Contacts of the helix formed by residues 849 - 863 (chain O) in PDB entry 5X0X
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 GLY 849 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17J T 5.2 0.6 + - - -
848O LYS* 1.3 73.6 - - - +
850O SER* 1.3 81.7 + - - +
853O GLU* 3.2 31.4 - - - +
854O ARG* 3.9 0.6 - - - +
875O TYR* 4.6 3.4 + - - -
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Residues in contact with SER 850 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J T 3.8 13.9 + - - -
848O LYS 3.6 2.1 - - - +
849O GLY* 1.3 93.1 + - - +
851O PRO* 1.3 77.0 - - - +
852O ASN* 3.0 28.8 + - - +
853O GLU* 3.6 2.9 + - - +
854O ARG* 2.8 23.0 + - - +
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Residues in contact with PRO 851 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J T 4.1 12.1 - - - +
18J G 5.1 16.4 - - - +
850O SER* 1.3 89.3 - - - +
852O ASN* 1.3 61.8 + - - +
853O GLU 3.5 0.2 - - - -
854O ARG* 3.2 25.6 + - + +
855O LYS* 2.9 37.4 + - + +
858O GLN* 5.1 0.5 - - - +
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Residues in contact with ASN 852 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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850O SER* 3.0 19.7 + - - +
851O PRO* 1.3 76.4 - - - +
853O GLU* 1.3 58.3 + - + +
855O LYS* 2.6 56.8 + - - +
856O ALA* 3.5 3.8 + - - +
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Residues in contact with GLU 853 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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848O LYS* 2.6 48.1 - - - +
849O GLY* 3.2 22.2 - - - +
850O SER* 3.6 1.8 + - - +
851O PRO 3.5 0.2 - - - -
852O ASN* 1.3 81.3 - - + +
854O ARG* 1.3 57.4 + - - +
856O ALA* 3.6 6.5 + - - +
857O LYS* 2.9 51.8 + - + +
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Residues in contact with ARG 854 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J T 2.8 27.3 + - - -
847O PHE* 3.7 18.2 - - + -
848O LYS 3.1 25.9 + - - +
849O GLY 3.9 0.2 - - - +
850O SER 2.8 23.5 + - - +
851O PRO* 3.1 33.3 + - + +
852O ASN 3.0 0.6 - - - -
853O GLU* 1.3 76.5 - - - +
855O LYS* 1.3 55.4 + - - +
857O LYS* 4.2 3.6 - - + -
858O GLN* 2.6 52.4 + - - +
875O TYR* 3.3 37.3 + - - -
878O LYS* 5.2 2.8 - - - +
879O GLU* 3.2 30.2 - - - +
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Residues in contact with LYS 855 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95J G 4.9 14.0 + - - -
851O PRO* 2.9 28.2 + - + +
852O ASN* 2.6 39.8 + - - +
854O ARG* 1.3 67.8 - - - +
856O ALA* 1.3 64.9 + - - +
858O GLN* 4.0 4.4 - - - +
859O ALA* 3.0 29.3 + - - +
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Residues in contact with ALA 856 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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852O ASN 3.5 3.6 + - - +
853O GLU* 3.7 9.6 - - - +
855O LYS* 1.3 79.6 - - - +
857O LYS* 1.3 62.1 + - + +
859O ALA* 3.8 2.3 - - - +
860O LYS* 2.8 31.9 + - - +
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Residues in contact with LYS 857 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845O ILE* 4.8 8.2 - - + +
846O SER* 3.5 36.4 + - - +
847O PHE* 4.4 17.7 - - + +
848O LYS* 4.7 7.1 - - - +
853O GLU* 2.9 47.1 + - + +
854O ARG* 4.2 4.7 - - + +
856O ALA* 1.3 78.0 - - + +
858O GLN* 1.3 64.5 + - - +
860O LYS* 3.0 16.6 - - + +
861O ILE* 2.9 27.3 + - - +
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Residues in contact with GLN 858 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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847O PHE* 4.5 3.1 - - + -
851O PRO 5.1 0.5 - - - +
854O ARG* 2.6 43.0 + - + +
855O LYS* 4.0 5.6 + - - +
857O LYS* 1.3 72.8 - - - +
859O ALA* 1.3 55.8 + - - +
861O ILE* 2.7 29.4 + - - +
862O ARG* 2.9 12.7 + - - +
879O GLU* 3.2 47.8 + - - +
882O LEU* 3.6 32.7 - - + +
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Residues in contact with ALA 859 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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855O LYS 3.0 18.3 + - - +
856O ALA* 4.2 2.0 - - - +
858O GLN* 1.3 76.8 - - - +
860O LYS* 1.3 61.8 + - - +
862O ARG* 3.8 14.1 - - - +
863O ALA* 3.3 20.1 + - - +
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Residues in contact with LYS 860 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843O ARG* 6.1 6.1 - - - +
845O ILE* 6.1 8.1 - - + -
856O ALA 2.8 15.5 + - - +
857O LYS* 3.0 22.4 - - + +
858O GLN 3.0 0.2 - - - -
859O ALA* 1.3 77.6 - - - +
861O ILE* 1.3 60.3 + - + +
863O ALA* 3.3 8.2 - - - +
865O GLU* 2.9 54.1 - - + +
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Residues in contact with ILE 861 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845O ILE* 3.5 34.8 - - + -
847O PHE* 3.5 22.9 - - + -
857O LYS 2.9 16.5 + - - +
858O GLN* 2.7 14.0 + - - +
860O LYS* 1.3 71.6 - - + +
862O ARG* 1.3 52.1 + - - +
863O ALA 2.9 5.2 - - - -
864O GLY* 2.6 31.2 + - - -
865O GLU 3.4 19.5 + - - +
866O PHE* 5.1 5.6 - - + -
869O VAL* 4.7 16.4 - - + -
882O LEU* 5.2 8.5 - - + -
883O LEU* 5.2 11.2 - - + -
886O VAL* 5.7 10.8 - - + -
888O TRP* 5.9 1.8 - - + -
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Residues in contact with ARG 862 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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858O GLN 2.9 14.5 + - - +
859O ALA* 3.8 14.1 - - - +
860O LYS 3.4 0.2 - - - -
861O ILE* 1.3 75.7 - - - +
863O ALA* 1.3 60.9 + - - +
864O GLY 3.0 1.6 + - - -
882O LEU* 4.6 23.2 - - + +
885O LYS* 5.8 6.6 - - - +
886O VAL* 5.7 6.1 - - - -
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Residues in contact with ALA 863 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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859O ALA 3.3 11.2 + - - +
860O LYS* 3.3 16.4 - - - +
862O ARG* 1.3 76.5 - - - +
864O GLY* 1.3 56.5 + - - +
865O GLU* 3.7 21.9 - - + +
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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