Contacts of the helix formed by residues 843 - 857 (chain A) in PDB entry 4D86
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 PRO 843 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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838A SER* 5.9 0.4 - - - +
842A GLY* 1.3 81.5 - - - +
844A GLU* 1.3 63.3 + - - +
845A LEU 3.2 0.8 + - - -
846A GLN* 3.6 8.2 + - + +
847A ALA* 3.0 25.7 + - + +
871A LYS* 5.1 7.6 - - - +
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Residues in contact with GLU 844 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841A ALA 4.9 0.9 - - - +
842A GLY 3.1 1.4 + - - -
843A PRO* 1.3 79.6 - - - +
845A LEU* 1.3 57.7 + - - +
847A ALA* 3.7 6.9 - - + +
848A ASP* 2.9 32.2 + - + +
868A LYS* 5.4 14.7 - - + +
870A GLY* 3.7 31.1 + - - +
871A LYS* 6.0 2.1 - - - +
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Residues in contact with LEU 845 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821A ASN* 5.7 0.4 - - - +
829A HIS* 4.1 17.3 - - + +
837A LEU* 4.2 11.4 - - + -
838A SER* 3.7 30.3 - - - +
841A ALA* 3.7 24.2 - - + -
842A GLY 3.4 4.7 + - - +
843A PRO 3.2 1.0 - - - -
844A GLU* 1.3 81.2 - - - +
846A GLN* 1.3 64.2 + - - +
848A ASP* 3.3 1.7 + - - +
849A CYS* 3.1 24.0 + - - -
867A SER* 3.4 13.2 - - - +
868A LYS 3.2 27.4 - - - +
869A ALA* 4.5 2.9 - - - -
870A GLY* 4.6 1.7 - - - +
872A LEU* 4.9 4.3 - - + -
877A VAL* 4.4 9.9 - - + -
879A HIS* 3.8 17.3 - - + +
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Residues in contact with GLN 846 (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 LEU 3.0 21.6 + - - -
828A LYS* 3.7 14.4 - - - +
829A HIS* 3.0 39.6 + - - +
838A SER* 4.5 11.6 + - - +
842A GLY 4.5 1.0 + - - -
843A PRO* 3.6 10.3 + - + +
845A LEU* 1.3 79.5 - - - +
847A ALA* 1.3 57.4 + - - +
849A CYS* 3.4 4.2 + - - +
850A ASP* 2.8 61.5 + - - +
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Residues in contact with ALA 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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843A PRO* 3.0 20.8 + - + +
844A GLU* 3.7 9.0 - - + +
845A LEU 3.2 0.4 - - - -
846A GLN* 1.3 77.2 - - - +
848A ASP* 1.3 61.7 + - - +
850A ASP* 3.4 10.1 + - - +
851A GLN* 3.2 21.5 + - - +
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Residues in contact with ASP 848 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844A GLU* 2.9 18.5 + - + +
845A LEU* 4.0 2.7 - - - +
847A ALA* 1.3 75.7 - - - +
849A CYS* 1.3 58.1 + - - +
851A GLN* 3.2 16.8 + - - +
852A ILE* 2.9 34.8 + - - +
855A ARG* 5.2 2.8 + - - -
867A SER* 3.4 10.4 - - - -
868A LYS* 2.9 66.6 + - + +
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Residues in contact with CYS 849 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826A ASP 5.4 0.2 - - - -
827A LEU* 3.7 32.9 - - + +
829A HIS* 3.4 17.3 - - - -
845A LEU* 3.1 18.9 + - - +
846A GLN* 3.6 5.8 - - - +
848A ASP* 1.3 74.0 - - - +
850A ASP* 1.3 64.4 + - - +
852A ILE* 3.3 4.9 + - - +
853A VAL* 3.0 29.5 + - - +
867A SER* 3.8 9.0 - - - -
879A HIS* 3.3 35.2 - - - -
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Residues in contact with ASP 850 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826A ASP 5.0 0.3 - - - +
828A LYS* 2.9 28.3 + - - +
846A GLN* 2.8 50.6 + - - +
847A ALA* 3.6 9.0 - - - +
848A ASP 3.3 0.2 - - - -
849A CYS* 1.3 72.3 - - - +
851A GLN* 1.3 58.2 + - - +
853A VAL* 3.4 6.2 + - - +
854A LYS* 3.0 28.9 + - - +
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Residues in contact with GLN 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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847A ALA 3.2 11.1 + - - +
848A ASP* 3.2 18.1 + - - +
850A ASP* 1.3 77.1 - - - +
852A ILE* 1.3 59.3 + - - +
854A LYS* 3.3 10.3 + - + +
855A ARG* 2.9 62.5 + - + +
868A LYS* 5.7 3.0 - - - +
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Residues in contact with ILE 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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827A LEU* 4.1 18.4 - - + -
848A ASP* 2.9 24.9 + - - +
849A CYS* 3.3 10.5 + - - +
851A GLN* 1.3 75.7 - - - +
853A VAL* 1.3 60.0 + - - +
855A ARG* 3.3 22.4 + - - +
856A GLU* 2.9 41.9 + - + +
857A GLY 5.8 0.2 - - - +
859A LEU* 5.3 4.7 - - + -
865A THR* 4.2 15.5 - - + +
866A ILE 3.3 27.4 - - - +
867A SER* 3.7 21.8 - - - -
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Residues in contact with VAL 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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825A GLU 4.5 3.8 - - - +
826A ASP* 3.5 36.3 - - + +
827A LEU* 3.9 14.8 - - + -
849A CYS 3.0 20.8 + - - +
850A ASP* 3.8 5.8 - - - +
852A ILE* 1.3 76.2 - - - +
854A LYS* 1.3 57.7 + - - +
857A GLY* 2.7 39.1 + - - +
858A ARG* 4.1 26.7 - - + +
859A LEU* 4.6 2.2 - - + -
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Residues in contact with LYS 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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850A ASP 3.0 18.7 + - - +
851A GLN* 3.6 10.3 - - + +
852A ILE 3.2 0.2 - - - -
853A VAL* 1.3 79.8 - - - +
855A ARG* 1.3 62.3 + - + +
857A GLY* 4.4 1.4 + - - -
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Residues in contact with ARG 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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848A ASP* 5.2 3.2 + - - -
851A GLN* 2.9 58.4 + - + +
852A ILE* 3.9 22.6 - - - +
854A LYS* 1.3 80.5 - - + +
856A GLU* 1.3 87.8 + - - +
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Residues in contact with GLU 856 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852A ILE* 2.9 23.7 + - + +
855A ARG* 1.3 109.5 + - - +
857A GLY* 1.3 64.0 + - - +
858A ARG 4.9 0.9 - - - +
1098A ARG* 5.2 13.7 - - - +
1102A THR* 5.8 3.6 - - - -
1103A SER* 5.5 2.3 + - - -
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Residues in contact with GLY 857 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852A ILE* 4.5 0.7 - - - +
853A VAL* 2.7 34.6 + - - +
854A LYS 4.4 1.6 + - - -
855A ARG 3.6 1.4 - - - -
856A GLU* 1.3 77.9 - - - +
858A ARG* 1.3 68.4 + - - +
859A LEU* 3.7 8.3 + - - +
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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