Contacts of the helix formed by residues 841 - 855 (chain N) 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 PRO 841 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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840N ASP* 1.3 74.6 - - - +
842N HIS* 1.3 53.8 + - - +
843N VAL 3.1 3.0 - - - -
844N LEU* 2.7 10.9 + - - -
845N LEU* 2.7 31.9 + - - -
873N ASP* 5.9 7.0 - - - +
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Residues in contact with HIS 842 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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815N SER* 5.3 6.8 - - - -
841N PRO* 1.3 74.3 - - - +
843N VAL* 1.3 56.0 + - - +
845N LEU* 3.7 3.6 - - - +
846N ALA* 2.8 25.2 + - - +
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Residues in contact with VAL 843 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811N GLY 5.5 3.2 + - - -
814N TRP 6.2 0.9 - - - -
815N SER* 5.7 7.6 - - - +
833N ALA 6.1 2.0 - - - -
840N ASP* 5.7 0.4 - - - +
841N PRO 3.1 3.0 - - - -
842N HIS* 1.3 73.5 - - - +
844N LEU* 1.3 58.9 + - - +
846N ALA* 3.8 0.4 - - - +
847N VAL* 2.9 28.2 + - - -
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Residues in contact with LEU 844 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839N HIS 5.2 5.9 + - - -
841N PRO* 2.7 15.3 + - - +
843N VAL* 1.3 73.1 - - - +
845N LEU* 1.3 59.9 + - - +
847N VAL* 3.6 1.3 + - - +
848N ALA* 3.1 19.6 + - - -
863N TRP* 4.8 15.7 - - - +
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Residues in contact with LEU 845 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841N PRO 2.7 17.8 + - - -
842N HIS* 4.0 3.1 - - - +
844N LEU* 1.3 71.2 - - - +
846N ALA* 1.3 57.3 + - - +
848N ALA* 3.2 2.7 + - - +
849N LYS* 2.9 25.1 + - - -
864N PHE* 5.8 6.5 - - - +
877N ALA* 6.5 0.7 - - - +
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Residues in contact with ALA 846 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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815N SER* 6.3 3.1 - - - +
818N ILE* 6.5 1.1 - - - -
842N HIS 2.8 18.3 + - - -
843N VAL* 3.8 0.7 - - - +
845N LEU* 1.3 74.4 - - - +
847N VAL* 1.3 59.6 + - - +
849N LYS* 3.3 2.2 + - - +
850N LEU* 2.9 25.8 + - - -
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Residues in contact with VAL 847 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843N VAL 2.9 16.0 + - - -
844N LEU* 4.0 1.1 - - - +
846N ALA* 1.3 76.8 - - - +
848N ALA* 1.3 61.8 + - - +
850N LEU* 3.3 10.2 + - - +
851N PHE* 3.5 7.1 + - - -
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Residues in contact with ALA 848 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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844N LEU 3.1 14.5 + - - -
845N LEU* 3.2 5.1 + - - +
847N VAL* 1.3 76.8 - - - +
849N LYS* 1.3 61.2 + - - +
851N PHE* 3.0 12.5 + - - -
852N TRP* 3.1 11.1 + - - -
860N ALA* 4.2 24.1 - - - +
863N TRP* 5.0 9.0 - - - +
864N PHE* 5.1 2.7 - - - +
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Residues in contact with LYS 849 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845N LEU 2.9 13.3 + - - -
846N ALA* 3.8 3.6 - - - +
848N ALA* 1.3 77.6 - - - +
850N LEU* 1.3 54.4 + - - +
852N TRP* 3.2 2.4 + - - +
853N SER* 2.7 33.8 + - - -
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Residues in contact with LEU 850 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822N ALA* 3.2 27.0 - - - +
823N ARG* 5.2 0.9 - - - -
846N ALA 2.9 14.9 + - - -
847N VAL* 3.3 5.8 + - - +
848N ALA 3.2 0.4 - - - -
849N LYS* 1.3 75.0 - - - +
851N PHE* 1.3 60.4 + - - +
853N SER* 4.4 0.8 - - - +
854N GLN* 3.6 11.8 + - - -
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Residues in contact with PHE 851 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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847N VAL 3.5 5.8 + - - -
848N ALA 3.0 8.3 + - - -
850N LEU* 1.3 74.1 - - - +
852N TRP* 1.3 52.2 + - - +
853N SER 3.1 1.6 - - - -
854N GLN* 2.8 9.6 + - - +
855N ARG 2.6 43.7 + - - -
856N LYS 5.3 0.9 - - - -
860N ALA* 5.5 5.4 - - - +
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Residues in contact with TRP 852 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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848N ALA 3.1 12.7 + - - -
849N LYS* 3.7 3.1 - - - +
851N PHE* 1.3 73.4 - - - +
853N SER* 1.3 63.8 + - - +
854N GLN 4.0 0.3 - - - -
855N ARG* 3.8 11.2 + - - -
857N ILE* 5.5 6.7 - - - +
860N ALA* 5.0 5.8 - - - +
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Residues in contact with SER 853 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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849N LYS 2.7 19.5 + - - -
850N LEU 4.4 1.6 - - - -
852N TRP* 1.3 75.1 - - - +
854N GLN* 1.3 61.8 + - - +
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Residues in contact with GLN 854 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822N ALA 5.5 0.6 + - - -
850N LEU 3.6 11.1 + - - -
851N PHE 2.8 9.5 + - - -
852N TRP 4.0 1.1 - - - -
853N SER* 1.3 76.8 - - - +
855N ARG* 1.3 55.7 + - - +
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Residues in contact with ARG 855 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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851N PHE* 2.6 31.0 + - - +
852N TRP* 3.8 6.6 + - - -
853N SER 3.6 0.4 - - - -
854N GLN* 1.3 73.7 - - - +
856N LYS* 1.3 68.0 + - - +
857N ILE* 3.4 2.4 + - - -
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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