Contacts of the helix formed by residues 844 - 858 (chain A) in PDB entry 4AY6
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 ASP 844 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464A GLN* 4.8 1.6 - - - +
469A TRP* 3.7 8.4 - - - +
472A TYR* 3.5 23.0 + - + +
842A LYS 3.9 0.6 + - - -
843A ILE* 1.3 76.3 - - - +
845A PRO* 1.4 71.0 - - + +
846A SER* 3.8 12.3 + - - -
847A THR* 2.7 53.6 + - - -
848A LEU 3.0 9.5 + - - -
916A LEU* 4.1 29.1 - - + +
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Residues in contact with PRO 845 (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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469A TRP* 3.6 49.3 - - + -
472A TYR* 3.9 33.9 - - + -
844A ASP* 1.4 88.5 - - + +
846A SER* 1.3 59.1 + - - +
848A LEU* 4.6 0.2 - - + -
849A GLN* 3.1 22.3 + - - +
883A MET* 3.7 13.1 - - + +
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Residues in contact with SER 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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844A ASP* 3.2 13.3 + - - -
845A PRO* 1.3 74.7 - - - +
847A THR* 1.3 68.5 + - - +
849A GLN* 2.9 19.0 + - - +
850A MET* 3.1 18.1 + - - +
963A ARG* 3.5 33.1 + - - -
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Residues in contact with THR 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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842A LYS 4.6 1.7 + - - -
843A ILE* 4.1 3.8 - - + -
844A ASP* 2.7 30.7 + - - -
846A SER* 1.3 79.4 - - - +
848A LEU* 1.3 62.9 + - - +
850A MET* 3.5 14.4 + - + +
851A TRP* 3.4 54.4 + - + +
914A THR* 4.1 7.4 - - + -
915A PRO* 3.3 31.9 - - + +
916A LEU* 4.4 3.8 + - - +
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Residues in contact with LEU 848 (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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469A TRP* 3.6 31.4 - - + -
843A ILE* 4.2 4.0 - - + +
844A ASP 3.0 13.2 + - - +
845A PRO 3.9 4.7 - - - +
847A THR* 1.3 75.3 - - - +
849A GLN* 1.3 66.4 + - - +
851A TRP* 2.9 29.8 + - + +
852A ALA* 2.9 23.4 + - + +
855A LEU* 6.5 0.2 - - + -
863A LEU* 4.9 7.0 - - + -
865A LEU* 5.8 0.7 - - + -
876A ILE* 4.0 27.6 - - + -
879A TYR* 4.2 15.7 - - + -
880A ALA* 4.5 9.9 - - + +
883A MET* 4.2 11.7 - - + -
885A LEU* 6.4 1.3 - - + -
890A ILE* 5.0 6.5 - - + -
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Residues in contact with GLN 849 (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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845A PRO 3.1 14.1 + - - +
846A SER* 2.9 13.1 + - - +
848A LEU* 1.3 75.2 - - - +
850A MET* 1.3 57.5 + - + +
852A ALA* 3.2 11.3 + - - +
853A ASN* 2.9 60.9 + - - +
856A LYS* 5.7 2.6 - - - +
883A MET* 3.8 32.7 + - + +
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Residues in contact with MET 850 (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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846A SER* 3.1 11.0 + - - +
847A THR* 3.5 30.3 - - + +
849A GLN* 1.3 75.5 - - + +
851A TRP* 1.3 70.0 + - + +
853A ASN* 3.3 4.1 + - - +
854A ILE* 3.0 29.1 + - - +
915A PRO* 3.7 25.4 - - + -
936A MET* 5.0 4.0 - - + +
963A ARG* 4.0 39.0 - - + +
966A TYR* 3.7 32.3 - - + -
967A GLU* 3.5 26.9 - - + +
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Residues in contact with TRP 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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836A ASN* 4.1 14.1 - - + -
843A ILE* 3.8 26.9 - - + -
847A THR* 3.5 33.3 + - + +
848A LEU* 2.9 22.4 + - + +
850A MET* 1.3 77.6 - - + +
852A ALA* 1.3 58.9 + - - +
854A ILE* 3.0 7.4 + - + +
855A LEU* 2.8 42.5 + - + +
863A LEU* 3.6 34.3 - - + -
865A LEU* 4.4 6.7 - - + -
912A LEU* 3.6 47.4 - - + +
913A ASP 4.4 0.2 - - - -
914A THR* 3.8 21.3 - - + -
966A TYR* 3.2 32.3 + + - -
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Residues in contact with ALA 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 LEU* 2.9 14.0 + - + +
849A GLN* 3.2 23.3 - - - +
851A TRP* 1.3 74.9 - - - +
853A ASN* 1.3 62.2 + - - +
855A LEU* 3.3 3.4 + - - +
856A LYS* 2.9 32.8 + - - +
883A MET* 4.1 18.8 - - + -
885A LEU* 3.9 27.7 - - + +
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Residues in contact with ASN 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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849A GLN* 2.9 37.9 + - - +
850A MET* 3.3 6.8 - - - +
852A ALA* 1.3 74.0 - - - +
854A ILE* 1.3 63.8 + - - +
856A LYS* 3.0 14.8 + - - +
857A ARG* 3.0 33.6 + - - +
967A GLU* 2.9 36.4 + - + +
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Residues in contact with ILE 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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834A TYR* 4.1 24.7 - - + +
850A MET 3.0 17.6 + - - +
851A TRP* 3.4 13.0 - - + +
853A ASN* 1.3 74.0 - - - +
855A LEU* 1.3 66.8 + - + +
857A ARG* 3.0 6.1 + - - +
858A VAL* 3.0 21.7 + - + +
912A LEU* 4.6 6.5 - - + -
966A TYR* 3.8 26.5 - - + -
967A GLU* 3.7 27.1 - - + +
970A ALA* 3.8 30.7 - - + -
971A VAL* 4.2 14.6 - - + -
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Residues in contact with LEU 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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834A TYR* 4.4 8.3 - - + -
851A TRP* 2.8 30.5 + - + +
852A ALA* 3.6 4.0 - - - +
854A ILE* 1.3 73.6 - - + +
856A LYS* 1.3 59.0 + - - +
858A VAL 2.9 12.6 - - - +
859A PRO* 4.6 0.2 - - - +
861A SER* 3.1 33.2 - - - +
862A VAL* 3.8 25.6 - - - +
863A LEU* 3.8 27.8 - - + +
885A LEU* 3.9 22.9 - - + -
889A ARG* 2.5 38.3 + - + +
890A ILE* 5.0 4.9 - - + -
912A LEU* 6.2 1.6 - - + -
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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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849A GLN* 5.7 2.0 - - - +
852A ALA* 2.9 29.0 + - - +
853A ASN* 3.0 13.7 + - - +
855A LEU* 1.3 75.2 - - - +
857A ARG* 1.3 63.8 + - + +
858A VAL 3.3 3.3 + - - -
859A PRO* 4.5 5.7 - - - +
883A MET 3.1 27.9 + - - -
884A GLY* 3.4 22.0 + - - -
885A LEU* 3.9 7.8 - - + +
889A ARG* 4.7 4.3 - - - +
1025B HIS 5.4 2.9 - - - +
1026B MET* 6.1 0.5 - - - -
1027B ILE* 3.6 27.3 + - + +
1028B LYS* 3.8 38.8 + - - +
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Residues in contact with ARG 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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853A ASN* 3.0 21.5 + - - +
854A ILE* 3.0 6.0 + - - +
856A LYS* 1.3 79.0 - - + +
858A VAL* 1.3 62.8 + - - +
859A PRO* 3.7 8.7 - - - +
964A GLN* 4.4 6.3 - - - +
967A GLU* 4.0 21.7 + - - +
968A ASP* 3.0 28.9 + - - +
971A VAL* 3.8 38.9 - - + +
975A THR* 4.6 4.7 - - - +
1028B LYS* 5.1 17.0 - - + +
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Residues in contact with VAL 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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832A ILE* 4.5 5.8 - - + -
834A TYR* 3.8 20.9 - - + +
854A ILE 3.0 15.5 + - - +
855A LEU 2.9 6.9 - - - +
856A LYS 3.2 0.4 - - - -
857A ARG* 1.3 82.9 - - - +
859A PRO* 1.3 66.6 - - + +
860A ASN* 3.2 5.3 + - + +
861A SER* 2.6 45.0 + - - +
971A VAL* 3.8 28.7 - - + +
974A GLY* 3.6 22.9 - - - +
975A THR* 3.9 8.7 - - + -
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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