2.9 19.5 + - + +
835B HIS* 3.5 4.0 - - - +
837B THR* 1.3 74.7 - - - +
839B THR* 1.3 57.0 + - - +
841B PHE* 3.4 2.6 + - - +
842B SER* 2.6 52.1 + - - -
866B LEU* 3.8 18.4 - - + +
870B ILE* 5.1 8.5 - - + -
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Residues in contact with THR 839 (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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595B TRP* 4.1 17.9 - - + -
835B HIS 2.5 25.4 + - - -
836B LYS* 3.4 12.0 - - - +
837B THR 3.2 0.2 - - - -
838B HIS* 1.3 77.1 - - - +
840B LEU* 1.3 58.1 + - - +
842B SER* 3.5 5.9 - - - -
843B LEU* 2.9 57.1 + - + +
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Residues in contact with LEU 840 (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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825A PRO* 5.5 7.6 - - + +
844A LEU* 6.3 2.9 - - + -
826B PHE* 5.8 6.5 - - + -
827B GLN 5.3 7.0 - - - +
828B LEU* 4.5 22.7 - - + -
832B THR* 6.1 1.6 - - + -
836B LYS 2.8 14.3 + - - +
837B THR* 3.1 11.6 + - + +
839B THR* 1.3 76.6 - - - +
841B PHE* 1.3 71.3 + - + +
843B LEU* 4.0 2.8 - - - +
844B LEU* 2.9 60.6 + - + +
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Residues in contact with PHE 841 (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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826B PHE* 5.7 2.9 - + - -
828B LEU* 6.5 0.2 - - + -
837B THR* 3.0 21.1 + - + +
838B HIS* 4.1 4.3 - - - +
840B LEU* 1.3 91.8 - - + +
842B SER* 1.3 61.3 + - - +
844B LEU* 4.5 11.7 - - + -
845B GLY* 2.8 23.0 + - - -
846B LEU* 3.2 26.8 + - + +
847B HIS 3.6 13.7 - - - -
848B LEU 3.3 30.3 - - - -
849B ALA* 3.5 22.9 - - + -
861B LEU* 3.9 10.3 - - + -
863B LEU* 5.4 5.2 - - + -
866B LEU* 3.6 40.6 - - + -
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Residues in contact with SER 842 (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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295B THR* 5.1 17.0 - - - -
838B HIS* 2.6 47.1 + - - -
839B THR* 3.5 7.9 - - - -
841B PHE* 1.3 77.4 - - - +
843B LEU* 1.3 65.6 + - - +
845B GLY* 3.1 16.3 + - - -
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Residues in contact with LEU 843 (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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296A TYR* 5.0 11.6 - - - -
843A LEU* 4.9 13.6 - - - +
295B THR* 4.6 11.7 - - + -
296B TYR* 3.6 49.4 - - + +
839B THR* 2.9 38.9 + - + +
840B LEU* 4.3 2.9 - - + +
842B SER* 1.3 78.6 - - - +
844B LEU* 1.3 64.7 + - - +
845B GLY 3.7 0.2 + - - -
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Residues in contact with LEU 844 (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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840A LEU* 6.3 3.6 - - + -
844A LEU* 5.7 9.6 - - + -
825B PRO* 5.8 6.1 - - + +
826B PHE* 4.6 18.8 - - + -
840B LEU* 2.9 49.5 + - + +
841B PHE* 4.2 10.5 - - + +
843B LEU* 1.3 78.4 - - - +
845B GLY* 1.3 60.2 + - - +
846B LEU* 3.5 41.4 - - + +
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Residues in contact with GLY 845 (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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841B PHE 2.8 12.2 + - - -
842B SER* 3.1 11.9 + - - -
844B LEU* 1.3 77.6 - - - +
846B LEU* 1.3 64.8 + - - +
847B HIS* 5.2 6.1 + - - -
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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