Contacts of the helix formed by residues 826 - 836 (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 LEU 826 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A BME 4.8 1.8 - - - -
697A LEU* 3.9 30.7 - - + -
701A LEU* 5.4 0.2 - - + -
821A GLN* 3.8 1.9 + - - -
824A ASP 3.8 4.0 + - - +
825A CYS* 1.3 74.0 - - - +
827A ASP* 1.3 64.2 + - - +
828A GLU* 4.0 20.2 - - - +
829A LEU* 3.1 22.2 + - + +
830A TYR* 3.1 10.0 + - - +
857A LEU* 4.0 25.1 - - + -
861A LEU* 4.0 19.3 - - + -
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Residues in contact with ASP 827 (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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821A GLN* 2.8 29.4 + - - +
825A CYS 4.1 0.7 - - - +
826A LEU* 1.3 71.2 - - - +
828A GLU* 1.3 64.8 + - - +
830A TYR* 3.3 3.9 + - - +
831A GLU* 2.8 46.7 + - + +
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Residues in contact with GLU 828 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826A LEU* 3.1 24.1 - - + +
827A ASP* 1.3 86.4 + - - +
829A LEU* 1.3 60.2 + - - +
831A GLU* 3.5 19.9 - - - +
832A ILE* 3.3 27.7 + - + +
857A LEU* 3.9 24.2 - - + +
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Residues in contact with LEU 829 (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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3A BME 3.6 31.2 - - - -
697A LEU* 4.6 6.1 - - + -
701A LEU* 3.6 28.9 - - + -
704A MET* 3.8 15.0 - - + -
790A MET* 3.4 30.7 - - + -
794A ALA* 4.5 0.2 - - + -
825A CYS* 4.4 2.2 - - + -
826A LEU* 3.1 17.3 + - + +
828A GLU* 1.3 75.2 - - - +
830A TYR* 1.3 66.1 + - - +
832A ILE* 3.1 14.7 + - + +
833A MET* 3.1 30.2 + - + +
854A LEU* 3.9 4.9 - - + -
857A LEU* 3.9 13.5 - - + +
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Residues in contact with TYR 830 (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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818A ARG* 4.9 0.7 + - - +
819A LEU 2.6 25.6 + - - -
820A LYS* 3.7 3.8 - - - -
821A GLN* 3.4 66.2 + - + -
822A PRO* 4.4 1.1 - - + -
825A CYS* 5.6 1.3 - - + +
826A LEU 3.1 7.6 + - - +
827A ASP* 3.3 6.9 + - - +
829A LEU* 1.3 74.1 - - - +
831A GLU* 1.3 57.7 + - + +
833A MET* 3.3 22.1 + - + +
834A TYR* 2.8 69.2 + + + +
837A TRP* 4.2 13.2 - + - -
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Residues in contact with GLU 831 (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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827A ASP* 2.8 37.4 + - + +
828A GLU* 3.5 21.5 + - - +
830A TYR* 1.3 78.1 - - + +
832A ILE* 1.3 60.9 + - + +
834A TYR* 3.8 5.0 - - - +
835A SER* 3.1 24.1 + - - -
838A ARG* 5.6 0.2 + - - -
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Residues in contact with ILE 832 (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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790A MET* 3.8 18.2 - - + -
828A GLU* 3.3 17.3 - - + +
829A LEU* 3.1 8.1 + - - +
831A GLU* 1.3 74.5 - - + +
833A MET* 1.3 65.3 + - - +
835A SER* 2.8 25.0 + - - -
836A CYS* 3.6 6.6 - - - -
850A LEU* 3.8 21.8 - - + +
853A GLN* 4.0 45.8 - - + +
854A LEU* 4.3 15.5 - - + -
857A LEU* 4.2 18.6 - - + -
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Residues in contact with MET 833 (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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787A GLY* 4.0 3.4 - - - +
790A MET* 3.7 35.9 - - + +
791A TRP* 4.0 27.6 - - - -
794A ALA* 3.7 29.6 - - + -
822A PRO* 4.4 11.0 - - + -
825A CYS* 5.2 2.0 - - + -
829A LEU* 3.1 29.9 + - + +
830A TYR* 3.4 25.8 - - - +
832A ILE* 1.3 77.6 - - - +
834A TYR* 1.3 59.2 + - - +
836A CYS* 3.0 28.3 + - - +
837A TRP* 3.5 22.1 - - + -
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Residues in contact with TYR 834 (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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816A GLY 4.7 6.4 + - - -
818A ARG* 4.1 25.7 - - + +
830A TYR* 2.8 56.2 + + + +
831A GLU* 3.8 6.7 - - - +
833A MET* 1.3 68.8 - - - +
835A SER* 1.3 60.7 + - - +
836A CYS 2.9 4.5 - - - -
837A TRP* 2.8 41.0 + + + +
838A ARG* 3.8 13.2 + - + +
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Residues in contact with SER 835 (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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831A GLU 3.1 14.4 + - - -
832A ILE* 2.8 18.9 + - - -
834A TYR* 1.3 76.1 - - - +
836A CYS* 1.3 59.7 + - - +
837A TRP 3.3 0.7 + - - -
838A ARG* 3.4 54.0 - - - +
844A ARG* 3.5 4.9 - - - +
845A PRO* 3.4 30.1 - - - +
850A LEU* 4.0 2.8 - - - +
853A GLN* 4.9 3.6 + - - -
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Residues in contact with CYS 836 (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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783A VAL* 3.4 36.3 - - - +
784A TRP* 3.2 15.2 + - - +
786A PHE* 4.3 4.3 - - - -
787A GLY* 3.7 20.0 - - - -
790A MET* 4.9 0.9 - - - -
832A ILE 3.6 15.5 - - - -
833A MET* 3.0 14.5 + - - +
834A TYR 2.8 1.0 + - - -
835A SER* 1.3 81.0 + - - +
837A TRP* 1.3 58.5 + - + +
838A ARG 3.6 0.7 - - - -
844A ARG* 3.1 20.3 + - - -
850A LEU* 3.7 25.1 - - - -
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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