Contacts of the helix formed by residues 826 - 848 (chain C) in PDB entry 6PUO
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 826 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816C VAL* 6.4 0.9 - - - -
820C ASP* 4.6 18.4 - - - -
822C GLN* 5.3 7.2 - - - -
824C VAL 3.2 6.7 + - - -
825C PRO* 1.3 78.4 - - - +
827C TRP* 1.3 64.7 + - - +
828C CYS* 3.3 11.0 - - - -
829C GLU* 3.4 18.3 + - - +
830C CYS* 3.5 9.9 + - - +
886C ARG* 4.0 5.7 - - - +
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Residues in contact with TRP 827 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826C SER* 1.3 73.7 - - - +
828C CYS* 1.3 62.6 + - - +
830C CYS* 3.1 11.5 + - - +
831C ALA* 3.0 24.3 + - - +
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Residues in contact with CYS 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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812C LEU* 4.7 8.0 - - + +
815C TYR* 5.5 8.7 - - - -
816C VAL* 3.7 28.2 - - + +
820C ASP* 5.6 4.5 - - + -
826C SER* 3.3 6.8 - - - -
827C TRP* 1.3 75.8 - - - +
829C GLU* 1.3 60.7 + - - +
831C ALA* 3.2 11.1 + - - +
832C ILE* 3.0 32.4 + - - +
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Residues in contact with GLU 829 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816C VAL* 4.8 7.8 - - + +
825C PRO* 5.2 2.5 - - + -
826C SER* 3.4 22.5 + - - +
827C TRP 3.2 0.2 - - - -
828C CYS* 1.3 78.1 - - - +
830C CYS* 1.3 57.9 + - - +
832C ILE* 3.2 16.6 - - + +
833C TYR* 2.9 28.8 + - - +
886C ARG* 4.7 16.2 - - - +
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Residues in contact with CYS 830 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826C SER 3.5 5.8 + - - +
827C TRP* 3.1 15.1 + - - +
829C GLU* 1.3 78.1 - - - +
831C ALA* 1.3 56.4 + - - +
833C TYR* 3.3 8.1 + - - +
834C LEU* 2.9 37.7 + - + +
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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
----------------------------------------------------------
812C LEU* 5.2 7.6 - - + -
827C TRP 3.0 12.9 + - - +
828C CYS* 3.2 14.1 + - + +
830C CYS* 1.3 76.7 - - - +
832C ILE* 1.3 60.1 + - + +
834C LEU* 3.3 17.6 - - + +
835C TRP* 3.0 34.6 + - + +
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Residues in contact with ILE 832 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809C PHE* 4.1 22.7 - - + -
812C LEU* 3.7 28.5 - - + -
813C PHE* 3.6 41.7 - - + +
816C VAL* 4.1 17.7 - - + -
828C CYS 3.0 11.4 + - - +
829C GLU* 3.2 22.4 - - + +
831C ALA* 1.3 74.7 - - - +
833C TYR* 1.3 57.8 + - - +
835C TRP* 3.5 8.7 - - + +
836C LEU* 3.0 30.1 + - - +
879C PHE* 5.1 9.2 - - + -
899C LEU* 6.0 2.5 - - + -
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Residues in contact with TYR 833 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829C GLU 2.9 19.5 + - - +
830C CYS* 3.5 9.6 - - - +
832C ILE* 1.3 78.6 - - - +
834C LEU* 1.3 58.2 + - - +
836C LEU* 3.4 3.0 + - - +
837C PHE* 2.9 27.8 + - - +
879C PHE* 4.8 15.4 - - + -
883C LEU* 5.3 9.2 - - + -
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Residues in contact with LEU 834 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830C CYS* 2.9 23.1 + - + +
831C ALA* 3.3 20.4 - - + +
833C TYR* 1.3 73.9 - - - +
835C TRP* 1.3 66.5 + - + +
837C PHE* 3.5 17.4 - - + +
838C SER* 2.9 29.5 + - - -
1083C PRO* 5.9 10.1 - - + +
1086C LEU* 5.4 5.4 - - + +
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Residues in contact with TRP 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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805C SER* 3.2 42.9 + - - -
806C TYR* 5.4 1.4 - - - +
808C ALA* 4.7 9.0 - - + -
809C PHE* 3.4 49.9 - + + +
812C LEU* 5.3 13.7 - - + -
831C ALA* 3.0 23.1 + - + +
832C ILE* 3.5 9.4 - - + +
833C TYR 3.2 0.2 - - - -
834C LEU* 1.3 83.8 - - + +
836C LEU* 1.3 58.0 + - - +
838C SER* 2.3 29.5 + - - -
839C LEU* 3.0 18.1 + - + +
1082C PRO* 4.3 8.5 - - + +
1083C PRO* 3.5 30.5 - - + +
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Residues in contact with LEU 836 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809C PHE* 4.6 14.3 - - + -
832C ILE 3.0 17.3 + - - +
833C TYR 3.9 2.9 - - - +
835C TRP* 1.3 77.2 - - - +
837C PHE* 1.3 57.4 + - - +
839C LEU* 3.3 23.0 + - + -
840C VAL* 3.0 40.3 + - + +
876C ILE* 5.4 4.9 - - + -
879C PHE* 3.6 48.7 - - + -
906C PHE* 3.9 36.3 - - + -
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Residues in contact with PHE 837 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833C TYR 2.9 17.7 + - - +
834C LEU* 3.5 16.8 - - + +
835C TRP 3.2 0.2 - - - -
836C LEU* 1.3 77.0 - - - +
838C SER* 1.3 60.7 + - - +
840C VAL* 3.3 14.0 - - + +
841C CYS* 2.9 38.1 + - + +
1086C LEU* 4.2 24.9 - - + -
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Residues in contact with SER 838 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834C LEU* 2.9 12.8 + - - -
835C TRP* 2.3 35.2 + - - -
837C PHE* 1.3 79.4 - - - +
839C LEU* 1.3 61.3 + - - +
841C CYS* 3.2 7.6 + - - +
842C GLU* 3.0 24.9 + - - +
1082C PRO* 3.3 31.8 + - - +
1083C PRO* 4.9 0.7 - - - +
1085C ILE* 4.5 5.4 - - - +
1086C LEU* 3.6 21.8 - - - -
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Residues in contact with LEU 839 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806C TYR* 4.4 26.9 - - + -
809C PHE* 5.3 7.2 - - + -
835C TRP* 3.0 16.7 + - + +
836C LEU* 3.6 28.3 - - + +
837C PHE 3.3 0.2 - - - -
838C SER* 1.3 81.3 + - - +
840C VAL* 1.3 64.5 + - + +
842C GLU* 3.3 7.4 + - - +
843C GLU* 3.0 30.5 + - + +
872C ASP* 6.1 4.7 - - + -
876C ILE* 5.7 5.2 - - + -
906C PHE* 5.3 7.6 - - + -
1082C PRO* 5.4 12.1 - - + -
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Residues in contact with VAL 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 LEU* 3.0 26.8 + - + +
837C PHE* 3.3 24.2 - - + +
839C LEU* 1.3 77.1 - - + +
841C CYS* 1.3 59.8 + - - +
843C GLU* 3.7 7.5 - - + +
844C MET* 2.9 29.8 + - - +
876C ILE* 3.7 43.1 - - + -
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Residues in contact with CYS 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 PHE* 2.9 33.2 + - + +
838C SER* 3.5 7.9 - - - +
839C LEU 3.2 0.2 - - - -
840C VAL* 1.3 76.2 - - - +
842C GLU* 1.3 60.2 + - - +
844C MET* 3.3 20.4 + - + +
845C ARG* 2.9 27.1 + - - +
1086C LEU* 4.4 8.5 - - + -
1089C HIS* 3.5 35.4 - - - -
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Residues in contact with GLU 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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838C SER 3.0 13.5 + - - +
839C LEU* 3.3 9.2 + - - +
841C CYS* 1.3 76.2 - - - +
843C GLU* 1.3 58.7 + - - +
845C ARG* 3.2 21.6 + - - +
846C GLN* 3.0 40.1 + - - +
1077C ARG* 4.4 28.9 + - - +
1078C PRO* 4.4 11.1 - - - +
1085C ILE* 3.7 21.4 - - + +
1089C HIS* 3.4 24.6 + - - +
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Residues in contact with GLU 843 (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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839C LEU* 3.0 21.3 + - + +
840C VAL* 3.7 10.1 - - + +
842C GLU* 1.3 76.5 - - - +
844C MET* 1.3 62.1 - - - +
846C GLN* 3.4 33.1 + - - +
847C LEU* 3.7 23.2 + - + +
863C TYR* 5.9 0.5 - - - +
869C ASN* 5.1 11.6 - - - +
872C ASP* 5.8 8.7 - - + -
873C VAL* 6.1 4.5 - - + -
876C ILE* 5.7 8.3 - - + -
909C ARG* 5.9 1.6 + - - -
1077C ARG* 6.0 0.3 + - - -
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Residues in contact with MET 844 (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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840C VAL 2.9 17.2 + - - +
841C CYS* 3.7 20.4 - - + +
842C GLU 3.3 0.2 - - - -
843C GLU* 1.3 73.9 - - - +
845C ARG* 1.3 70.2 + - - +
847C LEU* 3.2 16.6 + - + +
848C PHE* 3.7 41.7 + - + -
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Residues in contact with ARG 845 (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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841C CYS 2.9 17.5 + - - +
842C GLU* 3.2 24.4 + - - +
844C MET* 1.3 82.5 - - - +
846C GLN* 1.3 68.4 + - - +
847C LEU 3.3 0.7 + - - -
848C PHE* 3.4 14.4 + - - +
849C TYR* 4.0 35.9 + - - +
1076C GLY 3.9 17.0 + - - -
1077C ARG* 4.6 2.4 - - - +
1078C PRO* 3.8 27.6 - - - +
1089C HIS* 3.9 19.1 - - + +
1092C LEU* 3.8 37.7 - - + +
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Residues in contact with GLN 846 (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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842C GLU* 3.0 26.1 + - - +
843C GLU* 3.6 26.7 + - - +
844C MET 3.2 0.8 - - - -
845C ARG* 1.3 85.1 - - - +
847C LEU* 1.3 63.9 + - + +
849C TYR* 4.0 14.4 - - - +
859C LYS* 4.3 6.4 + - - -
1073C GLU* 2.5 43.9 + - + +
1077C ARG* 3.3 19.8 - - - +
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Residues in contact with LEU 847 (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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843C GLU* 3.7 27.1 - - + +
844C MET* 3.2 11.7 + - + +
845C ARG 3.2 1.0 - - - -
846C GLN* 1.3 83.0 - - + +
848C PHE* 1.3 72.7 + - + +
849C TYR 3.2 6.0 + - - -
850C ASP* 4.6 0.7 + - - +
856C LEU* 5.0 5.0 - - - +
859C LYS* 3.3 53.0 + - + +
860C ALA* 4.3 8.1 - - + -
863C TYR* 3.8 32.3 - - + -
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Residues in contact with PHE 848 (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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844C MET* 3.7 42.0 - - + -
845C ARG* 3.4 12.0 + - - +
847C LEU* 1.3 89.5 - - + +
849C TYR* 1.3 59.4 + - - +
850C ASP 3.6 1.6 - - - -
856C LEU* 4.7 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
------------------------------------------------------------
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