Contacts of the helix formed by residues 1017 - 1033 (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 LEU1017 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548C ILE* 3.9 29.4 - - + -
907C LEU* 3.6 32.1 - - + +
910C ILE* 5.0 4.9 - - + -
1013C THR* 3.0 24.1 + - + +
1016C VAL* 1.3 94.7 - - + +
1018C ALA* 1.3 68.0 + - - +
1020C PHE* 2.8 18.2 + - - +
1021C PHE* 2.9 23.8 + - + -
29F LEU* 4.2 11.0 - - + -
33F PHE* 5.9 2.9 - - + -
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Residues in contact with ALA1018 (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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904C VAL* 3.6 23.6 - - + -
907C LEU* 3.7 11.7 - - + +
941C ASN* 4.6 10.1 - - + -
945C ILE* 4.5 1.1 - - - +
1013C THR 3.7 3.0 + - - -
1014C ALA* 2.8 29.4 - - - +
1015C THR* 3.5 1.7 + - - +
1016C VAL 3.5 0.4 - - - -
1017C LEU* 1.3 77.7 - - - +
1019C ILE* 1.3 58.9 + - + +
1022C VAL* 2.8 40.9 + - + +
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Residues in contact with ILE1019 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527C TYR* 2.9 43.4 + - + +
531C VAL* 4.2 1.2 - - - +
941C ASN* 5.6 1.8 - - + +
945C ILE* 4.3 7.0 - - + -
972C LEU* 4.0 23.8 - - + -
975C ILE* 4.2 36.3 - - + -
976C LEU* 4.7 5.8 - - + -
1015C THR* 3.2 22.8 + - + +
1016C VAL* 3.4 10.3 - - - +
1018C ALA* 1.3 78.7 - - + +
1020C PHE* 1.3 60.7 + - + +
1023C PRO* 3.4 14.1 - - - +
26F ILE* 3.5 31.2 - - + -
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Residues in contact with PHE1020 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527C TYR* 3.4 31.9 - + - -
530C SER* 4.1 16.2 - - - -
531C VAL* 3.9 19.6 - - + +
534C ILE* 4.1 15.3 - - + +
1016C VAL 3.3 22.4 - - - -
1017C LEU* 2.8 7.8 + - - +
1019C ILE* 1.3 83.5 - - + +
1021C PHE* 1.3 64.8 + - + +
1022C VAL 3.6 0.2 - - - -
1023C PRO* 3.6 9.2 - - - +
1024C VAL* 3.7 16.1 + - - +
26F ILE* 3.8 25.8 - - + -
29F LEU* 3.7 23.8 - - + -
30F GLY* 4.1 8.3 - - - -
33F PHE* 3.5 35.9 - + + -
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Residues in contact with PHE1021 (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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541C TYR* 3.9 17.5 - + + -
544C LEU* 3.3 29.6 - - + -
545C TYR* 3.6 37.5 - + + -
548C ILE* 4.1 13.9 - - + -
907C LEU* 3.4 26.2 - - + -
1017C LEU* 2.9 21.9 + - + -
1020C PHE* 1.3 85.3 - - + +
1022C VAL* 1.3 63.0 + - - +
1024C VAL* 3.1 10.9 + - + +
1025C PHE* 3.0 48.2 + + + -
33F PHE* 3.9 24.7 - + - -
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Residues in contact with VAL1022 (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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900C SER 4.9 2.7 - - - +
904C VAL* 3.4 39.0 - - + -
942C ALA* 3.8 22.9 - - + -
945C ILE* 4.0 18.2 - - + -
946C VAL* 3.9 25.1 - - + +
1018C ALA* 2.8 27.4 + - + +
1021C PHE* 1.3 68.5 - - - +
1023C PRO* 1.3 67.4 - - + +
1025C PHE* 3.2 11.7 + - + +
1026C PHE* 3.0 22.0 + - - +
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Residues in contact with PRO1023 (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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531C VAL* 4.1 16.8 - - + -
535C LEU* 4.3 5.2 - - + -
945C ILE* 4.2 8.1 - - + -
964C THR* 3.8 22.0 - - + -
968C VAL* 3.5 27.8 - - + -
1018C ALA 3.6 1.1 - - - +
1019C ILE 3.4 21.8 - - - +
1020C PHE 3.6 5.4 - - - +
1021C PHE 3.6 2.9 - - - -
1022C VAL* 1.3 96.5 - - + +
1024C VAL* 1.3 60.1 + - - +
1026C PHE* 3.6 5.2 + - + +
1027C VAL* 3.2 30.0 + - - +
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Residues in contact with VAL1024 (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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531C VAL* 6.4 0.2 - - + -
534C ILE* 3.5 32.5 - - + -
535C LEU* 4.3 9.6 - - + -
538C THR* 4.0 19.5 - - + -
541C TYR* 4.7 11.0 - - + -
542C LEU* 4.0 19.1 - - + -
1020C PHE 3.7 10.5 - - - +
1021C PHE* 3.1 12.0 + - + +
1023C PRO* 1.3 76.5 - - + +
1025C PHE* 1.3 69.5 + - + +
1027C VAL* 3.4 0.5 + - - +
1028C VAL* 2.9 47.5 + - + +
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Residues in contact with PHE1025 (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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541C TYR 5.7 0.2 - - - -
542C LEU* 4.8 12.8 - - + -
545C TYR* 3.2 49.1 - + + -
900C SER* 3.7 20.2 - - - +
903C LEU* 3.6 44.4 - - + -
904C VAL* 4.0 7.6 - - + -
907C LEU* 4.6 2.2 - - + -
1021C PHE* 3.0 37.1 + + + -
1022C VAL* 3.2 15.7 + - + +
1024C VAL* 1.3 82.2 - - + +
1026C PHE* 1.3 60.1 + - - +
1028C VAL* 4.1 2.2 - - - -
1029C VAL* 2.9 35.0 + - - +
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Residues in contact with PHE1026 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897C ILE* 5.1 5.2 - - + -
900C SER* 3.7 13.4 - - - -
945C ILE* 5.9 2.7 - - + -
946C VAL* 3.7 41.5 - - + -
949C ALA* 3.2 32.8 - - + -
950C LYS* 3.8 17.9 - - + -
953C MET* 4.2 7.2 - - - -
960C LEU* 3.8 18.6 - - + -
963C ALA* 5.9 0.2 - - + -
964C THR* 3.7 18.6 - - + -
1022C VAL* 3.0 16.1 + - + +
1023C PRO* 3.8 5.4 - - + +
1024C VAL 3.2 0.2 - - - -
1025C PHE* 1.3 75.9 - - - +
1027C VAL* 1.3 58.3 + - - +
1029C VAL* 4.0 0.7 - - - +
1030C ARG* 3.0 63.0 + - + +
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Residues in contact with VAL1027 (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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535C LEU* 3.8 23.6 - - + +
538C THR* 4.9 2.9 - - + +
960C LEU* 3.7 20.5 - - + +
961C ILE* 4.1 7.0 - - + -
964C THR* 3.4 25.4 - - - +
1023C PRO 3.2 19.3 + - - +
1024C VAL 3.9 2.5 - - - +
1026C PHE* 1.3 81.2 - - - +
1028C VAL* 1.3 62.9 + - + +
1031C ARG* 3.0 66.1 + - - +
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Residues in contact with VAL1028 (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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538C THR* 4.0 25.4 - - - +
542C LEU* 4.4 24.5 - - + -
1024C VAL* 2.9 36.3 + - + +
1025C PHE* 4.1 3.4 - - - +
1027C VAL* 1.3 78.8 - - + +
1029C VAL* 1.3 65.5 + - + +
1031C ARG* 4.2 5.6 - - - +
1032C ARG* 3.2 23.9 + - + +
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Residues in contact with VAL1029 (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* 3.8 29.2 - - - +
899C PHE* 4.3 26.0 - - + -
900C SER* 3.4 19.3 - - - +
903C LEU* 4.4 10.8 - - + -
1025C PHE* 2.9 25.9 + - - +
1026C PHE 4.1 0.2 - - - +
1028C VAL* 1.3 79.3 - - + +
1030C ARG* 1.3 63.3 + - + +
1032C ARG* 3.2 2.6 + - - -
1033C PHE* 2.9 46.2 + - + -
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Residues in contact with ARG1030 (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* 4.3 18.8 + - - +
897C ILE* 6.2 1.1 - - - -
900C SER* 5.5 0.9 - - - +
950C LYS* 6.1 1.8 - - - -
953C MET* 3.3 31.2 - - - +
960C LEU* 4.3 15.9 - - + -
1026C PHE* 3.0 59.2 + - + +
1027C VAL 3.9 2.7 - - - +
1029C VAL* 1.3 77.5 - - + +
1031C ARG* 1.3 62.4 + - - +
1033C PHE* 3.0 36.2 + - - +
1103C D12 5.8 5.7 - - - +
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Residues in contact with ARG1031 (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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535C LEU 4.7 7.9 + - - -
538C THR* 4.3 12.3 + - - -
960C LEU* 3.5 17.8 - - + +
961C ILE* 2.9 41.0 - - - +
1027C VAL* 3.0 32.6 + - - +
1028C VAL* 4.2 5.4 - - - +
1030C ARG* 1.3 73.2 - - - +
1032C ARG* 1.3 66.3 + - - +
1033C PHE* 3.4 2.6 + - - +
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Residues in contact with ARG1032 (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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1028C VAL* 3.2 19.5 + - + +
1029C VAL* 3.2 5.9 + - - +
1031C ARG* 1.3 78.8 - - - +
1033C PHE* 1.3 85.2 + - + +
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Residues in contact with PHE1033 (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* 5.1 6.3 - - - -
899C PHE* 6.1 3.4 - + - -
1029C VAL* 2.9 46.8 + - + +
1030C ARG* 3.0 32.5 + - - +
1031C ARG 4.4 2.4 - - - +
1032C ARG* 1.3 102.8 - - + +
1103C D12 4.3 41.1 - - + -
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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
------------------------------------------------------------
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