Contacts of the helix formed by residues 905 - 920 (chain B) in PDB entry 6AHU
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 ARG 905 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286A G 3.9 20.8 + - - -
287A A 5.2 7.1 + - - -
301A G 4.4 18.1 + - - +
302A G 5.6 6.0 + - - +
902B ASP* 3.7 23.1 + - + +
903B PRO 3.2 1.2 - - - -
904B PHE* 1.3 76.7 - - - +
906B SER* 1.3 65.0 + - - +
908B ILE* 3.2 24.8 + - + +
909B LEU* 3.9 24.3 + - - +
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Residues in contact with SER 906 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A G 4.2 31.5 + - - -
301A G 4.5 9.5 + - - -
903B PRO 4.0 9.9 + - - -
904B PHE 3.3 0.8 - - - -
905B ARG* 1.3 81.4 - - - +
907B LYS* 1.3 61.2 + - - +
908B ILE 3.3 0.9 + - - -
909B LEU* 4.1 5.0 + - - +
910B LYS* 3.6 17.3 + - - +
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Residues in contact with LYS 907 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903B PRO 5.3 3.8 - - - +
904B PHE* 3.6 32.5 + - + +
905B ARG 3.2 0.6 - - - -
906B SER* 1.3 77.6 - - - +
908B ILE* 1.3 63.6 + - + +
910B LYS* 3.8 13.1 - - + +
911B GLN* 3.2 24.4 + - - +
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Residues in contact with ILE 908 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904B PHE* 3.3 21.3 - - + +
905B ARG* 3.2 17.3 + - + +
907B LYS* 1.3 80.3 - - + +
909B LEU* 1.3 63.4 + - + +
910B LYS 3.2 0.9 - - - -
911B GLN* 3.1 7.7 + - + +
912B LYS* 2.9 55.4 + - + +
943B LEU 3.4 20.0 - - - +
944B THR* 3.3 34.3 - - + +
945B LEU* 5.7 4.9 - - + -
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Residues in contact with LEU 909 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905B ARG* 3.9 25.2 + - - +
906B SER* 4.1 6.2 + - - +
908B ILE* 1.3 77.8 - - + +
910B LYS* 1.3 62.7 + - - +
912B LYS* 4.0 19.5 - - + +
913B GLU* 3.3 45.3 + - + +
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Residues in contact with LYS 910 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906B SER 3.6 18.8 + - - +
907B LYS* 3.8 12.1 - - + +
908B ILE 3.2 0.2 - - - -
909B LEU* 1.3 79.5 - - - +
911B GLN* 1.3 56.5 + - - +
913B GLU* 4.4 2.0 - - - +
914B LYS* 3.3 35.3 + - + +
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Residues in contact with GLN 911 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907B LYS 3.2 17.5 + - - +
908B ILE* 3.1 9.7 + - + +
910B LYS* 1.3 77.2 - - - +
912B LYS* 1.3 61.7 + - + +
914B LYS* 3.5 10.6 + - - +
915B LYS* 3.1 39.2 + - + +
918B GLU* 5.8 1.4 + - - -
941B GLU* 5.0 15.3 + - - +
943B LEU 6.1 0.7 - - - +
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Residues in contact with LYS 912 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A G 5.1 8.5 + - - -
330A C 5.0 4.9 + - - -
331A C 4.1 21.9 + - - +
908B ILE* 2.9 40.8 + - + +
909B LEU* 4.5 19.0 - - + +
911B GLN* 1.3 78.4 - - + +
913B GLU* 1.3 63.9 + - + +
915B LYS* 3.4 7.4 + - - +
916B LYS* 3.3 26.5 + - - +
944B THR* 5.6 7.5 - - - +
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Residues in contact with GLU 913 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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909B LEU* 3.3 32.1 + - + +
910B LYS* 4.7 1.8 - - - +
912B LYS* 1.3 78.2 - - + +
914B LYS* 1.3 60.5 + - - +
916B LYS* 3.5 18.9 - - + +
917B ARG* 3.4 22.9 + - - +
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Residues in contact with LYS 914 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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910B LYS* 3.3 32.2 + - + +
911B GLN* 3.5 13.9 + - - +
912B LYS 3.3 0.4 - - - -
913B GLU* 1.3 76.7 - - - +
915B LYS* 1.3 65.1 + - - +
917B ARG* 3.3 6.8 + - + +
918B GLU* 3.2 35.5 + - + +
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Residues in contact with LYS 915 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A C 4.5 3.4 + - - -
332A U 3.3 29.9 + - - +
911B GLN* 3.1 28.7 + - + +
912B LYS* 3.4 7.8 + - - +
914B LYS* 1.3 78.3 - - - +
916B LYS* 1.3 60.9 + - - +
918B GLU* 3.4 22.0 - - - +
919B LYS* 3.3 46.8 - - - +
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Residues in contact with LYS 916 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A A 3.3 75.5 + - + +
4A G 2.5 32.4 + - - -
912B LYS 3.3 17.1 + - - +
913B GLU* 3.5 21.8 - - + +
915B LYS* 1.3 77.8 - - - +
917B ARG* 1.3 66.9 + - + +
919B LYS* 4.1 1.6 - - - -
920B ARG* 3.7 12.6 + - - +
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Residues in contact with ARG 917 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A U 3.4 23.0 + - - -
3A A 2.9 41.1 + - - -
913B GLU 3.4 16.8 + - - +
914B LYS* 3.3 10.0 + - + +
915B LYS 3.2 0.8 - - - -
916B LYS* 1.3 84.9 - - - +
918B GLU* 1.3 62.4 + - - +
919B LYS 3.2 1.1 + - - -
920B ARG 3.8 15.9 + - - +
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Residues in contact with GLU 918 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911B GLN* 5.8 1.0 + - - -
914B LYS* 3.2 24.1 + - + +
915B LYS* 3.4 29.3 - - - +
917B ARG* 1.3 76.1 - - - +
919B LYS* 1.3 63.6 + - + +
920B ARG 4.6 2.0 - - - +
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Residues in contact with LYS 919 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A A 4.1 20.6 - - - +
332A U 3.6 17.6 + - - -
333A C 3.8 28.8 + - - +
915B LYS* 3.3 52.5 + - - +
916B LYS 4.4 3.1 - - - +
917B ARG 3.2 0.4 - - - -
918B GLU* 1.3 84.2 - - + +
920B ARG* 1.3 64.9 + - - +
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Residues in contact with ARG 920 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A A 4.6 18.9 + - - -
2A U 3.2 50.6 + - - +
3A A 3.4 59.8 + - + +
335A G 5.4 5.7 + - - -
916B LYS 3.7 7.1 + - - +
917B ARG* 3.8 13.8 - - - +
918B GLU 4.6 1.4 - - - +
919B LYS* 1.3 83.4 - - - +
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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