Contacts of the helix formed by residues 826 - 844 (chain u) 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 ASP 826 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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822u ARG 4.0 7.2 + - - +
823u MET 3.5 0.7 + - - +
825u LEU* 1.3 76.4 - - - +
827u ARG* 1.3 53.6 + - - +
828u ARG* 3.3 2.9 - - + +
829u ASN* 3.0 20.5 + - + +
830u TYR* 2.5 34.2 + - - +
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Residues in contact with ARG 827 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825u LEU 3.4 5.9 + - - +
826u ASP* 1.3 71.9 - - - +
828u ARG* 1.3 57.7 + - - +
830u TYR* 3.6 9.7 - - + +
831u ARG* 2.9 31.9 + - - +
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Residues in contact with ARG 828 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786u LYS* 5.4 5.0 - - - +
826u ASP* 3.3 3.0 - - + +
827u ARG* 1.3 77.5 - - - +
829u ASN* 1.3 56.4 + - - +
831u ARG* 4.4 3.0 - - - +
832u GLN* 3.4 22.0 + - - +
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Residues in contact with ASN 829 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786u LYS* 5.6 10.1 - - + -
823u MET* 3.2 30.4 - - + +
826u ASP* 3.0 19.2 + - + +
828u ARG* 1.3 78.1 - - - +
830u TYR* 1.3 62.3 + - - +
831u ARG 3.4 0.2 - - - -
832u GLN* 4.0 4.7 - - - +
833u LEU* 3.5 22.3 + - - +
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Residues in contact with TYR 830 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823u MET 3.6 5.6 - - - -
824u ALA* 3.7 22.7 - - + +
826u ASP 2.5 19.9 + - - +
827u ARG* 3.2 12.1 + - + +
829u ASN* 1.3 76.6 - - - +
831u ARG* 1.3 61.6 + - - +
833u LEU* 3.8 8.5 + - - +
834u VAL* 3.9 11.3 + - - +
867u MET* 5.8 6.0 - - + +
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Residues in contact with ARG 831 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827u ARG 2.9 16.6 + - - +
828u ARG* 5.0 2.2 - - - +
830u TYR* 1.3 74.8 - - - +
832u GLN* 1.3 60.6 + - - +
834u VAL* 3.5 4.5 + - - +
835u ASP* 2.9 31.1 + - + +
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Residues in contact with GLN 832 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786u LYS* 5.3 8.5 - - + +
789u LEU* 4.6 17.8 - - + +
790u LYS* 5.6 4.0 - - + +
828u ARG 3.4 21.8 + - - +
829u ASN* 3.8 4.7 + - - +
830u TYR 3.4 0.6 - - - -
831u ARG* 1.3 77.2 - - - +
833u LEU* 1.3 59.5 + - - +
835u ASP* 3.7 6.4 - - - +
836u THR* 2.9 31.2 + - - -
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Residues in contact with LEU 833 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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789u LEU* 5.5 5.1 - - - +
818u PHE 6.1 1.3 - - - +
823u MET* 5.8 6.1 - - + +
829u ASN 3.5 16.5 + - - +
830u TYR* 4.1 4.5 - - - +
831u ARG 3.3 0.4 - - - -
832u GLN* 1.3 78.0 - - - +
834u VAL* 1.3 58.6 + - - +
836u THR* 3.3 5.4 + - - -
837u THR* 2.9 28.9 + - - -
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Residues in contact with VAL 834 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830u TYR 3.9 8.7 + - - +
831u ARG* 3.5 6.3 + - - +
832u GLN 3.4 0.2 - - - -
833u LEU* 1.3 78.9 - - - +
835u ASP* 1.3 56.9 + - - +
837u THR* 3.7 7.5 - - - -
838u VAL* 3.0 30.3 + - - +
867u MET* 5.1 3.6 - - + +
870u GLU* 5.0 11.0 - - + +
871u THR* 4.7 22.7 - - - +
874u LYS* 5.7 5.2 - - + +
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Residues in contact with ASP 835 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793u LYS* 4.5 7.9 - - - +
831u ARG* 2.9 21.1 + - + +
832u GLN* 3.8 7.4 - - - +
833u LEU 3.3 0.4 - - - -
834u VAL* 1.3 75.6 - - - +
836u THR* 1.3 58.7 + - - +
838u VAL* 4.2 6.1 - - - +
839u GLU* 4.2 11.3 + - - +
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Residues in contact with THR 836 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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789u LEU* 3.4 24.9 - - - -
792u VAL* 5.3 4.4 - - - -
793u LYS* 4.0 21.0 - - - -
832u GLN 2.9 16.0 + - - -
833u LEU* 3.8 5.2 - - - -
835u ASP* 1.3 77.9 - - - +
837u THR* 1.3 59.3 + - - +
838u VAL 3.2 0.2 - - - -
839u GLU* 3.2 5.9 + - - +
840u LEU* 3.0 27.2 + - - +
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Residues in contact with THR 837 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833u LEU 2.9 18.7 + - - -
834u VAL* 3.2 9.4 + - - -
836u THR* 1.3 73.8 - - - +
838u VAL* 1.3 60.2 + - - +
840u LEU* 3.7 8.9 - - - +
841u ALA* 2.9 30.3 + - - +
871u THR* 5.3 11.2 - - - -
875u ILE* 5.8 0.4 - - - +
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Residues in contact with VAL 838 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834u VAL 3.0 15.9 + - - +
835u ASP* 4.2 8.5 - - - +
836u THR 3.2 0.2 - - - -
837u THR* 1.3 76.5 - - - +
839u GLU* 1.3 57.2 + - - +
841u ALA* 3.2 7.9 + - - +
842u ASN* 2.9 25.7 + - - +
874u LYS* 5.1 17.5 - - + +
875u ILE* 5.8 7.0 - - - +
878u ASN* 6.0 5.4 - - + +
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Residues in contact with GLU 839 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793u LYS* 4.2 23.8 - - + +
796u CYS 4.3 8.8 - - - +
797u GLY* 6.0 0.7 - - - -
835u ASP 4.2 7.3 + - - +
836u THR 3.2 8.4 + - - +
838u VAL* 1.3 76.0 - - - +
840u LEU* 1.3 61.1 + - - +
842u ASN* 3.2 10.3 + - + +
843u LYS* 2.9 29.1 + - - +
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Residues in contact with LEU 840 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796u CYS* 5.7 2.7 - - - -
836u THR 3.0 16.3 + - - +
837u THR* 3.7 9.6 - - - +
839u GLU* 1.3 78.1 - - - +
841u ALA* 1.3 57.4 + - - +
843u LYS* 4.0 4.2 - - - +
844u VAL* 2.9 32.9 + - - +
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Residues in contact with ALA 841 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837u THR 2.9 17.6 + - - +
838u VAL* 3.6 4.9 - - - +
840u LEU* 1.3 73.8 - - - +
842u ASN* 1.3 66.1 + - - +
845u GLY* 3.1 40.6 + - - +
846u ALA* 5.1 2.5 - - - -
849u ILE* 5.0 10.5 - - + -
875u ILE* 4.4 23.1 - - + -
879u LEU* 5.3 10.3 - - + +
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Residues in contact with ASN 842 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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838u VAL 2.9 13.3 + - - +
839u GLU* 3.2 13.4 + - - +
841u ALA* 1.3 78.5 - - - +
843u LYS* 1.3 61.1 + - - +
844u VAL 5.0 0.3 - - - -
879u LEU* 6.2 2.2 - - - -
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Residues in contact with LYS 843 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796u CYS* 4.3 21.3 - - + +
797u GLY* 5.5 2.7 - - - -
801u VAL 6.0 2.5 - - - +
802u GLU 6.0 0.3 - - - -
803u ALA* 5.3 6.5 - - - +
839u GLU 2.9 16.3 + - - +
840u LEU* 4.0 5.2 - - - +
842u ASN* 1.3 79.6 - - - +
844u VAL* 1.3 63.9 + - + +
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Residues in contact with VAL 844 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803u ALA* 5.2 18.5 - - + +
806u ILE* 5.5 11.0 - - + -
807u LYS* 5.8 6.7 - - + -
840u LEU* 2.9 17.1 + - + +
842u ASN 5.0 0.4 - - - -
843u LYS* 1.3 81.1 - - + +
845u GLY* 1.3 58.6 + - - +
848u GLU* 5.2 11.4 - - + -
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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