Contacts of the helix formed by residues 892 - 907 (chain r) 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 GLN 892 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415r VAL* 5.9 0.3 - - - +
416r PHE* 5.7 11.0 - - + +
419r GLY* 5.8 6.5 - - - -
620r LEU 4.5 3.6 + - - -
621r HIS 5.2 3.4 - - - +
622r ASP 4.0 20.2 - - - +
623r ASP* 4.5 14.1 - - - +
625r GLY 5.7 0.2 - - - -
626r PRO* 4.8 9.4 - - + +
890r GLU 3.9 2.2 + - - -
891r SER* 1.3 71.5 - - - +
893r MET* 1.3 62.8 - - - +
894r VAL* 3.1 4.6 + - - -
895r SER* 3.1 22.8 + - - -
896r LYS* 4.1 1.6 + - - +
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Residues in contact with MET 893 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626r PRO* 4.2 22.5 - - + +
629r GLU* 5.2 7.6 - - + -
891r SER* 3.1 8.8 - - - +
892r GLN* 1.3 76.0 - - - +
894r VAL* 1.3 62.6 + - - +
896r LYS* 3.1 5.2 + - - +
897r LEU* 2.9 22.7 + - - -
923r ALA* 5.8 3.8 - - + -
925r LEU* 3.9 27.4 - - + +
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Residues in contact with VAL 894 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411r LEU* 4.7 17.2 - - + +
414r LEU* 4.4 21.5 - - + +
415r VAL* 4.8 7.2 - - + -
891r SER 4.8 3.2 + - - +
892r GLN 3.1 1.9 + - - +
893r MET* 1.3 77.4 - - - +
895r SER* 1.3 63.4 + - - +
896r LYS 3.4 0.2 + - - -
897r LEU* 3.4 21.1 + - - +
925r LEU* 5.6 1.0 - - - +
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Residues in contact with SER 895 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411r LEU* 5.6 2.7 - - - -
415r VAL* 4.6 17.9 - - - +
892r GLN* 3.1 15.8 + - - -
894r VAL* 1.3 79.7 - - - +
896r LYS* 1.3 61.4 + - - +
898r PRO* 5.0 3.3 - - - +
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Residues in contact with LYS 896 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626r PRO* 4.0 23.3 - - + -
892r GLN 5.1 0.4 - - - +
893r MET 3.1 8.0 + - - +
895r SER* 1.3 78.6 - - - +
897r LEU* 1.3 55.3 + - - +
898r PRO* 3.2 2.9 - - - -
899r ASP* 2.7 37.1 + - + -
900r MET* 3.1 13.5 + - + +
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Residues in contact with LEU 897 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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893r MET 2.9 13.1 + - - +
894r VAL* 3.4 20.2 + - - +
895r SER 3.4 0.2 - - - -
896r LYS* 1.3 75.3 - - - +
898r PRO* 1.3 62.0 - - - +
900r MET* 3.5 8.1 + - - +
901r LEU* 3.1 24.8 + - - +
957r VAL* 6.1 2.2 - - - +
960r ALA* 4.1 8.7 - - + +
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Residues in contact with PRO 898 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894r VAL 5.1 0.2 - - - -
895r SER 5.0 3.0 - - - +
896r LYS 2.9 3.4 - - - -
897r LEU* 1.3 76.2 - - - +
899r ASP* 1.3 62.3 + - - +
901r LEU* 3.6 2.1 + - - +
902r ASN* 3.3 22.3 + - - +
960r ALA* 3.7 27.6 - - + +
963r MET* 4.5 15.0 - - + -
964r LEU* 5.2 7.2 - - + +
995r ASN* 5.8 9.7 - - + +
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Residues in contact with ASP 899 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896r LYS* 2.7 20.9 + - + +
898r PRO* 1.3 73.0 - - - +
900r MET* 1.3 62.3 + - - +
902r ASN* 3.5 7.1 + - - +
903r ALA* 3.4 21.7 + - - +
993r ILE 5.8 1.6 - - - +
994r THR* 5.4 13.0 - - - -
995r ASN* 5.6 7.6 - - + +
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Residues in contact with MET 900 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626r PRO* 6.0 1.8 - - + +
630r ALA* 5.4 12.1 - - + -
896r LYS* 3.1 14.2 + - + +
897r LEU* 3.9 11.4 - - - +
898r PRO 3.4 0.2 - - - -
899r ASP* 1.3 77.5 - - - +
901r LEU* 1.3 64.9 + - - +
903r ALA* 3.6 5.1 + - - +
904r GLU* 3.4 18.4 + - - +
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Residues in contact with LEU 901 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897r LEU 3.1 18.4 + - - +
898r PRO 3.8 4.3 - - - +
899r ASP 3.3 0.2 - - - -
900r MET* 1.3 74.3 - - - +
902r ASN* 1.3 69.9 + - - +
904r GLU* 3.0 15.9 + - - +
905r ILE* 3.0 12.1 + - - +
910r VAL* 5.7 0.7 - - - +
916r ALA* 6.4 2.5 - - + -
957r VAL* 6.0 4.0 - - + +
960r ALA* 4.5 15.0 - - + -
961r ALA 5.9 0.2 - - - +
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Residues in contact with ASN 902 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898r PRO 3.3 10.6 + - - +
899r ASP* 3.6 11.7 - - - +
901r LEU* 1.3 77.7 - - - +
903r ALA* 1.3 52.0 + - - +
905r ILE* 2.7 30.4 + - - +
906r VAL* 2.8 17.4 + - - +
964r LEU* 5.4 6.7 - - + -
969r LEU* 5.0 15.9 - - + -
985r GLY* 5.5 7.9 - - - +
988r ALA* 6.2 2.5 - - + -
989r SER* 5.1 3.4 - - - +
995r ASN* 6.3 2.9 - - + -
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Residues in contact with ALA 903 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598r ARG* 5.1 13.8 - - + +
899r ASP 3.4 12.9 + - - +
900r MET* 4.0 5.6 - - - +
902r ASN* 1.3 78.2 - - - +
904r GLU* 1.3 56.8 + - - +
906r VAL* 3.5 11.9 - - - +
907r LEU* 3.1 25.5 + - - +
989r SER* 3.9 19.9 - - - +
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Residues in contact with GLU 904 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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900r MET 3.4 11.1 + - - +
901r LEU* 3.0 12.5 + - - +
903r ALA* 1.3 76.6 - - - +
905r ILE* 1.3 62.7 + - - +
907r LEU* 3.5 4.1 + - - +
908r GLY 3.2 2.3 + - - -
909r ASN* 2.9 37.9 + - + +
910r VAL* 3.3 14.2 + - + -
919r TRP* 5.9 6.3 - - + -
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Residues in contact with ILE 905 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901r LEU 3.0 9.1 + - - +
902r ASN* 2.7 16.4 + - - +
904r GLU* 1.3 72.8 - - - +
906r VAL* 1.3 59.6 + - - +
908r GLY* 3.0 18.7 + - - -
910r VAL* 3.8 21.4 - - + +
970r VAL* 6.0 4.9 - - + -
979r PHE* 4.8 14.8 - - + -
980r GLN 6.2 0.4 - - - -
981r VAL* 4.7 16.7 - - + +
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Residues in contact with VAL 906 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598r ARG* 5.8 4.9 - - + +
902r ASN 2.8 10.9 + - - +
903r ALA* 3.5 16.8 - - - +
905r ILE* 1.3 79.1 - - - +
907r LEU* 1.3 58.2 + - - +
908r GLY 3.5 0.3 + - - -
981r VAL* 5.0 10.1 - - + +
985r GLY 5.0 2.5 - - - +
986r ARG* 4.7 15.9 - - + +
989r SER* 3.9 17.3 - - - -
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Residues in contact with LEU 907 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597r THR 5.7 4.5 - - - +
598r ARG* 5.6 8.7 - - - +
903r ALA 3.1 16.5 + - - +
904r GLU* 3.5 6.7 + - - +
905r ILE 3.2 0.4 - - - -
906r VAL* 1.3 76.4 - - - +
908r GLY* 1.3 60.6 + - - +
909r ASN* 3.2 8.8 + - + +
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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