Contacts of the helix formed by residues 888 - 902 (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 LEU 888 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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847u ALA* 5.9 4.9 - - + -
851u SER* 5.6 11.2 - - - -
854u VAL* 5.8 1.4 - - - +
884u ILE* 5.0 8.7 - - + -
885u ASP* 3.4 15.3 + - + +
886u HIS 3.2 0.6 - - - -
887u LYS* 1.3 80.6 - - - +
889u GLU* 1.3 66.3 + - - +
890u GLU 3.4 2.5 - - - -
891u GLN* 3.3 19.4 + - - +
892u LEU* 3.4 13.0 + - - +
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Residues in contact with GLU 889 (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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884u ILE* 5.8 6.3 - - + +
885u ASP 3.6 12.3 + - - +
886u HIS* 4.3 5.2 + - - +
888u LEU* 1.3 75.6 - - - +
890u GLU* 1.3 61.5 + - - +
892u LEU* 3.4 6.3 + - - +
893u ILE* 3.0 30.2 + - - +
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Residues in contact with GLU 890 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2003A THR* 4.9 8.7 - - - -
886u HIS 5.0 5.8 + - - +
888u LEU 3.4 0.6 - - - +
889u GLU* 1.3 77.7 - - - +
891u GLN* 1.3 58.1 + - - +
893u ILE* 4.0 5.3 - - - +
894u ASP* 2.9 33.1 + - - +
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Residues in contact with GLN 891 (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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2001A SER* 5.4 8.7 - - - +
2003A THR* 5.8 2.9 - - - -
854u VAL* 4.9 18.8 - - + +
887u LYS 5.6 1.6 - - - +
888u LEU* 3.3 14.7 + - - +
889u GLU 3.2 0.6 - - - -
890u GLU* 1.3 79.3 - - - +
892u LEU* 1.3 56.0 + - - +
894u ASP* 3.8 3.6 - - - +
895u GLY* 2.9 25.3 + - - -
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Residues in contact with LEU 892 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854u VAL* 5.2 14.3 - - + +
857u LEU* 5.8 0.8 - - - +
888u LEU 3.4 9.6 + - - +
889u GLU* 4.1 7.2 - - - +
890u GLU 3.4 0.2 - - - -
891u GLN* 1.3 76.4 - - - +
893u ILE* 1.3 59.7 + - - +
895u GLY* 3.3 1.5 + - - +
896u ILE* 2.9 31.5 + - - +
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Residues in contact with ILE 893 (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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889u GLU 3.0 17.9 + - - +
890u GLU* 4.0 5.6 - - - +
892u LEU* 1.3 76.0 - - - +
894u ASP* 1.3 57.5 + - - +
896u ILE* 3.4 3.8 + - - +
897u LEU* 3.0 30.9 + - - +
928u TYR* 5.4 12.3 - - + -
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Residues in contact with ASP 894 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2003A THR* 4.1 25.8 - - - -
2004A GLN* 5.0 4.0 - - + +
890u GLU 2.9 18.8 + - - +
891u GLN* 4.0 3.6 - - - +
893u ILE* 1.3 75.7 - - - +
895u GLY* 1.3 58.1 + - - +
897u LEU* 3.8 5.4 - - - +
898u TYR* 2.9 29.8 + - - +
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Residues in contact with GLY 895 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854u VAL 5.5 0.4 - - - -
857u LEU* 3.7 32.2 - - - +
858u LYS* 5.9 2.0 - - - -
891u GLN 2.9 18.4 + - - -
892u LEU 3.8 1.6 - - - -
894u ASP* 1.3 78.1 - - - +
896u ILE* 1.3 56.6 + - - +
898u TYR* 3.4 4.9 + - - -
899u ALA* 2.9 28.9 + - - +
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Residues in contact with ILE 896 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857u LEU* 4.7 1.1 - - - +
892u LEU 2.9 16.9 + - - +
893u ILE* 4.2 3.8 - - - +
895u GLY* 1.3 73.9 - - - +
897u LEU* 1.3 61.1 + - - +
899u ALA* 3.8 7.0 - - - +
900u PHE* 2.9 28.1 + - - +
914u PHE* 5.9 9.6 - - + -
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Residues in contact with LEU 897 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893u ILE 3.0 18.9 + - - +
894u ASP* 3.8 6.3 - - - +
896u ILE* 1.3 77.9 - - - +
898u TYR* 1.3 57.0 + - - +
900u PHE* 3.2 7.9 + - - +
901u GLN* 2.9 28.6 + - - +
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Residues in contact with TYR 898 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857u LEU 4.9 6.3 - - - +
858u LYS* 5.5 8.5 - - + -
894u ASP 2.9 18.7 + - - +
895u GLY* 3.8 5.8 - - - +
897u LEU* 1.3 77.2 - - - +
899u ALA* 1.3 60.4 + - - +
901u GLN* 3.6 7.3 + - - +
902u GLU* 3.4 23.7 + - - +
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Residues in contact with ALA 899 (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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857u LEU* 4.4 12.5 + - + +
865u ARG* 5.1 14.8 - - + +
895u GLY 2.9 17.4 + - - +
896u ILE* 3.8 7.9 - - - +
897u LEU 3.2 0.2 - - - -
898u TYR* 1.3 75.7 - - - +
900u PHE* 1.3 62.3 + - - +
902u GLU* 3.6 9.8 + - - +
903u GLN* 3.6 17.8 + - - +
910u MET* 6.0 5.6 - - + +
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Residues in contact with PHE 900 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896u ILE 2.9 17.9 + - - +
897u LEU* 3.2 8.5 + - - +
899u ALA* 1.3 77.8 - - - +
901u GLN* 1.3 62.0 + - - +
902u GLU 3.5 0.2 + - - -
903u GLN* 4.2 8.3 + - - +
910u MET* 6.1 4.9 - - + -
950u GLN* 6.1 1.2 - - - +
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Residues in contact with GLN 901 (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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1758A PRO* 4.1 28.7 - - + +
1759A THR* 5.9 2.2 - - - -
897u LEU 2.9 15.9 + - - +
898u TYR* 4.0 8.1 - - - +
899u ALA 3.3 0.4 - - - -
900u PHE* 1.3 78.0 - - - +
902u GLU* 1.3 58.6 + - + +
903u GLN 3.7 2.2 + - - +
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Residues in contact with GLU 902 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1758A PRO* 6.2 3.1 - - + -
862u GLU* 5.7 4.3 - - - +
898u TYR 3.4 13.9 + - - +
899u ALA* 3.6 5.5 + - - +
900u PHE 3.3 0.6 - - - -
901u GLN* 1.3 82.0 - - + +
903u GLN* 1.3 58.8 + - - +
904u THR 4.3 0.2 + - - -
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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