Contacts of the helix formed by residues 895 - 903 (chain C) in PDB entry 5NC5
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 TRP 895 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B ILE* 3.2 39.4 - - + +
13B TRP* 4.1 21.1 - - + -
14B VAL* 4.5 7.9 - - + -
17B ILE* 3.9 22.9 - - + -
1103B D10 3.7 27.6 - - + +
885C PHE* 4.0 25.5 - + + -
886C LEU* 5.0 1.8 - - + -
889C ALA* 3.9 21.8 - - + -
894C SER* 1.3 72.3 + - - +
896C SER* 1.3 62.3 + - - +
898C PRO* 3.8 5.7 - - - +
899C PHE* 3.9 14.6 + - - +
1103C D12 3.4 83.6 - - + +
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Residues in contact with SER 896 (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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894C SER* 3.0 7.2 + - - -
895C TRP* 1.3 78.0 - - - +
897C ILE* 1.3 76.3 + - - +
898C PRO 3.1 2.0 - - - -
899C PHE* 2.8 16.0 + - - +
900C SER* 3.0 14.6 + - - -
1029C VAL* 3.8 23.7 - - - +
1030C ARG* 4.3 19.8 + - - -
1033C PHE* 5.1 5.8 - - - -
1103C D12 4.1 22.9 - - - +
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Residues in contact with ILE 897 (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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888C LEU* 6.0 1.3 - - + -
892C TYR* 3.5 42.6 - - + -
894C SER* 3.2 14.3 + - - +
896C SER* 1.3 81.6 + - - +
898C PRO* 1.3 73.0 - - + +
900C SER* 3.3 8.2 + - - -
901C VAL* 3.0 29.1 + - + +
943C ILE* 6.0 0.9 - - + -
946C VAL* 3.5 30.3 - - + +
947C GLU* 5.5 2.0 - - - +
950C LYS* 3.5 38.4 - - + +
1026C PHE* 5.1 5.2 - - + -
1030C ARG* 6.2 0.9 - - - -
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Residues in contact with PRO 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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885C PHE* 3.2 35.4 - - + +
888C LEU* 3.9 14.1 - - + +
889C ALA* 3.5 26.5 - - + +
892C TYR* 5.3 0.7 - - + -
894C SER* 3.0 27.4 - - - +
895C TRP* 3.8 3.4 - - - +
896C SER 3.4 2.0 - - - -
897C ILE* 1.3 98.0 - - + +
899C PHE* 1.3 57.1 + - - +
901C VAL* 3.1 5.3 + - + +
902C MET* 2.9 32.4 + - - +
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Residues in contact with PHE 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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885C PHE* 3.8 15.7 - + + -
895C TRP 3.9 9.8 + - - +
896C SER* 2.8 14.1 + - - +
898C PRO* 1.3 76.4 - - - +
900C SER* 1.3 59.5 + - - +
902C MET* 4.5 3.4 - - + +
903C LEU* 3.1 61.7 + - + +
1029C VAL* 4.3 17.9 - - + -
1033C PHE* 6.1 3.4 - + - -
1115C D10 5.6 6.7 - - + -
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Residues in contact with SER 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 SER 3.0 12.1 + - - -
897C ILE* 3.6 12.5 - - - -
899C PHE* 1.3 76.9 - - - +
901C VAL* 1.3 62.6 + - - +
903C LEU 4.2 0.5 + - - -
942C ALA* 4.9 2.4 - - - +
946C VAL* 4.4 14.1 - - - +
1022C VAL* 4.9 2.4 - - - +
1025C PHE* 3.6 31.7 + - - +
1026C PHE* 3.7 25.8 + - - -
1029C VAL* 3.4 26.4 - - - +
1030C ARG* 5.5 0.7 - - - +
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Residues in contact with VAL 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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888C LEU* 3.8 24.5 - - + -
897C ILE* 3.0 26.5 + - + +
898C PRO 3.6 2.9 - - - +
900C SER* 1.3 77.4 - - - +
902C MET* 1.3 57.4 + - - +
903C LEU 3.1 1.6 - - - -
904C VAL* 2.6 40.5 + - - +
939C ALA* 3.9 22.9 - - + +
942C ALA* 3.7 27.1 - - + -
943C ILE* 4.3 12.6 - - + +
946C VAL* 4.2 14.4 - - + -
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Residues in contact with MET 902 (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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881C LEU* 3.5 48.7 - - + +
884C VAL* 4.0 27.8 - - + -
885C PHE* 3.7 28.9 - - + -
888C LEU* 4.6 9.2 - - - -
898C PRO 2.9 21.0 + - - +
899C PHE* 4.8 3.6 - - + +
901C VAL* 1.3 80.5 - - - +
903C LEU* 1.3 64.5 + - - +
904C VAL 2.9 0.8 + - - -
905C VAL* 3.3 24.6 + - + +
906C PRO* 4.1 0.5 - - - +
935C ILE* 4.8 1.6 - - + -
939C ALA* 5.4 2.2 - - + -
1115C D10 4.6 7.0 - - + -
1116C D10 3.5 27.6 - - + +
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Residues in contact with LEU 903 (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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545C TYR* 2.4 54.2 + - + +
899C PHE* 3.1 50.2 + - + +
900C SER 4.4 0.9 - - - +
901C VAL 3.0 1.4 + - - -
902C MET* 1.3 77.2 - - - +
904C VAL* 1.3 60.6 + - - +
905C VAL 3.3 0.2 - - - -
906C PRO* 3.3 2.2 - - - +
1025C PHE* 3.6 38.3 - - + -
1029C VAL* 4.4 9.0 - - + -
1116C D10 4.8 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