Contacts of the helix formed by residues 822 - 842 (chain C) in PDB entry 6CIM
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 822 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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820C ASN 3.5 4.1 + - - -
821C ALA* 1.3 76.3 - - - +
823C LYS* 1.3 66.9 + - - +
824C GLU* 3.6 11.8 + - - +
825C GLU* 3.4 25.4 + - - +
826C ARG* 3.3 23.2 + - - +
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Residues in contact with LYS 823 (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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822C SER* 1.3 75.9 - - - +
824C GLU* 1.3 64.1 + - + +
826C ARG* 3.4 9.0 + - - +
827C LYS* 2.9 37.9 + - - +
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Residues in contact with GLU 824 (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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822C SER* 3.3 7.5 + - - +
823C LYS* 1.3 79.9 - - + +
825C GLU* 1.3 59.8 + - + +
827C LYS* 3.2 15.4 + - + +
828C ARG* 2.9 42.9 + - + +
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Residues in contact with GLU 825 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818C HIS* 5.3 8.0 - - - -
821C ALA* 3.5 13.7 - - - +
822C SER* 3.4 32.8 + - - +
823C LYS 3.3 0.4 - - - -
824C GLU* 1.3 78.5 - - + +
826C ARG* 1.3 57.7 + - - +
828C ARG* 3.2 33.2 + - - +
829C TRP* 2.9 48.9 + - + +
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Residues in contact with ARG 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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806C LYS* 5.9 7.4 - - - +
809C GLN* 4.0 10.7 - - - +
810C LEU* 3.9 14.9 - - + +
815C VAL* 3.5 29.6 - - - +
818C HIS 4.3 0.2 + - - -
819C PRO 3.9 18.0 + - - -
821C ALA* 3.4 30.2 + - + +
822C SER 3.3 12.8 + - - +
823C LYS* 3.8 8.5 - - - +
825C GLU* 1.3 75.0 - - - +
827C LYS* 1.3 58.1 + - - +
829C TRP* 3.2 30.1 + - + +
830C GLN* 2.9 28.1 + - - +
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Residues in contact with LYS 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 LYS* 2.9 24.1 + - - +
824C GLU* 3.4 21.1 - - + +
825C GLU 3.2 0.2 - - - -
826C ARG* 1.3 76.0 - - - +
828C ARG* 1.3 58.5 + - + +
830C GLN* 3.3 15.3 + - + +
831C ALA* 2.9 26.5 + - - +
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Residues in contact with ARG 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 GLU* 2.9 28.3 + - + +
825C GLU* 3.2 43.5 + - - +
827C LYS* 1.3 73.3 - - + +
829C TRP* 1.3 66.7 + - + +
831C ALA* 3.3 7.4 + - + +
832C THR* 2.9 33.9 + - - +
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Residues in contact with TRP 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 GLN* 3.7 19.9 - - + +
810C LEU* 4.0 25.1 - - + -
812C ILE* 4.1 7.6 - - + +
813C GLY* 3.3 41.9 + - - +
815C VAL* 4.0 20.4 - - + -
818C HIS* 4.6 9.6 - + + -
821C ALA* 3.5 29.4 - - + -
825C GLU* 2.9 39.9 + - + +
826C ARG* 3.2 30.9 + - + +
828C ARG* 1.3 82.8 - - + +
830C GLN* 1.3 62.9 + - - +
832C THR* 3.2 8.5 + - - -
833C LEU* 3.0 22.5 + - - +
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Residues in contact with GLN 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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805C TYR* 3.5 27.0 + - + +
809C GLN* 3.7 33.3 + - - +
826C ARG 2.9 12.4 + - - +
827C LYS* 3.6 17.2 - - - +
829C TRP* 1.3 77.1 - - - +
831C ALA* 1.3 58.3 + - - +
833C LEU* 3.3 3.0 + - - +
834C ASP* 2.9 43.5 + - - +
846C ILE 5.4 4.8 + - - -
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Residues in contact with ALA 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 LYS* 2.9 17.1 + - + +
828C ARG* 3.6 9.6 - - + +
830C GLN* 1.3 72.3 - - - +
832C THR* 1.3 61.1 + - - +
834C ASP* 3.7 9.0 - - - +
835C LYS* 2.9 49.2 + - + +
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Residues in contact with THR 832 (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 ILE* 3.9 21.1 - - + -
828C ARG* 2.9 17.5 + - - +
829C TRP* 3.4 10.0 - - - -
831C ALA* 1.3 76.2 - - - +
833C LEU* 1.3 63.4 + - - +
835C LYS* 3.3 13.8 + - - +
836C HIS* 3.0 23.7 + - - +
869C LEU* 4.4 20.6 - - + -
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Residues in contact with LEU 833 (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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805C TYR* 4.0 25.6 - - + +
808C PHE* 3.6 9.6 - - + -
809C GLN* 3.6 33.2 - - + +
812C ILE* 3.6 28.0 - - + -
829C TRP 3.0 11.2 + - - +
830C GLN 3.7 7.6 - - - +
832C THR* 1.3 77.4 - - - +
834C ASP* 1.3 59.2 + - - +
836C HIS 3.9 0.2 - - - -
837C LEU* 2.9 52.8 + - + +
866C VAL* 3.8 24.5 - - + -
869C LEU* 4.7 4.3 - - + -
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Residues in contact with ASP 834 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805C TYR* 2.9 30.1 + - - -
830C GLN* 2.9 37.8 + - - +
831C ALA* 3.7 8.0 - - - +
833C LEU* 1.3 78.0 - - - +
835C LYS* 1.3 62.4 + - + +
837C LEU* 3.3 5.5 + - - +
838C ARG* 2.9 25.3 + - - +
843C LEU 4.3 3.3 - - - +
845C PRO* 3.6 37.3 - - + +
846C ILE 5.4 0.5 + - - +
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Residues in contact with LYS 835 (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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828C ARG 5.8 0.2 + - - -
831C ALA* 2.9 37.1 + - + +
832C THR* 3.7 12.3 + - - +
834C ASP* 1.3 75.3 - - - +
836C HIS* 1.3 59.5 + - - +
838C ARG* 3.2 13.0 + - - +
839C LYS* 2.9 26.7 + - - +
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Residues in contact with HIS 836 (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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832C THR* 3.0 11.9 + - + +
833C LEU 4.2 1.1 - - - +
835C LYS* 1.3 76.4 - - - +
837C LEU* 1.3 58.9 + - + +
839C LYS* 3.2 16.1 + - + +
840C ARG* 2.9 72.9 + - + +
865C ALA* 3.4 28.8 + - + -
866C VAL* 6.2 0.4 - - + -
868C GLU* 3.7 17.5 + - + +
869C LEU* 3.4 44.1 - - + +
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Residues in contact with LEU 837 (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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805C TYR* 5.2 8.3 - - + -
808C PHE* 5.5 0.4 - - + -
833C LEU* 2.9 45.6 + - + +
834C ASP* 3.8 5.6 - - - +
836C HIS* 1.3 74.8 - - + +
838C ARG* 1.3 62.4 + - - +
840C ARG* 5.1 0.4 - - - -
841C MET* 2.9 36.8 + - + +
842C ASN 3.1 5.7 + - - -
843C LEU* 3.3 34.1 + - + +
857C LEU* 3.8 14.1 - - + -
862C THR* 3.7 28.0 - - + +
865C ALA* 4.8 7.6 - - + -
866C VAL* 4.0 13.2 - - + -
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Residues in contact with ARG 838 (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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834C ASP 2.9 14.4 + - - +
835C LYS* 3.2 14.3 + - - +
837C LEU* 1.3 77.9 - - - +
839C LYS* 1.3 61.7 + - - +
842C ASN* 3.2 25.5 + - - +
843C LEU 3.6 19.6 + - - +
844C LYS* 3.2 38.5 - - - +
845C PRO* 3.1 32.6 - - - +
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Residues in contact with LYS 839 (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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835C LYS 2.9 16.1 + - - +
836C HIS* 3.2 17.6 + - + +
838C ARG* 1.3 80.7 - - - +
840C ARG* 1.3 85.7 + - + +
842C ASN 4.7 0.3 + - - -
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Residues in contact with ARG 840 (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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836C HIS* 2.9 49.9 + - + +
837C LEU* 5.1 0.2 - - - -
839C LYS* 1.3 104.0 - - - +
841C MET* 1.3 60.2 + - - +
842C ASN 3.5 0.2 - - - -
865C ALA* 4.1 19.2 - - + +
868C GLU* 3.2 33.7 + - - -
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Residues in contact with MET 841 (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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837C LEU* 2.9 29.2 + - + +
840C ARG* 1.3 74.7 - - + +
842C ASN* 1.3 71.8 + - - +
843C LEU* 4.3 7.9 - - + +
856C LYS 6.0 0.7 - - - +
861C GLU* 6.5 0.7 - - - -
862C THR* 5.1 12.1 - - + +
865C ALA* 5.5 4.7 - - + -
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Residues in contact with ASN 842 (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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837C LEU 3.1 2.8 + - - -
838C ARG* 3.2 23.0 + - - +
839C LYS 4.5 0.6 - - - +
840C ARG 3.5 2.0 - - - +
841C MET* 1.3 79.9 - - - +
843C LEU* 1.3 58.6 + - - +
844C LYS* 4.0 22.4 + - - +
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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