Contacts of the helix formed by residues 861 - 879 (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 ALA 861 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261 VAL* 4.0 22.4 - - + +
821u HIS* 6.0 3.6 - - + -
859u ASP* 3.2 10.8 - - + +
860u GLU* 1.3 80.2 - - - +
862u GLU* 1.3 64.1 + - - +
863u GLN* 4.7 1.1 - - + +
864u TYR* 4.0 22.4 - - + +
865u ARG* 3.5 20.4 + - - +
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Residues in contact with GLU 862 (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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860u GLU 4.2 0.6 + - - -
861u ALA* 1.3 72.5 - - - +
863u GLN* 1.3 61.0 + - - +
865u ARG* 3.5 5.3 + - - +
866u LYS* 2.9 27.9 + - - +
902u GLU 5.7 4.9 - - - +
903u GLN* 6.0 2.0 - - - -
904u THR* 5.6 12.8 - - - +
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Residues in contact with GLN 863 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824u ALA* 4.3 21.2 - - + +
825u LEU* 6.0 1.6 - - - -
861u ALA* 4.7 1.2 - - + +
862u GLU* 1.3 76.9 - - - +
864u TYR* 1.3 60.5 + - - +
866u LYS* 3.3 8.1 + - - +
867u MET* 2.9 27.9 + - - +
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Residues in contact with TYR 864 (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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820u GLN 5.4 5.6 - - - +
821u HIS* 5.4 9.2 - - + -
824u ALA* 4.6 9.7 - - + +
856u ASP* 5.4 2.2 - - - +
859u ASP* 5.3 7.0 - - + -
861u ALA* 4.0 21.3 + - + +
862u GLU 3.3 0.4 - - - -
863u GLN* 1.3 76.2 - - - +
865u ARG* 1.3 59.8 + - - +
867u MET* 3.2 9.0 + - - +
868u VAL* 3.0 26.9 + - - +
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Residues in contact with ARG 865 (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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856u ASP 4.6 13.6 + - - +
857u LEU* 4.8 13.2 - - - +
859u ASP* 5.4 5.8 - - + +
861u ALA 3.5 16.3 + - - +
862u GLU* 3.5 5.5 + - - +
863u GLN 3.4 0.2 - - - -
864u TYR* 1.3 78.3 - - - +
866u LYS* 1.3 57.2 + - - +
868u VAL* 3.4 7.3 + - - +
869u MET* 2.9 29.3 + - - +
899u ALA* 5.1 11.9 - - + -
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Residues in contact with LYS 866 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862u GLU 2.9 19.0 + - - +
863u GLN* 3.5 10.1 - - - +
864u TYR 3.2 0.4 - - - -
865u ARG* 1.3 74.4 - - - +
867u MET* 1.3 58.6 + - - +
869u MET* 3.4 6.5 + - - +
870u GLU* 2.9 29.8 + - - +
909u VAL* 6.5 0.9 - - + -
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Residues in contact with MET 867 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824u ALA* 4.4 14.1 - - + -
830u TYR* 5.8 5.4 - - + +
834u VAL* 5.1 3.5 - - - +
863u GLN 2.9 14.4 + - - +
864u TYR* 3.2 11.6 + - - +
866u LYS* 1.3 74.5 - - - +
868u VAL* 1.3 59.7 + - - +
870u GLU* 3.3 6.3 + - - +
871u THR* 2.9 28.8 + - - -
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Residues in contact with VAL 868 (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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853u ILE* 4.6 19.7 - - + +
856u ASP* 4.8 17.3 - - + +
857u LEU* 5.3 4.5 - - + +
864u TYR 3.0 16.0 + - - +
865u ARG* 3.8 8.1 - - - +
867u MET* 1.3 75.5 - - - +
869u MET* 1.3 58.0 + - - +
871u THR* 3.3 8.8 + - - -
872u ILE* 2.9 28.6 + - - +
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Residues in contact with MET 869 (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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865u ARG 2.9 18.2 + - - +
866u LYS* 3.6 8.5 - - - +
867u MET 3.2 0.2 - - - -
868u VAL* 1.3 78.3 - - - +
870u GLU* 1.3 56.4 + - - +
872u ILE* 3.8 6.4 - - - +
873u GLU* 2.9 30.3 + - - +
909u VAL 5.8 2.2 - - - +
910u MET* 5.3 16.8 - - + -
913u GLY* 5.2 4.3 - - - -
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Residues in contact with GLU 870 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834u VAL* 5.0 11.4 - - + +
866u LYS 2.9 17.0 + - - +
867u MET* 3.7 7.2 - - - +
869u MET* 1.3 73.4 - - - +
871u THR* 1.3 61.0 + - - +
873u GLU* 4.1 4.9 - - - +
874u LYS* 3.0 33.1 + - - +
909u VAL* 6.2 4.3 - - + -
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Residues in contact with THR 871 (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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834u VAL* 4.7 14.7 - - - +
837u THR* 5.3 11.4 - - - -
853u ILE* 6.4 1.8 - - - -
867u MET 2.9 14.7 + - - -
868u VAL* 3.4 13.0 - - - -
869u MET 3.3 0.2 - - - -
870u GLU* 1.3 76.9 - - - +
872u ILE* 1.3 56.9 + - - +
874u LYS* 3.9 2.4 - - - +
875u ILE* 3.0 32.9 + - - +
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Residues in contact with ILE 872 (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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850u ILE* 6.4 3.6 - - + -
868u VAL 2.9 16.3 + - - +
869u MET* 3.8 6.5 - - - +
871u THR* 1.3 76.8 - - - +
873u GLU* 1.3 56.1 + - - +
875u ILE* 4.0 3.7 - - - +
876u MET* 2.9 35.1 + - - +
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Residues in contact with GLU 873 (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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869u MET 2.9 18.0 + - - +
870u GLU* 4.1 5.4 - - - +
871u THR 3.4 0.2 - - - -
872u ILE* 1.3 75.6 - - - +
874u LYS* 1.3 57.8 + - - +
876u MET* 4.4 2.2 - - - +
877u GLY* 2.9 26.5 + - - -
909u VAL 5.5 1.1 - - - +
912u ASN 5.0 0.7 - - - +
913u GLY* 3.7 30.7 - - - +
916u THR* 4.6 13.8 - - - -
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Residues in contact with LYS 874 (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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834u VAL* 5.7 5.4 - - + +
838u VAL* 5.1 16.3 - - + +
870u GLU 3.0 18.3 + - - +
871u THR* 4.1 2.9 - - - +
873u GLU* 1.3 75.9 - - - +
875u ILE* 1.3 60.0 + - - +
877u GLY* 5.1 0.2 - - - -
878u ASN* 2.9 31.7 + - - +
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Residues in contact with ILE 875 (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 5.8 0.7 - - - +
838u VAL* 5.8 4.9 - - - +
841u ALA* 4.4 22.9 - - + -
846u ALA* 5.8 9.0 - - + +
850u ILE* 6.4 1.8 - - + -
871u THR 3.0 19.5 + - - +
872u ILE* 4.1 3.6 - - - +
874u LYS* 1.3 77.5 - - - +
876u MET* 1.3 57.7 + - - +
878u ASN* 4.8 2.2 - - - -
879u LEU* 2.8 37.4 + - + +
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Residues in contact with MET 876 (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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872u ILE 2.9 19.3 + - - +
873u GLU* 4.4 2.2 - - - +
875u ILE* 1.3 76.5 - - - +
877u GLY* 1.3 59.4 + - - +
878u ASN 3.5 0.2 - - - -
880u GLY* 3.5 34.2 + - - +
881u ALA* 5.7 1.6 - - + -
916u THR* 5.4 7.0 - - - +
917u VAL* 5.4 8.3 - - + -
920u ALA* 4.3 18.6 - - + +
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Residues in contact with GLY 877 (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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873u GLU 2.9 18.3 + - - -
874u LYS 3.9 0.7 - - - -
876u MET* 1.3 78.2 - - - +
878u ASN* 1.3 60.2 + - - +
880u GLY 5.0 0.2 - - - -
916u THR* 5.3 8.0 - - - -
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Residues in contact with ASN 878 (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* 6.0 5.8 - - + +
874u LYS 2.9 18.9 + - - +
875u ILE* 4.1 2.2 - - - +
877u GLY* 1.3 80.0 - - - +
879u LEU* 1.3 65.5 + - - +
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Residues in contact with LEU 879 (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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841u ALA* 5.3 12.1 - - + +
842u ASN* 6.2 1.6 - - - -
846u ALA* 4.7 17.9 - - + +
875u ILE* 2.8 21.4 + - + +
877u GLY 5.2 0.2 - - - -
878u ASN* 1.3 77.3 - - + +
880u GLY* 1.3 59.4 + - - +
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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