Contacts of the helix formed by residues 113 - 118 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109E GLU 5.9 2.5 - - - -
113E GLY* 5.5 11.4 - - - -
109G GLU 3.8 3.2 + - - -
110G TYR 3.3 13.8 + - - -
111G ALA 3.1 1.4 - - - -
112G CYS* 1.3 75.7 - - - +
114G ALA* 1.3 62.6 + - - -
115G PRO* 3.4 6.3 - - - -
116G GLU* 3.3 19.1 + - - +
117G LEU* 3.3 15.2 + - - +
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Residues in contact with ALA 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G PRO* 4.5 3.6 - - + +
65G ALA* 4.5 2.7 - - + -
111G ALA 3.3 4.9 + - - +
112G CYS 3.2 1.0 - - - -
113G GLY* 1.3 76.1 - - - +
115G PRO* 1.3 66.2 - - + +
117G LEU* 3.0 10.3 + - - +
118G LEU* 2.8 41.9 + - + +
161G MET* 5.9 0.4 - - - -
164G VAL* 3.4 49.1 - - + +
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Residues in contact with PRO 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446E TYR* 3.4 50.3 - - + +
123F SER* 4.8 1.2 + - - -
61G PRO* 4.2 14.6 - - + +
62G LEU* 4.1 29.4 - - + +
65G ALA* 4.5 1.6 - - + -
112G CYS 4.1 7.9 - - - +
113G GLY* 3.4 5.6 - - - -
114G ALA* 1.3 95.9 - - + +
116G GLU* 1.3 62.1 + - - +
118G LEU* 3.5 9.5 + - + +
119G LYS* 3.6 13.9 + - - +
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Residues in contact with GLU 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E TYR* 3.0 27.8 + - + -
116E GLU* 4.3 18.2 - - + +
117E LEU* 3.5 28.6 - - + +
446E TYR* 4.5 2.5 - - - +
465E PRO* 5.7 0.2 - - - +
121F GLU* 4.7 3.6 - - - +
113G GLY* 3.3 13.9 + - - +
115G PRO* 1.3 78.6 - - - +
117G LEU* 1.3 64.3 + - + +
119G LYS* 2.8 59.9 + - - +
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Residues in contact with LEU 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E GLU* 3.6 29.4 - - + +
110G TYR* 3.1 68.9 - - + +
113G GLY* 3.4 12.8 - - - +
114G ALA* 3.0 9.8 + - - +
116G GLU* 1.3 78.8 - - + +
118G LEU* 1.3 57.5 + - + +
119G LYS 3.3 6.3 + - - +
136G PHE* 5.4 2.4 - - - -
161G MET* 3.8 13.9 - - + -
465G PRO* 6.0 0.4 - - + -
468G VAL* 3.6 30.6 - - + +
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Residues in contact with LEU 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F HIS 4.3 1.6 - - - +
123F SER* 5.4 2.2 - - - -
124F ARG* 5.4 3.1 + - - +
61G PRO* 3.9 22.0 - - + -
64G ARG* 3.6 26.0 - - - +
114G ALA* 2.8 22.6 + - + +
115G PRO* 3.9 6.3 - - + +
116G GLU 3.2 0.6 - - - -
117G LEU* 1.3 76.1 - - + +
119G LYS* 1.3 62.7 + - - +
120G GLY* 3.4 2.8 + - - -
135G GLU* 5.9 0.3 - - - -
136G PHE* 4.1 27.4 + - + +
164G VAL 4.1 9.0 - - - +
165G CYS* 3.9 28.0 - - - +
468G VAL* 4.1 8.1 - - + -
472G THR* 4.0 18.4 - - + -
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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