Contacts of the helix formed by residues 918 - 931 (chain B) in PDB entry 4E4N
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 HIS 918 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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886B PHE* 3.2 57.7 - + + -
910B LEU* 3.3 26.9 - - + +
917B ASN* 1.3 89.1 + - - +
919B ILE* 1.3 65.2 + - - +
920B ALA 3.3 2.5 - - - -
921B ASP* 3.2 26.4 + - + +
922B LEU* 3.1 17.2 + - - +
1039B ASP* 5.1 10.5 - - - -
1041B ARG* 6.2 1.1 - - - -
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Residues in contact with ILE 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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910B LEU* 3.5 16.2 - - + +
917B ASN* 3.3 27.0 + - - +
918B HIS* 1.3 77.3 - - - +
920B ALA* 1.3 72.2 + - + +
922B LEU* 3.2 4.9 + - - +
923B LYS* 3.0 43.5 + - + +
950B ASN* 3.1 38.1 - - + +
951B GLY* 3.9 8.1 - - - +
952B ILE* 4.6 7.4 - - + -
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Residues in contact with ALA 920 (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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917B ASN 5.3 1.7 + - - +
918B HIS* 3.3 1.2 - - - +
919B ILE* 1.3 87.3 - - + +
921B ASP* 1.3 60.1 + - - +
923B LYS* 3.4 10.7 + - - +
924B LYS* 3.0 45.5 + - - +
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Residues in contact with ASP 921 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918B HIS* 3.2 31.7 + - + +
919B ILE 3.2 0.6 - - - -
920B ALA* 1.3 78.7 - - - +
922B LEU* 1.3 59.1 + - - +
924B LYS* 3.4 19.3 + - - +
925B GLU* 3.0 28.8 + - - +
1023B GLY 5.4 9.4 - - - +
1026B LYS* 4.5 13.8 + - - -
1039B ASP* 5.8 0.2 - - - +
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Residues in contact with LEU 922 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908B LYS* 4.2 30.5 - - + +
909B SER* 4.3 1.3 - - - -
910B LEU* 3.8 33.0 - - + +
918B HIS 3.1 10.3 + - - +
919B ILE* 3.2 8.3 + - - +
921B ASP* 1.3 78.9 - - - +
923B LYS* 1.3 58.1 + - - +
925B GLU* 3.1 24.9 + - - +
926B ILE* 2.9 46.8 + - + +
952B ILE* 3.3 32.1 - - + +
953B LYS* 4.8 0.2 - - - -
954B LEU* 4.4 8.1 - - + -
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Residues in contact with LYS 923 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919B ILE* 3.0 39.4 + - + +
920B ALA* 3.7 11.4 - - - +
922B LEU* 1.3 75.0 - - - +
924B LYS* 1.3 57.0 + - + +
926B ILE* 3.4 11.7 + - - +
927B GLU* 3.1 30.0 + - - +
950B ASN 3.2 26.1 + - - -
952B ILE* 3.7 29.9 - - + +
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Residues in contact with LYS 924 (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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920B ALA* 3.0 32.4 + - - +
921B ASP* 3.6 17.5 + - - +
923B LYS* 1.3 73.9 - - + +
925B GLU* 1.3 65.0 + - - +
927B GLU* 3.2 6.9 + - - +
928B ILE* 3.0 34.1 + - + +
1026B LYS* 5.4 6.0 - - - +
1035B PTR 5.0 12.9 + - - -
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Residues in contact with GLU 925 (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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908B LYS* 2.6 47.1 + - - +
921B ASP 3.0 12.9 + - - +
922B LEU* 3.4 20.4 - - - +
924B LYS* 1.3 76.2 - - - +
926B ILE* 1.3 58.1 + - - +
928B ILE* 3.3 8.4 + - - +
929B LEU* 2.9 30.8 + - + +
954B LEU* 4.1 14.9 - - + +
956B MET* 5.9 0.5 - - - +
1021B ASP* 4.4 0.5 - - - +
1022B PHE* 3.7 30.1 + - + +
1023B GLY* 3.5 20.0 + - - +
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Residues in contact with ILE 926 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922B LEU* 2.9 30.6 + - + +
923B LYS* 3.5 7.9 - - - +
924B LYS 3.2 0.2 - - - -
925B GLU* 1.3 76.2 - - - +
927B GLU* 1.3 66.4 + - + +
929B LEU* 3.4 1.2 + - - +
930B ARG* 2.8 33.5 + - + +
940B TYR* 3.9 14.2 - - + +
943B ILE* 3.6 25.1 - - + -
952B ILE* 3.6 37.0 - - + -
954B LEU* 3.7 40.6 - - + +
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Residues in contact with GLU 927 (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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923B LYS 3.1 18.3 + - - +
924B LYS* 3.2 6.9 + - - +
926B ILE* 1.3 79.5 - - + +
928B ILE* 1.3 64.6 + - + +
930B ARG* 2.8 45.3 + - - -
931B ASN* 2.7 37.0 + - - +
999B TYR* 5.3 0.3 + - - -
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Residues in contact with ILE 928 (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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924B LYS* 3.0 24.4 + - + +
925B GLU* 3.6 10.3 - - - +
927B GLU* 1.3 77.4 - - + +
929B LEU* 1.3 64.0 + - - +
931B ASN* 3.2 13.7 + - - +
932B LEU* 3.4 30.8 + - + +
999B TYR* 3.7 44.8 + - + +
1022B PHE* 4.7 9.4 - - + +
1025B THR* 3.6 43.3 - - + +
1026B LYS* 5.1 0.7 - - - -
1027B ALA 5.5 0.4 - - - +
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Residues in contact with LEU 929 (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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925B GLU* 2.9 18.1 + - + +
926B ILE* 4.1 3.8 - - - +
928B ILE* 1.3 79.1 - - + +
930B ARG* 1.3 63.6 + - - +
931B ASN 3.1 1.2 + - - -
932B LEU* 3.1 19.5 + - + +
937B ILE* 3.9 9.4 - - + -
938B VAL* 3.5 27.6 - - + +
940B TYR* 4.0 16.7 + - + +
954B LEU* 4.3 13.7 - - + -
956B MET* 3.7 38.4 - - + -
1022B PHE* 3.8 33.4 - - + -
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Residues in contact with ARG 930 (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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926B ILE* 2.8 20.8 + - - +
927B GLU* 2.8 42.6 + - - +
929B LEU* 1.3 75.7 - - - +
931B ASN* 1.3 74.3 + - - +
932B LEU 3.8 0.9 + - - +
933B TYR* 3.5 22.2 + - - -
940B TYR* 3.6 51.9 - - + +
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Residues in contact with ASN 931 (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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927B GLU* 2.7 43.2 + - - +
928B ILE* 3.2 6.1 + - - +
929B LEU 3.1 0.8 - - - -
930B ARG* 1.3 99.9 + - - +
932B LEU* 1.3 63.9 + - - +
933B TYR* 3.8 19.5 + - + -
993B TYR* 4.0 5.2 + - - -
997B ARG* 5.0 8.0 + - - -
999B TYR* 6.0 1.8 - - - +
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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