Contacts of the helix formed by residues 808 - 821 (chain C) in PDB entry 4OQB
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 SER 808 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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804C VAL* 4.0 7.8 - - - +
805C ASP* 3.2 26.8 + - - +
806C ARG 3.8 0.2 - - - +
807C ASP* 1.3 80.2 - - - +
809C GLU* 1.3 65.8 + - - +
810C GLU* 3.3 21.7 + - - +
811C ALA* 3.4 19.0 + - - +
812C GLU* 3.5 12.5 + - - +
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Residues in contact with GLU 809 (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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807C ASP 4.8 6.0 - - - +
808C SER* 1.3 74.5 + - - +
810C GLU* 1.3 63.9 + - - +
812C GLU* 3.3 38.3 + - - +
813C ILE* 3.6 12.4 - - - +
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Residues in contact with GLU 810 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804C VAL* 4.1 20.0 - - + +
808C SER* 3.3 19.2 + - - +
809C GLU* 1.3 77.3 - - - +
811C ALA* 1.3 64.8 + - - +
813C ILE* 3.2 30.5 + - + +
814C ILE* 3.4 13.8 + - - +
838C LYS* 4.9 8.8 - - - +
964C LEU* 4.9 10.7 - - + +
1001C TYR* 3.0 36.2 + - - +
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Residues in contact with ALA 811 (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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804C VAL* 3.8 14.4 - - + +
805C ASP 3.2 26.9 - - - +
806C ARG* 4.2 1.3 - - - +
808C SER* 3.4 8.9 + - - +
809C GLU 3.3 0.6 - - - -
810C GLU* 1.3 79.5 - - - +
812C GLU* 1.3 63.1 + - - +
814C ILE* 3.4 9.1 + - - +
815C ARG* 3.2 45.1 + - - +
836C ILE* 5.0 7.8 - - + +
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Residues in contact with GLU 812 (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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806C ARG 4.8 1.6 - - - +
807C ASP 5.3 3.3 - - - +
808C SER 3.7 11.4 - - - +
809C GLU* 3.3 30.8 + - - +
810C GLU 3.3 0.4 - - - -
811C ALA* 1.3 75.6 - - - +
813C ILE* 1.3 59.3 + - + +
815C ARG* 3.7 23.9 + - - +
816C LYS* 3.0 29.9 + - - +
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Residues in contact with ILE 813 (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 GLU 3.6 11.2 - - - +
810C GLU* 3.4 21.3 - - + +
811C ALA 3.2 0.6 - - - -
812C GLU* 1.3 76.3 - - + +
814C ILE* 1.3 56.0 + - + +
816C LYS* 3.3 8.7 + - - +
817C TYR* 2.8 31.8 + - + +
962C ILE* 4.7 18.8 - - + -
963C SER 5.0 2.5 - - - +
964C LEU* 4.4 23.1 - - + -
969C VAL* 4.7 15.5 - - + -
971C LEU* 3.5 21.4 - - + +
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Residues in contact with ILE 814 (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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804C VAL* 5.8 0.2 - - + -
810C GLU* 3.4 13.6 + - - +
811C ALA* 3.4 8.4 + - - +
812C GLU 3.4 0.2 - - - -
813C ILE* 1.3 76.5 - - + +
815C ARG* 1.3 54.8 + - - +
817C TYR* 2.9 10.2 + - + +
818C VAL* 2.7 34.8 + - + +
836C ILE* 3.4 49.8 - - + -
859C LEU* 6.2 0.2 - - + -
861C TRP* 4.5 0.4 - - + -
921C LEU* 4.2 14.1 - - + -
1001C TYR* 3.8 38.8 - - + -
1003C LEU* 3.4 22.7 - - + -
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Residues in contact with ARG 815 (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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806C ARG* 3.0 72.1 + - - +
811C ALA* 3.2 31.5 + - - +
812C GLU* 3.7 29.3 + - - +
814C ILE* 1.3 78.4 - - - +
816C LYS* 1.3 56.1 + - - +
818C VAL* 3.8 7.5 - - - +
819C LYS* 3.0 30.5 + - - +
833C VAL* 4.4 27.3 - - + +
836C ILE* 4.9 8.5 - - + +
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Residues in contact with LYS 816 (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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812C GLU 3.0 20.5 + - - +
813C ILE* 3.3 8.1 - - - +
815C ARG* 1.3 75.0 - - - +
817C TYR* 1.3 56.0 + - - +
819C LYS* 4.5 3.1 - - + -
820C ASN* 2.7 66.5 + - - +
962C ILE* 5.9 4.0 - - - +
971C LEU* 4.3 22.4 - - + +
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Residues in contact with TYR 817 (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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813C ILE 2.8 18.5 + - - +
814C ILE* 2.9 11.0 + - + +
816C LYS* 1.3 72.2 - - - +
818C VAL* 1.3 57.1 + - - +
820C ASN* 4.8 0.4 - - - -
821C THR* 2.6 35.4 + - + -
859C LEU* 3.0 27.5 + - + -
860C LEU* 3.9 2.4 - - - -
861C TRP* 3.2 38.4 - + + -
899C ASP* 3.2 33.4 + - - -
921C LEU* 3.6 22.4 - - + -
969C VAL* 4.0 11.4 - - + -
970C PRO* 3.4 27.2 - - + +
971C LEU* 3.5 27.1 - - + +
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Residues in contact with VAL 818 (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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814C ILE 2.7 21.9 + - - +
815C ARG 3.8 4.0 - - - +
817C TYR* 1.3 73.1 - - - +
819C LYS* 1.3 68.4 + - + +
820C ASN 3.4 0.5 + - - -
821C THR 3.7 3.3 + - - -
822C HIS* 4.0 6.6 + - - +
831C LEU* 4.1 25.1 - - + +
832C GLU* 6.0 0.2 - - - -
833C VAL* 3.7 33.4 - - + +
861C TRP* 3.4 25.6 - - + -
901C VAL* 3.4 29.6 - - + +
1003C LEU* 3.7 7.9 - - + -
1005C LEU* 4.9 1.8 - - + -
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Residues in contact with LYS 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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815C ARG 3.0 18.6 + - - +
816C LYS* 3.9 4.0 - - + +
818C VAL* 1.3 80.2 - - - +
820C ASN* 1.3 72.6 + - - +
822C HIS* 4.2 10.7 + - - +
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Residues in contact with ASN 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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816C LYS* 2.7 58.9 + - - +
819C LYS* 1.3 89.4 - - - +
821C THR* 1.3 57.9 + - + +
822C HIS* 3.2 10.1 + - - +
900C MET* 5.0 0.7 - - - +
971C LEU* 3.1 29.5 - - - +
972C GLY* 4.6 1.8 - - - -
973C THR* 3.9 37.3 + - + +
974C GLY 5.2 0.5 + - - -
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Residues in contact with THR 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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817C TYR* 2.6 46.5 + - + +
818C VAL 4.1 3.6 - - - -
819C LYS 3.6 0.2 - - - -
820C ASN* 1.3 74.1 - - + +
822C HIS* 1.3 58.3 + - - +
861C TRP* 3.7 3.8 + - - -
899C ASP 3.8 9.9 - - - +
900C MET* 3.5 28.3 - - + +
901C VAL* 3.1 31.2 + - - +
902C SER 3.8 0.5 + - - -
956C PRO* 4.7 1.6 - - + -
970C PRO 3.9 5.8 - - - +
971C LEU* 4.0 4.9 - - - -
972C GLY 3.8 20.2 - - - +
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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