Contacts of the helix formed by residues 846 - 860 (chain A) in PDB entry 2P0C
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 THR 846 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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715A SER* 5.9 2.2 - - - -
780A LYS* 3.9 16.8 - - - +
783A VAL* 4.8 2.2 - - - -
845A PRO* 1.3 77.8 - - - +
847A PHE* 1.3 59.3 + - - +
848A SER* 3.0 23.2 + - - -
849A VAL* 3.2 18.1 + - + +
850A LEU* 3.0 28.0 + - - +
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Residues in contact with PHE 847 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708A ALA* 4.1 9.4 - - + +
711A MET* 3.5 53.2 - - + -
712A GLU* 3.7 22.0 - - - +
715A SER* 4.1 17.5 + - - -
724A LEU* 4.8 0.2 - - + -
779A SER* 4.1 5.6 - - - -
782A ASP* 3.7 15.5 - - + -
783A VAL* 3.6 36.3 - - + +
786A PHE* 3.5 32.5 - + + -
846A THR* 1.3 71.0 - - - +
848A SER* 1.3 59.1 + - - +
850A LEU* 3.8 12.5 - - + +
851A ARG* 2.8 34.1 + - - +
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Residues in contact with SER 848 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A GLU* 3.4 33.3 - - - +
716A ASN* 5.9 1.8 - - - -
846A THR* 3.0 17.3 + - - -
847A PHE* 1.3 78.8 - - - +
849A VAL* 1.3 60.9 + - - +
851A ARG* 3.9 8.2 + - - +
852A LEU* 3.4 22.3 + - - +
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Residues in contact with VAL 849 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845A PRO* 3.8 17.9 - - + -
846A THR* 3.2 26.1 + - - +
848A SER* 1.3 76.5 + - - +
850A LEU* 1.3 66.7 + - - +
852A LEU* 3.2 6.5 + - - +
853A GLN* 2.9 46.5 + - + +
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Residues in contact with LEU 850 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708A ALA* 5.1 0.4 - - + -
783A VAL* 3.8 24.9 - - + -
786A PHE* 3.8 33.4 - - + -
832A ILE* 3.8 21.5 - - + -
835A SER* 4.0 2.7 - - - +
836A CYS* 3.7 16.8 - - - -
845A PRO* 3.5 21.3 - - + -
846A THR 3.0 22.1 + - - +
847A PHE* 3.8 17.3 - - + +
849A VAL* 1.3 74.8 - - - +
851A ARG* 1.3 64.8 + - - +
853A GLN* 3.1 12.6 + - - +
854A LEU* 3.0 30.5 + - + +
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Residues in contact with ARG 851 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705A VAL* 4.6 3.4 - - + +
708A ALA* 3.9 16.5 - - + +
709A LEU* 3.5 35.5 - - + +
712A GLU* 2.8 41.1 + - - +
847A PHE 2.8 22.5 + - - +
848A SER* 3.9 13.7 + - - +
850A LEU* 1.3 74.8 - - - +
852A LEU* 1.3 74.8 + - - +
854A LEU* 3.4 3.8 + - - +
855A GLU* 2.8 73.5 + - + +
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Residues in contact with LEU 852 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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848A SER 3.4 13.6 + - - +
849A VAL* 3.2 6.8 + - - +
851A ARG* 1.3 88.0 - - - +
853A GLN* 1.3 60.8 + - + +
855A GLU* 3.4 18.1 + - + +
856A LYS* 3.0 45.4 + - + +
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Residues in contact with GLN 853 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832A ILE* 4.0 28.6 - - + +
835A SER* 4.9 5.0 + - - -
845A PRO* 4.9 1.9 - - - +
849A VAL* 2.9 33.9 + - + +
850A LEU* 3.1 30.3 + - - +
852A LEU* 1.3 76.3 - - + +
854A LEU* 1.3 56.5 + - - +
856A LYS* 3.7 4.1 + - - +
857A LEU* 3.0 27.5 + - - +
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Residues in contact with LEU 854 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701A LEU* 3.8 27.6 - - + +
704A MET* 4.0 18.8 - - + +
705A VAL* 3.8 17.6 - - + +
708A ALA* 4.3 5.6 - - + -
786A PHE* 3.6 36.8 - - + -
790A MET* 3.6 24.9 - - + -
829A LEU* 3.9 3.8 - - + -
832A ILE* 4.3 12.6 - - + -
850A LEU 3.0 18.9 + - - +
851A ARG 3.9 1.8 - - - +
853A GLN* 1.3 74.8 - - - +
855A GLU* 1.3 61.3 + - - +
857A LEU* 3.5 4.8 + - + +
858A LEU* 2.9 30.0 + - - +
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Residues in contact with GLU 855 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705A VAL* 4.0 26.8 - - + +
709A LEU* 4.6 7.6 - - - +
851A ARG* 2.8 58.0 + - - +
852A LEU* 3.7 13.4 - - + +
854A LEU* 1.3 76.7 - - - +
856A LYS* 1.3 57.7 + - + +
858A LEU* 3.4 6.9 + - + +
859A GLU* 2.9 32.2 + - - +
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Residues in contact with LYS 856 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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852A LEU* 3.0 35.4 + - + +
853A GLN* 4.2 4.3 - - - +
855A GLU* 1.3 73.7 - - + +
857A LEU* 1.3 65.1 + - - +
859A GLU* 3.4 18.8 + - - +
860A SER* 3.1 22.9 + - - -
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Residues in contact with LEU 857 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701A LEU* 4.0 26.0 - - + -
826A LEU* 4.0 18.6 - - + -
828A GLU* 3.9 25.1 - - + +
829A LEU* 3.9 36.6 - - + +
832A ILE* 4.2 11.0 - - + -
853A GLN 3.0 20.4 + - - +
854A LEU* 3.8 5.6 - - + +
856A LYS* 1.3 76.8 - - - +
858A LEU* 1.3 62.5 + - - +
860A SER* 2.8 31.5 + - - +
861A LEU* 3.5 8.2 + - + +
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Residues in contact with LEU 858 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698A GLN* 3.6 39.0 - - + +
701A LEU* 4.1 17.0 - - + +
702A LYS* 4.3 35.4 - - + +
705A VAL* 4.6 10.1 - - + -
854A LEU 2.9 18.2 + - - +
855A GLU* 3.8 6.3 - - + +
857A LEU* 1.3 76.0 - - - +
859A GLU* 1.3 63.2 + - - +
861A LEU* 3.3 19.4 + - + +
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Residues in contact with GLU 859 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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855A GLU 2.9 19.8 + - - +
856A LYS* 3.5 20.7 - - - +
858A LEU* 1.3 77.4 - - - +
860A SER* 1.3 59.7 + - - +
861A LEU* 3.2 4.1 + - - -
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Residues in contact with SER 860 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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856A LYS 3.1 14.2 + - - -
857A LEU* 2.8 30.3 + - - +
859A GLU* 1.3 75.2 - - - +
861A LEU* 1.3 63.1 + - - +
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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