Contacts of the helix formed by residues 113 - 118 (chain J) in PDB entry 4ZZ7
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 GLY 113 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109J GLU 3.8 2.0 + - - -
110J TYR 3.2 10.7 + - - -
111J ALA 3.0 2.0 + - - -
112J CYS* 1.3 75.9 - - - +
114J ALA* 1.3 63.8 + - - +
115J PRO* 3.2 6.6 - - - -
116J GLU* 3.3 10.7 + - - +
117J LEU* 3.2 26.1 + - - +
109L GLU 6.1 1.1 - - - -
113L GLY* 5.5 10.9 - - - -
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Residues in contact with ALA 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61J PRO 4.5 3.8 - - - +
65J ALA* 4.4 2.9 - - + -
111J ALA 3.0 16.2 + - - +
112J CYS 3.2 0.6 - - - -
113J GLY* 1.3 75.9 - - - +
115J PRO* 1.3 66.4 - - + +
117J LEU* 2.8 12.4 + - - +
118J LEU* 2.8 41.4 + - + +
161J MET* 5.9 0.9 - - - -
164J VAL* 3.5 37.7 - - + +
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Residues in contact with PRO 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123I SER* 4.8 1.4 + - - -
61J PRO* 4.1 12.8 - - + +
62J LEU* 3.9 32.8 - - + +
65J ALA* 4.6 2.0 - - + -
112J CYS 4.1 7.4 - - - +
113J GLY* 3.3 5.2 - - - -
114J ALA* 1.3 95.7 - - + +
116J GLU* 1.3 59.6 + - - +
118J LEU* 3.7 3.5 + - + +
119J LYS* 3.5 21.3 + - - +
446L TYR* 3.4 49.6 - - + +
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Residues in contact with GLU 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121I GLU* 4.3 5.9 - - - +
113J GLY* 3.3 11.1 + - - +
115J PRO* 1.3 79.2 - - - +
117J LEU* 1.3 64.4 + - + +
118J LEU 3.4 0.9 + - - -
119J LYS* 2.8 49.3 + - - +
110L TYR* 2.8 40.2 + - + -
116L GLU* 4.3 21.8 - - + +
117L LEU* 3.7 20.6 - - + +
446L TYR* 4.6 2.7 - - - +
465L PRO* 4.8 0.2 - - - +
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Residues in contact with LEU 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110J TYR* 3.2 66.4 - - + +
113J GLY* 3.2 15.7 - - - +
114J ALA* 2.8 10.4 + - - +
116J GLU* 1.3 80.1 - - + +
118J LEU* 1.3 59.6 + - + +
119J LYS 3.4 4.2 + - - +
136J PHE* 5.3 2.6 - - - -
161J MET* 3.7 14.8 - - + -
468J VAL* 3.5 28.4 - - + +
116L GLU* 3.6 30.3 - - + +
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Residues in contact with LEU 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122I HIS 4.3 1.2 - - - +
123I SER* 6.0 0.4 - - - -
124I ARG* 5.5 3.8 + - - +
61J PRO* 4.0 19.1 - - + -
64J ARG* 3.6 26.7 - - - +
114J ALA* 2.8 23.0 + - + +
115J PRO* 4.2 6.1 - - + +
116J GLU 3.3 0.2 - - - -
117J LEU* 1.3 76.5 - - + +
119J LYS* 1.3 65.2 + - - +
120J GLY* 3.1 3.6 + - - -
135J GLU* 5.9 0.2 - - - -
136J PHE* 4.3 24.4 + - + +
164J VAL 3.8 11.2 - - - +
165J CYS* 3.8 26.9 - - + +
468J VAL* 3.9 12.3 - - + -
472J THR* 4.0 14.1 - - + -
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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