Contacts of the helix formed by residues 936 - 949 (chain B) in PDB entry 3LZB
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 LYS 936 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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696A SER 5.2 4.6 + - - -
802B ASN* 5.9 1.3 - - - +
805B GLU* 3.0 37.9 + - - -
870B GLN* 4.4 16.4 + - - +
873B VAL* 4.7 1.3 - - - -
934B ARG 4.7 3.1 - - - +
935B PRO* 1.3 76.3 - - - +
937B PHE* 1.3 61.1 + - - +
938B ARG* 3.9 35.9 - - + +
939B GLU* 2.9 31.3 + - + +
940B LEU* 2.8 28.9 + - - +
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Residues in contact with PHE 937 (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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798B ALA* 4.0 10.9 - - + +
801B MET* 3.4 54.7 - - + -
802B ASN* 3.8 22.9 - - + +
805B GLU* 3.8 17.3 - - + +
869B HIS* 3.8 13.9 - - + -
872B ASP* 3.7 25.6 - - + -
873B VAL* 3.7 18.6 - - + -
876B TYR* 3.7 25.6 - + + -
935B PRO 4.2 0.6 + - - -
936B LYS* 1.3 74.7 - - - +
938B ARG* 1.3 53.9 + - - +
940B LEU* 2.9 16.5 + - + +
941B ILE* 2.8 40.6 + - - +
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Residues in contact with ARG 938 (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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1A ITI 6.3 2.7 - - - -
696A SER 4.2 18.0 + - - +
697A GLY* 5.8 1.0 - - - -
775A LEU* 5.6 2.0 - - - +
776A ASP* 3.9 30.0 + - - +
779A ARG* 3.7 24.0 - - - +
802B ASN* 4.0 23.3 - - - +
936B LYS* 3.9 40.1 - - + +
937B PHE* 1.3 78.3 - - - +
939B GLU* 1.3 67.2 + - + +
941B ILE* 3.4 12.4 + - + +
942B ILE* 3.2 31.9 + - + +
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Residues in contact with GLU 939 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779A ARG* 4.7 22.6 + - - +
889A LYS* 4.6 15.4 + - - +
925B LYS* 3.6 21.0 + - - -
934B ARG 4.8 0.5 - - - +
935B PRO* 3.7 10.1 - - + +
936B LYS* 2.9 41.3 + - + +
938B ARG* 1.3 86.3 + - - +
940B LEU* 1.3 58.7 + - - +
942B ILE* 3.2 11.6 + - - +
943B GLU* 2.9 31.1 + - - +
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Residues in contact with LEU 940 (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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798B ALA* 4.2 11.8 - - + +
873B VAL* 4.3 9.4 - - + -
876B TYR* 3.8 32.1 - - + +
922B ILE* 3.6 32.3 - - + -
926B CYS* 4.2 11.0 - - - -
935B PRO* 3.9 19.3 - - + -
936B LYS 2.8 17.5 + - - +
937B PHE* 2.9 28.4 + - + +
939B GLU* 1.3 74.9 - - - +
941B ILE* 1.3 63.6 + - - +
943B GLU* 4.6 2.5 - - + +
944B PHE* 3.1 34.6 + - + +
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Residues in contact with ILE 941 (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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795B VAL* 4.5 5.4 - - + +
798B ALA* 3.8 21.5 - - + +
799B LYS* 3.8 34.3 - - + +
802B ASN* 3.5 38.1 - - + +
937B PHE 2.8 19.5 + - - +
938B ARG* 3.6 9.6 - - + +
939B GLU 3.3 0.2 - - - -
940B LEU* 1.3 72.6 - - - +
942B ILE* 1.3 64.1 + - + +
944B PHE* 4.3 1.0 - - - +
945B SER* 2.6 41.6 + - - +
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Residues in contact with ILE 942 (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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776A ASP* 4.6 13.5 - - - +
779A ARG* 4.2 31.4 - - + +
780A GLU* 4.0 35.2 - - + +
782A LYS* 3.8 23.6 - - - +
938B ARG* 3.2 20.3 + - + +
939B GLU* 3.5 11.0 - - - +
941B ILE* 1.3 85.3 - - + +
943B GLU* 1.3 63.5 + - + +
945B SER* 3.3 6.7 + - - -
946B LYS* 3.0 22.3 + - - +
949B ARG* 4.4 3.3 + - - +
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Residues in contact with GLU 943 (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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782A LYS* 4.1 14.5 + - - +
922B ILE* 3.8 25.1 - - + -
939B GLU 2.9 19.8 + - - +
940B LEU* 4.1 5.8 - - + +
942B ILE* 1.3 74.0 - - + +
944B PHE* 1.3 61.0 + - - +
946B LYS* 3.4 5.4 + - - +
947B MET* 3.0 32.2 + - + +
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Residues in contact with PHE 944 (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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791B LEU* 3.7 25.5 - - + +
794B CYS* 3.5 32.1 - - + -
795B VAL* 3.5 20.4 - - + +
876B TYR* 3.5 27.8 - + - -
880B VAL* 4.4 13.7 - - + -
884B MET* 4.5 4.7 - - + -
919B VAL* 4.8 9.0 - - + -
922B ILE* 3.9 35.2 - - + -
923B MET* 5.8 1.1 - - + -
940B LEU* 3.1 28.1 + - + +
943B GLU* 1.3 75.3 - - - +
945B SER* 1.3 55.7 + - - +
947B MET* 3.6 12.5 - - - +
948B ALA* 2.6 36.6 + - - +
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Residues in contact with SER 945 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795B VAL* 3.7 21.4 - - - +
799B LYS* 5.0 1.6 - - - -
941B ILE* 2.6 30.1 + - - +
942B ILE* 3.3 8.1 - - - -
944B PHE* 1.3 76.0 - - - +
946B LYS* 1.3 63.9 + - - +
948B ALA* 3.3 4.6 + - - +
949B ARG* 3.2 39.4 + - - +
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Residues in contact with LYS 946 (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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782A LYS* 2.8 52.3 - - - +
783A ASP* 5.0 8.3 + - - +
784A ASN* 5.0 6.7 - - - +
942B ILE 3.0 9.5 + - - +
943B GLU 3.5 9.2 - - - +
944B PHE 3.2 0.2 - - - -
945B SER* 1.3 81.1 - - - +
947B MET* 1.3 67.1 + - + +
949B ARG* 3.2 44.5 + - - +
950B ASP* 3.8 3.8 + - - +
954B TYR* 4.4 17.6 - - - +
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Residues in contact with MET 947 (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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791B LEU* 4.1 8.0 - - + +
918B ASP* 3.8 30.5 - - + +
919B VAL* 3.7 22.9 - - - -
922B ILE* 3.6 31.6 - - + -
943B GLU* 3.0 18.6 + - + +
944B PHE* 3.9 15.5 - - - +
946B LYS* 1.3 73.4 - - + +
948B ALA* 1.3 67.6 + - - +
949B ARG 3.0 2.5 - - - -
950B ASP 3.1 22.3 + - - +
951B PRO* 3.1 5.5 - - - +
954B TYR* 3.4 37.0 - - + -
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Residues in contact with ALA 948 (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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788B GLN* 2.9 21.5 + - - +
791B LEU* 4.0 21.7 - - + +
792B ASN* 3.6 23.6 - - - +
795B VAL* 4.4 2.9 - - + -
944B PHE 2.6 22.5 + - - +
945B SER* 3.8 8.1 - - - +
946B LYS 3.2 0.8 - - - -
947B MET* 1.3 75.3 - - - +
949B ARG* 1.3 51.1 + - - +
950B ASP 3.1 0.9 - - - -
951B PRO* 2.7 21.6 - - - +
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Residues in contact with ARG 949 (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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780A GLU* 4.9 13.3 + - - +
782A LYS* 6.1 0.2 - - - +
942B ILE* 4.4 3.0 + - - +
945B SER* 3.2 20.7 + - - +
946B LYS* 3.2 62.5 + - - +
947B MET 3.0 0.4 - - - -
948B ALA* 1.3 74.6 - - - +
950B ASP* 1.3 59.2 + - + +
951B PRO* 3.5 2.8 - - - +
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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