Contacts of the helix formed by residues 842 - 853 (chain C) in PDB entry 6AH0
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 CYS 842 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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838C ALA* 6.4 0.7 - - - -
839C PRO 3.1 9.5 + - - -
841C ASP* 1.3 76.3 - - - +
843C VAL* 1.3 63.5 + - - +
844C SER 3.2 2.5 - - - -
845C ALA* 3.1 7.8 + - - +
846C VAL* 3.0 18.9 + - - -
891C THR* 6.1 5.6 - - - +
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Residues in contact with VAL 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 PRO 3.7 5.3 + - - -
840C ALA 3.5 11.9 + - - -
842C CYS* 1.3 77.8 - - - +
844C SER* 1.3 57.2 + - - +
846C VAL* 3.2 2.6 + - - +
847C TYR* 2.9 25.8 + - - -
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Residues in contact with SER 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 ALA 5.0 1.2 + - - -
841C ASP 4.8 2.8 + - - -
842C CYS* 3.2 0.8 - - - +
843C VAL* 1.3 76.6 - - - +
845C ALA* 1.3 56.3 + - - +
847C TYR* 3.2 3.5 + - - +
848C THR* 2.9 25.6 + - - -
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Residues in contact with ALA 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 ASP 5.4 0.6 + - - -
842C CYS* 3.1 10.0 + - - +
844C SER* 1.3 75.1 - - - +
846C VAL* 1.3 63.0 + - - +
848C THR* 3.2 2.8 + - - +
849C VAL* 3.0 19.9 + - - -
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Residues in contact with VAL 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 CYS 3.0 12.7 + - - -
843C VAL* 3.2 4.8 + - - +
845C ALA* 1.3 74.8 - - - +
847C TYR* 1.3 63.0 + - - +
849C VAL* 3.2 2.8 + - - +
850C LEU* 3.0 19.4 + - - -
887C LEU* 6.4 1.6 - - - +
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Residues in contact with TYR 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 VAL 2.9 13.6 + - - -
844C SER* 3.2 4.0 + - - +
846C VAL* 1.3 76.5 - - - +
848C THR* 1.3 56.1 + - - +
850C LEU* 3.2 2.9 + - - +
851C ALA* 2.9 26.2 + - - -
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Residues in contact with THR 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 SER 2.9 14.1 + - - -
845C ALA* 3.2 3.8 + - - +
847C TYR* 1.3 76.8 - - - +
849C VAL* 1.3 61.2 + - - +
851C ALA* 3.2 2.9 + - - +
852C ARG* 2.9 20.8 + - - -
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Residues in contact with VAL 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 ALA 3.0 13.8 + - - -
846C VAL 3.2 2.9 + - - -
848C THR* 1.3 75.9 - - - +
850C LEU* 1.3 64.0 - - - +
852C ARG* 3.2 3.5 + - - +
853C ARG* 3.0 19.2 + - - -
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Residues in contact with LEU 850 (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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846C VAL 3.0 13.8 + - - -
847C TYR* 3.7 3.1 - - - +
849C VAL* 1.3 77.9 - - - +
851C ALA* 1.3 59.4 + - - +
853C ARG* 3.2 7.8 + - - +
855C GLY* 2.9 34.2 + - - -
856C HIS 4.8 3.6 - - - +
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Residues in contact with ALA 851 (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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847C TYR 2.9 14.7 + - - -
848C THR* 3.7 2.9 - - - +
850C LEU* 1.3 77.7 - - - +
852C ARG* 1.3 62.0 + - - +
853C ARG 3.4 0.3 + - - -
854C ARG* 3.5 9.0 + - - -
855C GLY 4.8 1.8 - - - +
856C HIS 5.5 1.3 - - - +
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Residues in contact with ARG 852 (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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848C THR 2.9 14.1 + - - -
849C VAL* 3.2 4.9 + - - +
851C ALA* 1.3 77.2 - - - +
853C ARG* 1.3 58.0 + - - +
854C ARG 3.6 0.5 + - - -
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Residues in contact with ARG 853 (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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849C VAL 3.0 13.4 + - - -
850C LEU* 3.2 2.8 + - - +
852C ARG* 1.3 76.6 - - - +
854C ARG* 1.3 60.2 + - - +
855C GLY* 3.6 2.4 - - - -
875C ILE* 5.9 0.3 - - - -
876C PRO* 5.3 4.5 - - - +
879C ASP* 4.5 24.1 - - - +
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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