Contacts of the helix formed by residues 833 - 845 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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599A SER* 5.9 3.2 - - - -
603A ILE* 3.4 26.7 - - + +
604A PHE* 4.7 9.2 - - + -
831A GLN 4.5 5.6 - - - +
832A THR* 1.3 74.7 - - - +
834A LEU* 1.3 54.4 + - - +
835A HIS* 4.4 6.9 + - - +
836A LYS* 2.9 39.0 + - + +
837A THR* 2.7 33.1 + - - -
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Residues in contact with LEU 834 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590A LEU* 6.2 0.2 - - + -
603A ILE* 3.6 31.5 - - + +
604A PHE 5.4 0.2 - - - +
605A VAL* 5.1 12.3 - - + +
608A ILE* 6.2 1.6 - - + -
832A THR 3.7 1.8 + - - -
833A THR* 1.3 69.8 - - - +
835A HIS* 1.3 64.9 + - + +
837A THR* 3.9 9.4 - - + -
838A HIS* 2.9 31.1 + - + +
861A LEU* 6.4 0.7 - - + -
866A LEU* 4.2 28.7 - - + +
869A ALA* 3.6 35.2 - - + +
870A ILE* 3.7 33.2 - - + +
872A GLY 5.7 2.7 - - - -
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Residues in contact with HIS 835 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A TRP* 3.0 54.8 + + + +
598A LEU* 2.5 35.0 + - + -
599A SER* 3.9 19.5 - - - -
603A ILE* 3.9 24.8 - - + +
833A THR* 4.7 6.3 - - - +
834A LEU* 1.3 80.7 - - + +
836A LYS* 1.3 54.4 + - + +
838A HIS* 3.5 4.2 + - - +
839A THR* 2.5 37.0 + - - -
870A ILE* 4.8 16.0 - - + +
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Residues in contact with LYS 836 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832A THR* 4.1 14.0 - - + +
833A THR* 2.9 29.6 + - + +
835A HIS* 1.3 76.4 - - + +
837A THR* 1.3 59.8 + - - +
839A THR* 3.3 9.7 + - - +
840A LEU* 2.8 27.5 + - - +
822B ASP* 5.0 11.9 + - - -
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Residues in contact with THR 837 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605A VAL* 4.2 5.2 - - + +
828A LEU* 4.8 11.9 - - + -
832A THR* 3.3 24.9 + - - +
833A THR 2.7 22.9 + - - -
834A LEU* 3.7 11.7 - - + -
835A HIS 3.3 0.2 - - - -
836A LYS* 1.3 70.8 - - - +
838A HIS* 1.3 59.5 + - - +
840A LEU* 3.1 10.9 + - + +
841A PHE* 3.0 40.0 + - + -
861A LEU* 4.4 30.7 - - + -
866A LEU* 4.5 5.2 - - + -
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Residues in contact with HIS 838 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590A LEU* 3.6 34.8 - - + +
591A PRO 3.1 26.2 + - - -
595A TRP* 3.6 34.1 - + + +
834A LEU* 2.9 20.4 + - + +
835A HIS* 3.5 3.6 - - - +
837A THR* 1.3 75.5 - - - +
839A THR* 1.3 56.6 + - - +
841A PHE* 3.4 2.5 + - - +
842A SER* 2.6 53.5 + - - -
866A LEU* 3.8 17.1 - - + +
870A ILE* 5.1 7.6 - - + -
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Residues in contact with THR 839 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595A TRP* 4.1 17.6 - - + -
835A HIS 2.5 24.6 + - - -
836A LYS* 3.4 11.3 - - - -
838A HIS* 1.3 78.7 - - - +
840A LEU* 1.3 57.1 + - - +
842A SER* 3.3 5.9 + - - -
843A LEU* 2.9 58.4 + - + +
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Residues in contact with LEU 840 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826A PHE* 5.8 5.6 - - + -
827A GLN 5.3 7.2 - - - +
828A LEU* 4.5 22.9 - - + -
832A THR* 6.1 1.8 - - + -
836A LYS 2.8 14.3 + - - +
837A THR* 3.1 12.5 + - + +
839A THR* 1.3 76.4 - - - +
841A PHE* 1.3 71.0 + - + +
843A LEU* 4.3 3.4 - - + +
844A LEU* 2.9 61.4 + - + +
825B PRO* 5.5 8.5 - - + +
844B LEU* 6.3 3.1 - - + -
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Residues in contact with PHE 841 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826A PHE* 5.7 2.9 - + - -
828A LEU* 6.5 0.2 - - + -
837A THR* 3.0 19.5 + - + +
838A HIS* 4.1 4.3 - - - +
840A LEU* 1.3 91.4 - - + +
842A SER* 1.3 60.7 + - - +
844A LEU* 4.5 9.9 - - + -
845A GLY* 2.8 23.9 + - - -
846A LEU* 3.2 26.4 + - + +
847A HIS 3.6 12.8 - - - -
848A LEU 3.3 30.5 - - - -
849A ALA* 3.5 22.4 - - + -
861A LEU* 3.9 11.2 - - + -
863A LEU* 5.4 5.2 - - + -
866A LEU* 3.6 41.3 - - + -
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Residues in contact with SER 842 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A THR* 5.1 18.4 - - - -
838A HIS* 2.6 48.1 + - - -
839A THR* 3.5 8.7 - - - -
841A PHE* 1.3 77.1 - - - +
843A LEU* 1.3 66.5 + - - +
845A GLY* 3.1 16.8 + - - -
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Residues in contact with LEU 843 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A THR* 4.6 12.6 - - + -
296A TYR* 3.6 49.5 - - + +
839A THR* 2.9 38.3 + - + +
840A LEU* 4.3 2.9 - - - +
842A SER* 1.3 79.9 - - - +
844A LEU* 1.3 63.5 + - + +
296B TYR* 5.0 12.0 - - - -
843B LEU* 4.9 14.0 - - - +
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Residues in contact with LEU 844 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825A PRO* 5.8 5.8 - - + +
826A PHE* 4.6 19.5 - - + -
840A LEU* 2.9 50.6 + - + +
841A PHE* 4.2 9.9 - - + +
843A LEU* 1.3 77.8 - - + +
845A GLY* 1.3 61.1 + - - +
846A LEU* 3.5 41.3 + - + +
840B LEU* 6.3 2.7 - - + -
844B LEU* 5.7 9.4 - - + -
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Residues in contact with GLY 845 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841A PHE 2.8 12.6 + - - -
842A SER* 3.1 11.9 + - - -
844A LEU* 1.3 77.8 - - - +
846A LEU* 1.3 64.6 + - - +
847A HIS* 5.2 6.2 + - - -
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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