Contacts of the helix formed by residues 887 - 901 (chain C) in PDB entry 1U6G
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 ASN 887 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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850C ASP* 3.2 24.4 + - - +
852C SER* 3.2 25.3 + - - -
883C ILE 4.0 3.0 + - - -
884C SER 3.2 3.5 + - - +
886C GLY* 1.3 77.6 - - - +
888C LEU* 1.3 62.4 + - - +
889C PRO* 2.8 24.0 - - - +
890C GLU* 3.0 22.3 + - - +
891C TYR* 3.2 32.3 + - + -
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Residues in contact with LEU 888 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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884C SER 3.2 20.4 + - - +
885C VAL* 4.0 13.8 + - + +
887C ASN* 1.3 72.9 - - - +
889C PRO* 1.3 64.7 - - + +
892C LEU* 3.0 48.1 + - + +
916C ILE* 4.0 24.0 - - + -
920C ALA* 4.8 9.4 - - + -
921C SER* 5.4 4.9 - - - +
924C GLY* 3.3 37.5 - - - +
925C LEU* 4.1 17.0 - - + -
928C TYR* 4.3 4.9 - - + -
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Residues in contact with PRO 889 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887C ASN* 2.8 22.4 - - - +
888C LEU* 1.3 84.7 - - + +
890C GLU* 1.3 55.4 - - + +
891C TYR 3.1 5.4 - - - -
893C PRO* 2.9 25.7 - - + +
928C TYR* 3.0 27.1 - - + +
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Residues in contact with GLU 890 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852C SER* 3.4 29.8 + - - +
855C LEU* 5.3 4.9 - - - +
858C LYS* 2.9 35.7 + - - -
887C ASN* 3.0 30.7 + - + +
889C PRO* 1.3 78.9 - - + +
891C TYR* 1.3 60.8 + - + +
893C PRO* 4.6 0.7 - - - -
894C PHE* 4.4 1.1 - - - +
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Residues in contact with TYR 891 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851C LEU* 2.9 31.1 + - - +
852C SER* 3.7 11.9 + - - -
854C GLN 4.9 0.3 + - - -
855C LEU* 5.7 0.4 - - + -
857C LEU* 3.8 14.5 - - + +
858C LYS* 3.2 40.4 - - + -
880C LEU* 5.2 5.4 - - + -
883C ILE* 3.5 40.1 - - + +
884C SER* 3.5 23.3 - - - +
886C GLY* 5.7 0.2 - - - -
887C ASN* 3.2 35.4 + - + +
889C PRO 3.1 0.8 - - - -
890C GLU* 1.3 82.8 - - + +
892C LEU* 1.3 67.4 + - - +
893C PRO* 3.4 2.9 - - - -
894C PHE* 3.0 12.3 + + - +
895C VAL* 2.9 24.4 + - + +
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Residues in contact with LEU 892 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884C SER 4.7 1.2 + - - -
888C LEU* 3.0 37.7 + - + +
891C TYR* 1.3 77.5 - - - +
893C PRO* 1.3 66.4 - - + +
895C VAL* 3.0 8.4 + - + +
896C LEU* 3.0 41.7 + - + +
913C LEU* 5.4 1.8 - - + -
916C ILE* 4.2 19.7 - - + -
925C LEU* 4.1 11.4 - - + -
928C TYR* 3.4 42.0 - - + -
932C ILE* 3.6 16.6 - - + -
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Residues in contact with PRO 893 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888C LEU 3.7 0.4 - - - +
889C PRO* 2.9 31.0 - - + +
890C GLU 4.6 0.4 - - - -
891C TYR 3.5 2.9 - - - +
892C LEU* 1.3 93.1 - - + +
894C PHE* 1.3 51.5 + - - +
896C LEU* 3.5 8.4 + - + +
897C GLN* 2.7 37.1 + - - +
928C TYR* 4.1 17.9 - - + -
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Residues in contact with PHE 894 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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858C LYS* 3.3 67.1 - - + +
862C LEU* 4.1 17.9 - - + -
880C LEU* 4.9 13.5 - - + -
890C GLU 4.4 1.3 + - - +
891C TYR* 3.0 15.0 - + - +
893C PRO* 1.3 80.7 - - - +
895C VAL* 1.3 65.1 + - + +
897C GLN* 2.9 11.0 - - + +
898C GLU* 2.8 62.9 + - + +
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Residues in contact with VAL 895 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880C LEU* 4.1 24.0 - - + -
884C SER* 3.5 23.1 - - - +
891C TYR 2.9 18.1 + - - +
892C LEU* 3.0 8.7 + - + +
894C PHE* 1.3 73.7 - - + +
896C LEU* 1.3 69.9 + - + +
897C GLN 2.8 1.6 + - - -
898C GLU* 2.9 16.9 + - - +
899C ILE* 3.0 18.3 + - + +
909C LEU* 4.2 22.0 - - + +
912C SER* 4.9 3.6 - - - -
913C LEU* 4.2 20.0 - - + +
916C ILE* 4.1 12.6 - - + -
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Residues in contact with LEU 896 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892C LEU* 3.0 24.0 + - + +
893C PRO* 3.9 8.7 - - + +
895C VAL* 1.3 75.6 - - - +
897C GLN* 1.3 64.3 + - - +
899C ILE* 3.2 21.6 + - + +
900C THR* 3.3 10.2 + - - -
913C LEU* 3.4 33.4 - - + -
928C TYR* 5.6 2.5 - - + -
931C ASN* 4.3 19.3 - - + +
932C ILE* 3.6 41.5 - - + +
935C LEU* 4.2 22.5 - - + +
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Residues in contact with GLN 897 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893C PRO 2.7 20.4 + - - +
894C PHE* 2.9 20.9 - - + +
895C VAL 2.8 0.6 + - - -
896C LEU* 1.3 75.4 - - - +
898C GLU* 1.3 68.8 + - - +
900C THR* 3.2 5.9 + - - -
901C SER* 3.0 30.8 + - - -
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Residues in contact with GLU 898 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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862C LEU* 4.2 5.5 - - + +
894C PHE* 2.8 53.7 + - + +
895C VAL* 2.9 4.4 + - - +
897C GLN* 1.3 82.6 - - - +
899C ILE* 1.3 65.9 + - - +
900C THR 3.1 1.0 + - - -
901C SER* 3.6 12.9 + - - -
902C GLN* 2.6 60.3 + - - +
909C LEU* 3.6 21.5 - - + -
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Residues in contact with ILE 899 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895C VAL* 3.0 19.3 + - + +
896C LEU* 3.2 14.6 - - - +
897C GLN 3.2 0.4 - - - -
898C GLU* 1.3 77.4 - - - +
900C THR* 1.3 58.0 + - - +
902C GLN 4.0 3.1 - - - +
903C PRO* 4.3 1.7 - - - +
906C GLN* 3.9 14.9 - - + +
909C LEU* 3.8 34.5 - - + +
910C LEU* 3.9 22.2 - - + +
913C LEU* 3.6 31.6 - - + -
935C LEU* 3.4 16.8 - - + -
939C HIS* 3.3 35.0 - - + +
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Residues in contact with THR 900 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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896C LEU 3.3 13.2 + - - -
897C GLN* 3.2 5.3 + - - -
898C GLU 3.1 0.4 - - - -
899C ILE* 1.3 76.5 - - - +
901C SER* 1.3 71.4 + - - +
903C PRO* 4.5 5.4 - - - +
935C LEU* 3.6 17.0 - - + +
938C LYS* 4.8 14.4 - - + -
939C HIS* 4.0 17.5 - - + +
941C GLU* 5.3 3.4 - - - +
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Residues in contact with SER 901 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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897C GLN* 3.0 23.9 + - - -
898C GLU* 3.2 21.1 + - - -
900C THR* 1.3 84.6 - - - +
902C GLN* 1.3 62.7 + - - +
903C PRO* 3.0 13.2 - - - +
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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