Contacts of the helix formed by residues 951 - 962 (chain B) in PDB entry 1ZYC
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 MET 951 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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809B ARG* 4.7 0.4 - - - -
812B TYR* 4.6 9.6 - - + +
919B ILE* 3.6 34.8 - - + +
920B TYR* 4.5 6.3 - - + +
921B PRO* 5.4 1.8 - - + -
946B PHE* 3.3 39.9 - - + -
947B ASP* 2.9 34.6 + - + +
948B ASP* 4.8 0.4 - - - -
950B LYS* 1.3 98.6 - - - +
952B LYS* 1.3 54.7 + - - +
953B VAL 3.4 1.1 - - - -
954B GLU* 3.3 19.5 - - + -
955B LYS* 2.6 37.5 + - - +
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Residues in contact with LYS 952 (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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948B ASP* 3.3 21.2 + - - +
949B ASN* 3.0 21.5 + - - +
950B LYS 2.7 3.8 + - - +
951B MET* 1.3 79.3 - - - +
953B VAL* 1.3 66.8 + - + +
955B LYS* 3.3 12.6 + - - +
956B LYS* 3.4 11.6 + - + +
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Residues in contact with VAL 953 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809B ARG* 4.7 3.1 - - - +
813B TRP* 4.3 11.7 - - + -
950B LYS 4.2 3.6 - - - +
952B LYS* 1.3 83.2 - - + +
954B GLU* 1.3 79.9 + - - +
956B LYS* 3.0 29.5 + - + +
957B ILE* 3.4 9.4 + - + +
980B TRP* 3.5 35.7 - - + +
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Residues in contact with GLU 954 (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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809B ARG* 2.5 47.6 + - - -
812B TYR* 3.2 13.5 + - - +
813B TRP* 2.9 27.9 - - + -
915B PHE* 3.9 13.2 - - + -
919B ILE* 4.7 7.0 - - + -
950B LYS 2.7 10.6 - - - +
951B MET* 3.3 26.2 - - + -
953B VAL* 1.3 91.8 - - - +
955B LYS* 1.3 57.7 + - - +
957B ILE* 3.1 11.7 + - - +
958B ILE* 2.8 37.0 + - + +
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Residues in contact with LYS 955 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942B PHE* 3.5 24.5 - - + -
946B PHE* 3.6 14.6 - - + -
948B ASP* 3.8 25.0 + - - +
951B MET 2.6 23.8 + - - +
952B LYS* 3.5 7.9 - - - +
953B VAL 3.1 0.2 - - - -
954B GLU* 1.3 71.1 - - - +
956B LYS* 1.3 58.9 + - - +
958B ILE* 3.7 10.5 - - - +
959B ARG* 2.8 53.9 + - + +
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Residues in contact with LYS 956 (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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952B LYS* 3.4 7.2 + - + +
953B VAL* 3.0 18.8 + - + +
955B LYS* 1.3 81.4 - - - +
957B ILE* 1.3 59.7 + - + +
959B ARG* 3.9 5.6 - - + +
960B LEU* 3.3 37.0 + - + +
980B TRP* 4.2 29.6 - - + -
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Residues in contact with ILE 957 (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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813B TRP* 4.8 10.3 - - + -
816B PHE* 3.9 21.5 - - + -
915B PHE* 4.6 5.8 - - + -
953B VAL* 3.4 17.0 - - + +
954B GLU* 3.2 13.9 - - - +
955B LYS 3.0 0.2 - - - -
956B LYS* 1.3 74.2 - - - +
958B ILE* 1.3 68.2 + - - +
959B ARG 3.1 1.1 - - - -
960B LEU* 3.0 16.5 + - - +
961B LEU* 3.1 17.1 + - + +
975B LEU* 3.7 35.4 - - + +
980B TRP* 3.3 43.7 - - + +
981B LEU* 5.5 5.2 - - + -
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Residues in contact with ILE 958 (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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912B GLY* 3.6 23.6 - - - +
913B ILE* 5.4 0.2 - - - -
915B PHE* 3.7 18.2 - - + -
916B PHE* 4.2 17.9 - - + +
919B ILE* 3.2 34.1 - - + -
935B LEU* 5.4 0.4 - - + -
942B PHE* 4.4 10.3 - - + -
946B PHE* 4.2 7.4 - - + -
954B GLU* 2.8 30.2 + - + +
955B LYS* 3.7 7.6 - - - +
957B ILE* 1.3 73.8 - - - +
959B ARG* 1.3 54.8 + - - +
961B LEU* 3.4 5.2 + - - +
962B ILE* 2.8 54.2 + - + +
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Residues in contact with ARG 959 (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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940B ILE* 2.8 44.9 - - - +
942B PHE* 3.4 27.1 - - + -
955B LYS* 2.8 34.4 + - - +
956B LYS* 3.9 9.4 - - + +
958B ILE* 1.3 79.0 - - - +
960B LEU* 1.3 65.2 + - + +
962B ILE* 3.9 2.5 - - - +
963B ASP* 3.3 29.9 + - - +
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Residues in contact with LEU 960 (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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956B LYS* 3.3 27.1 + - + +
957B ILE* 3.0 8.3 + - - +
959B ARG* 1.3 80.8 - - + +
961B LEU* 1.3 67.0 + - - +
963B ASP* 3.2 15.2 + - + +
968B LYS 4.1 15.7 - - - +
969B ARG* 3.2 18.0 - - - +
970B PRO* 3.7 25.8 - - + -
975B LEU* 5.1 1.6 - - + -
980B TRP* 3.9 29.2 - - + -
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Residues in contact with LEU 961 (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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816B PHE* 4.3 3.8 - - + -
908B MET* 3.0 51.4 - - + +
909B TYR* 3.1 13.4 - - - -
911B LEU* 4.1 17.0 - - + -
912B GLY* 3.3 35.7 - - - +
915B PHE* 5.5 0.9 - - + -
957B ILE* 3.1 31.5 + - + +
958B ILE* 4.0 0.9 - - - +
960B LEU* 1.3 80.0 - - - +
962B ILE* 1.3 57.4 + - - +
969B ARG* 2.9 25.8 - - - -
970B PRO* 4.3 14.6 - - + +
975B LEU* 4.2 8.7 - - + -
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Residues in contact with ILE 962 (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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909B TYR* 3.2 38.2 + - + +
912B GLY 4.4 0.2 - - - -
913B ILE* 3.6 36.6 - - + +
916B PHE* 6.3 0.2 - - + -
935B LEU* 3.7 37.6 - - + +
940B ILE* 4.1 17.5 - - + +
942B PHE* 4.4 2.0 - - + -
958B ILE* 2.8 42.8 - - + +
959B ARG* 3.9 7.2 - - - +
961B LEU* 1.3 71.7 - - - +
963B ASP* 1.3 71.1 + - - +
964B HIS* 3.3 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