Contacts of the helix formed by residues 860 - 872 (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 THR 860 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C TYR* 3.3 13.9 - - - -
681C ASP* 3.1 39.8 + - - +
683C GLU* 3.6 26.9 - - + +
819C TYR* 3.1 31.1 + - - -
826C GLU* 4.5 1.3 - - - +
859C TRP* 1.3 73.0 - - - +
861C GLY* 1.3 76.6 + - - +
862C MET 3.2 0.5 + - - -
863C SER* 3.0 17.5 + - - -
864C TYR* 3.1 6.3 + - - -
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Residues in contact with GLY 861 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C TYR* 3.2 21.8 + - - -
674C LEU* 4.0 26.2 - - - -
681C ASP* 4.8 4.7 - - - -
860C THR* 1.3 84.3 + - - +
862C MET* 1.3 61.7 + - - -
864C TYR* 3.3 14.2 + - - +
865C GLN* 3.5 11.1 + - - +
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Residues in contact with MET 862 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563C PHE* 5.1 10.6 - - + +
669C PRO* 3.9 21.5 - - + -
671C ILE* 5.3 9.2 - - + +
674C LEU* 4.0 16.7 - - + +
675C GLY* 4.5 16.4 - - - -
677C ALA 2.8 29.8 - - - +
678C THR* 4.6 2.9 - - - +
679C GLY 3.8 29.2 - - - +
680C PHE 4.4 3.6 - - - +
681C ASP* 4.6 17.2 + - + +
828C LEU* 5.6 3.8 - - + -
860C THR 3.2 0.4 + - - +
861C GLY* 1.3 71.9 - - - -
863C SER* 1.4 61.2 + - - +
865C GLN* 3.2 11.9 + - - +
866C GLU* 3.1 24.3 + - - +
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Residues in contact with SER 863 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679C GLY 4.1 1.9 + - - -
680C PHE* 3.2 34.3 - - - +
681C ASP* 3.3 5.8 + - - +
841C MET* 3.8 13.4 - - - +
859C TRP* 3.6 28.0 - - - +
860C THR 3.0 7.9 + - - -
862C MET* 1.4 78.6 - - - +
864C TYR* 1.3 64.0 + - - +
866C GLU* 3.2 11.4 + - - +
867C ARG* 3.1 23.4 + - - +
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Residues in contact with TYR 864 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C MET* 3.5 43.5 + - - +
77C TYR* 3.8 26.2 - + + -
819C TYR* 4.6 1.3 - - - -
858C ASP* 4.2 4.0 - - - -
859C TRP* 3.3 28.5 - - - +
860C THR* 3.1 13.1 + - - +
861C GLY 3.3 11.4 + - - +
863C SER* 1.3 76.8 - - - +
865C GLN* 1.3 75.2 + - - +
867C ARG* 3.4 22.7 + - - +
868C LEU* 2.8 60.8 + - + +
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Residues in contact with GLN 865 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C PRO* 3.8 22.9 - - - +
76C MET* 4.2 9.1 - - - +
77C TYR* 4.8 1.2 + - - -
96C SER* 5.9 0.3 - - - -
461C GLY* 4.5 3.6 - - - -
462C SER* 3.2 37.9 + - - +
463C THR* 4.4 2.3 + - - +
563C PHE* 4.1 21.1 - - + -
671C ILE* 5.9 1.6 - - + -
674C LEU* 4.2 11.6 - - + +
861C GLY 3.5 14.2 + - - +
862C MET* 3.2 8.0 + - - +
863C SER 3.2 0.6 - - - -
864C TYR* 1.3 92.7 - - - +
866C GLU* 1.3 67.1 + - - +
868C LEU* 3.1 12.2 + - - +
869C SER* 2.9 26.5 + - - -
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Residues in contact with GLU 866 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561C SER* 4.0 2.8 + - - +
562C SER* 3.3 19.0 - - - -
563C PHE* 3.8 28.1 - - + +
680C PHE* 5.5 0.2 - - - +
837C THR* 2.4 32.7 + - - -
838C GLY* 3.5 9.5 + - - -
841C MET* 2.9 31.2 - - + +
862C MET 3.1 11.7 + - - +
863C SER* 3.2 13.6 + - - +
865C GLN* 1.3 76.0 - - - +
867C ARG* 1.3 66.0 + - - +
869C SER* 2.9 12.0 + - - -
870C GLY* 3.1 10.7 + - - -
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Residues in contact with ARG 867 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841C MET* 4.6 9.6 - - + +
845C GLU* 4.8 8.1 + - - +
857C TYR* 5.2 4.0 - - - -
858C ASP* 3.1 33.7 + - - +
859C TRP* 3.4 33.7 + - - +
863C SER 3.1 10.5 + - - +
864C TYR* 3.6 32.6 + - - +
865C GLN 3.3 0.2 - - - -
866C GLU* 1.3 80.9 - - - +
868C LEU* 1.3 66.8 + - - +
870C GLY* 3.7 0.9 + - - -
871C ASN* 3.1 44.8 + - - +
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Residues in contact with LEU 868 (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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76C MET* 5.8 0.7 - - - -
95C GLU* 5.4 7.4 - - - +
460C GLY 5.8 2.5 - - - +
461C GLY* 5.5 10.3 - - - -
463C THR* 5.6 2.0 - - - +
864C TYR* 2.8 67.1 + - + +
865C GLN* 3.1 14.3 + - - +
867C ARG* 1.3 83.2 - - + +
869C SER* 1.3 61.8 + - - +
871C ASN* 4.0 8.5 - - - +
872C GLN* 3.2 35.7 + - - +
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Residues in contact with SER 869 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463C THR* 3.1 40.2 - - - +
467C TYR* 4.5 0.2 + - - -
563C PHE* 3.9 9.3 - - - -
865C GLN 2.9 13.4 + - - -
866C GLU 2.9 3.5 + - - -
868C LEU* 1.3 79.3 - - - +
870C GLY* 1.3 59.9 + - - +
872C GLN* 3.6 18.7 - - - +
873C ALA* 3.8 4.3 + - - +
925C VAL* 3.7 12.0 - - - +
928C GLN* 3.4 20.7 + - - +
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Residues in contact with GLY 870 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866C GLU 3.1 11.2 + - - -
867C ARG 4.1 1.6 - - - -
869C SER* 1.3 74.8 - - - +
871C ASN* 1.3 64.8 + - - +
873C ALA* 3.1 17.2 + - - +
874C PRO* 3.4 9.0 - - - +
928C GLN* 4.6 4.7 - - - +
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Residues in contact with ASN 871 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867C ARG* 3.1 37.8 + - - +
868C LEU* 3.5 8.8 + - - +
870C GLY* 1.3 73.7 - - - +
872C GLN* 1.3 57.7 + - - +
874C PRO* 3.0 19.0 - - - +
875C SER* 4.6 3.8 + - - -
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Residues in contact with GLN 872 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459C PHE* 3.8 28.0 - - + -
460C GLY* 4.0 17.5 + - - +
463C THR* 3.4 35.2 - - - +
464C GLY 4.4 1.0 - - - +
467C TYR* 3.9 15.2 - - - +
868C LEU* 3.2 24.2 + - - +
869C SER* 3.6 7.4 - - - +
871C ASN* 1.3 80.0 - - - +
873C ALA* 1.3 70.1 + - - +
874C PRO* 3.1 0.7 - - - -
875C SER* 2.9 20.9 + - - -
876C LEU* 3.4 9.3 + - + +
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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
------------------------------------------------------------
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