Contacts of the helix formed by residues 834 - 851 (chain C) in PDB entry 4YZ9
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 834 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832C PHE 3.6 3.0 + - - -
833C TRP* 1.3 78.8 - - - +
835C LEU* 1.3 66.5 + - - +
836C GLU* 3.6 8.6 + - - +
837C LYS* 3.3 20.6 + - - +
838C GLN* 3.1 22.0 + - - +
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Residues in contact with LEU 835 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879A THR* 5.0 3.8 - - - +
880A VAL* 5.0 18.2 - - + -
881A PRO* 6.3 0.7 - - + -
800C HIS* 6.5 0.7 - - + -
801C GLU* 6.2 0.7 - - - +
834C SER* 1.3 75.4 - - - +
836C GLU* 1.3 61.4 + - - +
838C GLN* 3.4 19.3 + - - +
839C LEU* 3.1 20.3 + - - +
926C PRO* 4.3 1.7 - - - +
927C ASP* 3.8 38.1 - - + +
930C VAL* 3.6 25.4 - - + +
931C CYS* 3.7 30.3 - - - -
934C THR* 5.9 0.7 - - - +
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Residues in contact with GLU 836 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834C SER* 3.2 8.1 + - - +
835C LEU* 1.3 79.7 - - - +
837C LYS* 1.3 57.6 + - - +
839C LEU* 3.6 2.4 + - - +
840C GLN* 3.0 31.2 + - + +
926C PRO* 3.4 36.3 - - + +
927C ASP* 4.6 1.7 + - - +
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Residues in contact with LYS 837 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828C LYS* 4.9 13.3 - - - +
833C TRP* 3.5 47.8 - - + +
834C SER* 3.3 21.5 + - - +
836C GLU* 1.3 76.9 - - - +
838C GLN* 1.3 61.0 + - - +
840C GLN* 3.7 5.9 - - + +
841C PHE* 2.9 28.4 + - - +
959C PRO* 3.5 23.8 + - - +
960C TYR* 3.9 24.2 - - + +
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Residues in contact with GLN 838 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800C HIS* 3.0 32.4 + - - -
830C PRO 4.4 8.1 + - - -
833C TRP* 3.5 34.6 + - + -
834C SER 3.1 16.3 + - - +
835C LEU* 3.7 23.3 - - - +
837C LYS* 1.3 76.3 - - - +
839C LEU* 1.3 62.1 + - - +
841C PHE* 3.3 5.8 + - - +
842C PHE* 3.2 29.4 + - + -
930C VAL* 4.2 8.2 - - + +
934C THR* 4.1 9.5 + - - +
941C LEU* 3.8 20.4 - - + +
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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
----------------------------------------------------------
835C LEU 3.1 16.1 + - - +
836C GLU 4.0 4.0 - - - +
838C GLN* 1.3 76.7 - - - +
840C GLN* 1.3 62.1 + - - +
842C PHE* 3.3 7.1 + - + +
843C GLN* 3.1 21.0 + - - +
904C MET* 4.6 14.6 - - + +
908C LYS* 3.7 25.1 - - + +
925C LEU* 3.2 34.1 - - + -
926C PRO* 3.6 19.7 - - + +
929C PHE* 3.6 26.7 - - + -
930C VAL* 3.9 20.1 - - + +
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Residues in contact with GLN 840 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836C GLU* 3.0 22.9 + - + +
837C LYS* 3.7 9.0 - - + +
838C GLN 3.3 0.4 - - - -
839C LEU* 1.3 74.7 - - - +
841C PHE* 1.3 58.3 + - - +
843C GLN* 3.3 38.4 + - - +
844C ASP* 3.0 50.2 + - - +
908C LYS* 4.4 9.9 + - - +
960C TYR* 3.4 15.0 - - + +
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Residues in contact with PHE 841 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833C TRP* 3.8 11.9 - + + -
837C LYS 2.9 16.9 + - - +
838C GLN 3.6 4.0 - - - +
839C LEU 3.3 0.2 - - - -
840C GLN* 1.3 77.2 - - - +
842C PHE* 1.3 62.9 + + - +
844C ASP* 3.3 1.4 + - - +
845C VAL* 2.9 49.0 + - + +
941C LEU* 3.5 30.1 - - + -
944C THR* 3.8 22.9 - - + -
945C TYR* 3.8 25.6 - + + -
948C MET* 4.6 0.2 - - + -
957C PHE* 4.4 3.1 - + - -
960C TYR* 3.4 51.8 + + + -
961C TYR* 3.9 18.6 - + - -
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Residues in contact with PHE 842 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838C GLN* 3.2 21.1 + - + -
839C LEU* 3.3 10.1 + - + +
841C PHE* 1.3 85.1 - + - +
843C GLN* 1.3 61.7 + - - +
845C VAL* 3.3 4.1 + - - +
846C SER* 2.9 24.8 + - - -
901C LEU* 3.4 30.2 - - + +
904C MET* 3.5 34.1 - - + -
905C ARG* 5.7 0.7 - - - -
930C VAL* 4.2 8.5 - - + -
934C THR* 4.1 20.9 - - + -
940C LEU* 4.0 13.7 - - + -
941C LEU* 3.7 50.0 - - + -
944C THR* 4.1 10.1 - - + -
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Residues in contact with GLN 843 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839C LEU 3.1 13.5 + - - +
840C GLN* 3.4 29.2 + - - +
842C PHE* 1.3 76.1 - - - +
844C ASP* 1.3 63.8 + - - +
846C SER* 3.2 2.9 + - - -
847C ASP* 3.1 41.6 + - - +
905C ARG* 4.0 25.1 - - + +
908C LYS* 2.7 41.9 + - + +
909C HIS* 5.2 14.7 + - - -
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Residues in contact with ASP 844 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840C GLN* 3.0 33.1 + - - +
841C PHE 3.3 4.0 + - - +
843C GLN* 1.3 81.2 + - - +
845C VAL* 1.3 62.1 + - - +
847C ASP* 3.8 6.5 + - - +
848C ARG* 3.3 21.7 + - - +
956C LEU* 3.9 36.0 - - + +
957C PHE* 3.7 7.6 - - + -
960C TYR* 2.6 38.5 + - + -
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Residues in contact with VAL 845 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841C PHE* 2.9 51.0 + - + +
842C PHE* 3.7 5.2 - - - +
844C ASP* 1.3 75.9 - - - +
846C SER* 1.3 65.9 + - - +
848C ARG* 3.2 11.6 + - - +
849C ILE* 3.2 19.8 + - + +
862C LEU* 5.0 0.7 - - + -
901C LEU* 3.7 24.0 - - + -
944C THR* 3.7 10.5 - - + -
948C MET* 3.8 24.2 - - + -
957C PHE* 3.7 21.1 - - + -
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Residues in contact with SER 846 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842C PHE 2.9 15.3 + - - -
843C GLN 3.7 4.5 - - - -
845C VAL* 1.3 78.0 - - - +
847C ASP* 1.3 62.1 + - - +
848C ARG 3.4 0.2 + - - -
849C ILE* 3.4 15.4 + - - +
850C GLU* 3.1 24.8 + - - +
898C ARG 5.2 0.3 + - - -
901C LEU* 3.4 30.4 + - - -
902C ARG* 3.5 17.2 - - - +
905C ARG* 3.5 20.9 - - - +
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Residues in contact with ASP 847 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843C GLN* 3.1 34.1 + - - +
844C ASP* 4.1 9.1 - - - +
845C VAL 3.3 0.2 - - - -
846C SER* 1.3 75.3 - - - +
848C ARG* 1.3 64.6 + - - +
849C ILE 3.4 0.5 + - - -
850C GLU* 3.4 17.8 + - - +
851C LYS* 4.3 2.9 + - - +
905C ARG* 3.2 35.5 + - - -
956C LEU* 5.7 3.8 - - + -
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Residues in contact with ARG 848 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844C ASP 3.3 16.7 + - - +
845C VAL 3.2 6.1 + - - +
847C ASP* 1.3 80.5 - - - +
849C ILE* 1.3 61.1 + - + +
850C GLU 3.6 0.3 + - - -
851C LYS* 4.2 7.9 + - - +
852C GLU* 2.6 38.1 + - - +
858C ILE* 3.7 17.6 - - + +
948C MET* 4.2 4.7 - - + -
951C CYS* 3.9 8.4 - - - -
954C GLU* 2.6 42.3 + - - -
956C LEU* 5.0 6.7 - - + +
957C PHE* 3.8 22.7 - - + -
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Residues in contact with ILE 849 (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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845C VAL* 3.2 22.4 + - + +
846C SER* 3.4 15.7 - - - +
848C ARG* 1.3 77.1 - - + +
850C GLU* 1.3 65.7 + - - +
851C LYS 3.3 1.3 - - - -
852C GLU* 3.1 19.2 + - + +
858C ILE* 3.8 28.7 - - + -
859C VAL* 4.4 6.5 - - + +
862C LEU* 3.7 23.8 - - + -
898C ARG* 3.0 53.2 + - + +
901C LEU* 4.8 2.9 - - + -
948C MET* 4.4 14.8 - - + -
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Residues in contact with GLU 850 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846C SER* 3.1 15.3 + - - +
847C ASP* 3.7 14.8 - - - +
848C ARG 3.4 0.8 - - - -
849C ILE* 1.3 76.7 - - - +
851C LYS* 1.3 62.5 + - - +
852C GLU 3.9 2.1 - - - +
898C ARG* 3.3 22.5 + - - +
902C ARG* 2.9 38.6 + - - +
905C ARG* 5.9 2.1 + - - -
906C ASN* 5.7 0.2 - - - +
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Residues in contact with LYS 851 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847C ASP 4.3 3.0 + - - +
848C ARG* 4.2 7.4 + - - +
849C ILE 3.3 0.2 - - - -
850C GLU* 1.3 79.7 - - - +
852C GLU* 1.3 64.5 + - + +
853C SER 3.7 0.5 + - - -
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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