Contacts of the helix formed by residues 968 - 980 (chain A) in PDB entry 4Z02
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 PRO 968 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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966A ALA 3.6 3.3 - - - +
967A PRO* 1.4 86.6 - - + +
969A LEU* 1.3 64.2 + - - +
970A ASP* 3.2 21.1 - - - +
971A VAL* 3.1 23.9 + - + -
972A LEU* 3.2 11.2 + - - +
998A TRP* 3.5 27.1 - - + +
1106A UNX 3.8 13.2 - - - -
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Residues in contact with LEU 969 (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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967A PRO 3.9 0.6 + - - -
968A PRO* 1.3 71.9 - - - +
970A ASP* 1.3 57.1 + - - +
972A LEU* 3.3 17.8 + - + +
973A LYS* 3.0 29.4 + - - +
1106A UNX 3.4 16.7 - - - -
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Residues in contact with ASP 970 (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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968A PRO* 3.2 21.1 - - - +
969A LEU* 1.3 74.0 - - - +
971A VAL* 1.3 81.3 + - - +
973A LYS* 3.4 6.7 + - - +
974A ILE* 2.9 31.5 + - - +
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Residues in contact with VAL 971 (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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967A PRO* 4.2 10.5 - - + -
968A PRO* 3.1 25.0 + - + +
970A ASP* 1.3 89.5 + - - +
972A LEU* 1.3 65.7 + - - +
974A ILE* 3.3 8.8 - - + +
975A GLY 3.1 8.1 + - - -
988A LEU* 3.6 30.7 - - + -
998A TRP* 3.7 31.2 - - + +
1000A TRP* 2.8 27.3 + - + +
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Residues in contact with LEU 972 (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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950A PRO* 3.8 24.2 - - + -
967A PRO* 3.7 26.0 - - + +
968A PRO 3.2 10.9 + - - +
969A LEU* 3.5 20.6 - - + +
971A VAL* 1.3 76.7 - - - +
973A LYS* 1.4 60.8 + - - +
975A GLY* 3.3 2.6 + - - -
976A GLU* 3.2 22.1 + - - +
1000A TRP* 4.4 13.2 - - + -
1104A UNX 3.8 21.3 - - - -
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Residues in contact with LYS 973 (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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969A LEU 3.0 16.7 + - - +
970A ASP* 3.8 7.9 - - - +
971A VAL 3.3 0.2 - - - -
972A LEU* 1.4 73.3 - - - +
974A ILE* 1.3 63.9 + - - +
976A GLU* 3.4 16.3 + - - +
977A HIS* 3.2 20.8 + - - +
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Residues in contact with ILE 974 (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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970A ASP 2.9 17.7 + - - +
971A VAL* 3.3 22.4 - - + +
973A LYS* 1.3 75.8 - - - +
975A GLY* 1.3 56.5 + - - +
977A HIS* 3.2 23.8 + - + +
978A MET* 2.9 47.5 + - + +
1000A TRP* 4.3 9.6 - - + -
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Residues in contact with GLY 975 (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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971A VAL 3.1 10.7 + - - -
972A LEU 3.7 2.0 - - - -
973A LYS 3.3 0.2 - - - -
974A ILE* 1.3 76.7 - - - +
976A GLU* 1.3 54.8 + - - +
978A MET* 3.4 3.9 + - - +
979A GLN* 2.9 31.6 + - - +
986A LEU* 4.6 1.9 - - - +
1000A TRP* 3.3 44.1 - - - -
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Residues in contact with GLU 976 (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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972A LEU 3.2 11.6 + - - +
973A LYS* 3.6 20.8 + - - +
975A GLY* 1.3 74.8 - - - +
977A HIS* 1.3 61.3 + - - +
979A GLN* 3.5 11.3 + - - +
980A THR* 3.4 22.1 + - + +
1000A TRP* 5.7 0.2 - - - -
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Residues in contact with HIS 977 (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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973A LYS 3.2 11.0 + - - +
974A ILE* 3.2 27.1 + - + +
976A GLU* 1.3 75.3 - - - +
978A MET* 1.3 66.2 + - + +
980A THR* 2.6 34.0 + - - +
981A LYS* 3.9 24.6 + - + +
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Residues in contact with MET 978 (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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974A ILE* 2.9 43.1 + - + +
975A GLY 3.7 4.3 - - - +
977A HIS* 1.3 77.1 - - + +
979A GLN* 1.4 56.8 + - - +
981A LYS* 3.1 26.4 + - + +
982A SER* 3.4 12.8 + - - -
986A LEU* 3.7 15.6 - - + +
999A GLN* 3.9 15.3 - - - +
1000A TRP* 3.6 42.6 - - + +
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Residues in contact with GLN 979 (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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975A GLY 2.9 18.7 + - - +
976A GLU* 3.7 9.0 - - - +
977A HIS 3.3 0.4 - - - -
978A MET* 1.4 76.2 - - - +
980A THR* 1.4 57.0 + - + +
982A SER* 3.2 23.0 + - - +
983A ASP 5.0 0.6 + - - -
984A GLU 3.2 23.4 + - - -
985A LYS* 3.7 10.4 - - - +
986A LEU* 2.8 38.6 + - + +
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Residues in contact with THR 980 (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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976A GLU* 3.4 18.6 - - + +
977A HIS* 2.6 27.0 + - - +
979A GLN* 1.4 76.3 - - - +
981A LYS* 1.4 64.6 + - - +
982A SER 3.6 0.9 - - - -
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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