Contacts of the helix formed by residues 1006 - 1010 (chain D) in PDB entry 5ZX2
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 PRO1006 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1002D SER 3.2 23.6 - - - +
1003D ILE 3.7 9.9 - - - +
1004D GLY 3.7 0.7 - - - -
1005D GLU* 1.3 104.5 - - + +
1007D GLY* 1.3 51.0 + - - -
1008D THR 3.1 0.7 - - - -
1009D GLN* 2.7 45.7 + - - +
1010D LEU* 3.8 4.9 - - - +
1142D TYR* 3.7 15.0 - - + -
1147D VAL* 3.6 28.0 - - + -
1149D ILE* 3.8 11.0 - - + -
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Residues in contact with GLY1007 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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866D ARG* 4.4 0.7 - - - +
870D SER* 3.7 13.5 - - - -
1003D ILE 4.2 4.0 + - - -
1004D GLY* 2.9 20.2 + - - -
1005D GLU 3.1 0.2 - - - -
1006D PRO* 1.3 77.0 - - - +
1008D THR* 1.3 61.0 + - - +
1009D GLN 3.2 0.7 + - - -
1010D LEU* 3.4 23.5 + - - +
1028D LEU* 3.8 24.2 - - - +
1142D TYR* 5.0 3.4 - - - -
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Residues in contact with THR1008 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504D LEU* 5.1 14.0 - - + +
863D THR* 6.4 1.3 - - - -
866D ARG* 3.2 35.3 + - - +
867D THR* 3.7 36.6 - - - +
870D SER* 4.1 11.9 - - - +
1005D GLU 3.9 11.9 + - - +
1007D GLY* 1.3 76.2 - - - +
1009D GLN* 1.3 66.4 + - - +
1010D LEU 3.4 0.4 - - - -
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Residues in contact with GLN1009 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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866D ARG* 6.2 0.2 - - - -
1005D GLU* 4.7 9.7 + - - -
1006D PRO* 2.7 31.5 + - - +
1008D THR* 1.3 80.3 + - - +
1010D LEU* 1.3 63.5 + - + +
1011D THR* 3.5 10.4 + - - +
1145D GLN* 3.5 17.1 - - + +
1147D VAL* 3.4 25.4 - - + +
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Residues in contact with LEU1010 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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866D ARG* 3.1 22.7 - - - +
1006D PRO 3.8 15.9 - - - +
1007D GLY* 3.4 8.4 + - - +
1008D THR 3.4 1.6 - - - -
1009D GLN* 1.3 78.7 - - - +
1011D THR* 1.3 63.1 + - - +
1027D GLY 4.8 0.7 - - - -
1028D LEU* 4.0 27.0 - - + +
1031D VAL* 3.8 18.4 - - + -
1141D VAL* 3.7 25.1 - - + -
1142D TYR* 4.0 35.4 - - + +
1145D GLN* 3.8 28.3 - - + +
1147D VAL* 4.7 5.2 - - + -
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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