Contacts of the helix formed by residues 818 - 831 (chain C) in PDB entry 4YOC
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 818 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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816C ARG 3.5 3.0 + - - +
817C MET* 1.3 72.4 - - - +
819C TYR* 1.3 65.2 + - - +
820C PHE* 3.3 12.9 + - - +
821C GLN* 2.9 53.7 + - - +
822C VAL* 3.2 25.3 + - - +
857C TYR 5.9 0.4 - - - +
858C GLU 5.9 1.1 - - - +
859C GLY 4.0 13.5 - - - +
860C THR* 4.6 4.3 - - + +
861C LEU 5.6 0.2 - - - -
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Residues in contact with TYR 819 (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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818C ASN* 1.3 77.5 - - - +
820C PHE* 1.3 62.3 + - - +
822C VAL* 3.4 7.4 + - + +
823C ALA* 2.9 41.8 + - + +
834C PRO 5.6 1.0 + - - -
835C MET* 5.9 6.7 - - + -
837C LEU 3.8 3.1 + - - -
839C PHE* 3.4 36.6 + + - -
853C LEU* 4.0 34.2 + - + -
854C ARG 4.1 8.5 - - - -
855C HIS* 3.7 29.4 - - + +
857C TYR* 3.7 32.9 + + + +
859C GLY 4.1 4.8 + - - -
864C LEU* 5.9 2.2 - - + -
885C ILE* 3.6 25.0 - - + +
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Residues in contact with PHE 820 (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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818C ASN* 3.3 12.7 + - - +
819C TYR* 1.3 85.6 - - - +
821C GLN* 1.3 70.7 + - + +
823C ALA* 3.5 4.0 + - - +
824C LYS* 2.9 72.1 + - + +
834C PRO* 6.4 1.1 - - + -
835C MET* 6.4 2.0 - - + -
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Residues in contact with GLN 821 (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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816C ARG 4.5 0.7 - - - +
817C MET* 3.2 31.3 - - + +
818C ASN* 2.9 43.6 + - - +
820C PHE* 1.3 85.5 - - + +
822C VAL* 1.3 60.8 + - - +
824C LYS* 3.3 6.7 + - - +
825C THR* 2.9 31.7 + - - -
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Residues in contact with VAL 822 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798C PHE* 4.0 30.1 - - + -
813C LEU* 4.8 4.7 - - + -
817C MET* 3.9 25.8 - - + -
818C ASN 3.2 18.4 + - - +
819C TYR* 3.7 7.0 - - + +
821C GLN* 1.3 76.1 - - - +
823C ALA* 1.3 64.0 + - - +
825C THR* 3.1 5.6 + - - -
826C VAL* 2.9 23.0 + - - +
839C PHE* 4.4 14.6 - - + -
861C LEU* 4.5 24.7 - - + -
864C LEU* 5.9 6.3 - - + -
876C LEU* 5.6 2.2 - - + -
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Residues in contact with ALA 823 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819C TYR* 2.9 30.1 + - + +
820C PHE* 3.8 5.2 - - - +
822C VAL* 1.3 76.3 - - - +
824C LYS* 1.3 63.1 + - - +
827C ALA* 2.9 27.5 + - - +
834C PRO* 4.2 19.5 - - + +
835C MET* 6.5 0.7 - - + -
837C LEU* 4.0 3.5 - - - +
839C PHE* 3.8 27.8 - - + -
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Residues in contact with LYS 824 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820C PHE* 2.9 59.3 + - + +
821C GLN* 3.5 7.6 - - - +
822C VAL 3.2 0.2 - - - -
823C ALA* 1.3 76.9 - - - +
825C THR* 1.3 57.1 + - - +
828C GLN* 2.7 48.7 + - + +
833C ASP* 5.2 1.4 + - - -
834C PRO* 3.6 31.1 - - + +
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Residues in contact with THR 825 (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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811C VAL* 4.0 18.6 - - + -
813C LEU* 3.9 26.3 - - + +
817C MET* 3.8 11.1 - - - +
821C GLN 2.9 16.2 + - - -
822C VAL* 3.1 10.7 + - - -
824C LYS* 1.3 76.0 - - - +
826C VAL* 1.3 67.7 + - + +
828C GLN* 3.0 19.4 + - - +
829C ARG* 3.0 14.6 + - + +
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Residues in contact with VAL 826 (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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798C PHE* 3.5 48.0 - - + -
809C PHE* 4.1 13.9 - - + -
822C VAL 2.9 17.6 + - - +
823C ALA 4.1 0.2 - - - +
825C THR* 1.3 78.2 - - + +
827C ALA* 1.3 58.7 - - - +
829C ARG* 3.2 7.1 + - - +
830C LEU* 2.9 44.4 + - + +
837C LEU* 3.9 15.7 - - + -
839C PHE* 4.0 18.2 - - + -
878C TYR* 5.0 6.3 - - + -
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Residues in contact with ALA 827 (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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823C ALA 2.9 21.2 + - - +
824C LYS 3.5 3.8 - - - +
826C VAL* 1.3 77.0 - - - +
828C GLN* 1.3 59.8 + - - +
830C LEU 3.3 0.3 + - - -
831C ASN* 2.8 23.4 + - - -
832C THR* 2.9 36.4 + - - +
834C PRO* 3.6 25.8 - - + -
837C LEU* 3.7 11.4 - - + +
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Residues in contact with GLN 828 (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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824C LYS* 2.7 50.6 + - + +
825C THR* 3.0 9.8 + - - +
827C ALA* 1.3 81.6 - - - +
829C ARG* 1.3 62.1 + - - +
830C LEU 3.0 5.3 + - - -
831C ASN* 3.1 18.3 + - - +
832C THR 4.6 3.3 + - - +
834C PRO* 4.5 3.4 - - - +
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Residues in contact with ARG 829 (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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809C PHE* 3.5 44.4 - - + +
810C VAL 2.7 33.2 + - - +
811C VAL* 3.7 15.7 - - + +
825C THR* 3.0 14.9 + - + +
826C VAL* 3.2 4.7 + - - +
828C GLN* 1.3 76.7 - - - +
830C LEU* 1.3 63.9 + - + +
831C ASN* 3.6 0.7 - - - -
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Residues in contact with LEU 830 (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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809C PHE* 3.5 31.6 - - + -
826C VAL* 2.9 23.4 + - + +
827C ALA 4.0 2.7 - - - +
829C ARG* 1.3 86.6 - - + +
831C ASN* 1.3 72.1 + - - +
832C THR* 3.5 12.1 + - + -
837C LEU* 4.4 4.7 - - + -
878C TYR* 3.4 39.5 - - + +
880C GLN* 3.7 24.8 + - - +
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Residues in contact with ASN 831 (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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827C ALA 2.8 7.8 + - - -
828C GLN* 3.1 13.6 + - - +
829C ARG 3.6 0.9 - - - -
830C LEU* 1.3 82.0 - - - +
832C THR* 1.3 56.4 + - - +
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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