Contacts of the helix formed by residues 113 - 118 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F GLU 5.8 2.9 - - - -
110F TYR* 6.6 0.2 - - - -
113F GLY* 5.5 11.4 - - - -
109H GLU 3.8 2.0 + - - -
110H TYR 3.0 16.5 + - - -
111H ALA 4.0 0.2 - - - -
112H CYS* 1.3 76.0 - - - +
114H ALA* 1.3 62.0 + - - +
115H PRO* 3.4 5.2 - - - -
116H GLU* 3.2 20.8 + - - +
117H LEU* 3.3 14.9 + - - +
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Residues in contact with ALA 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61H PRO 4.3 4.7 - - - +
65H ALA* 4.6 0.4 - - + -
111H ALA 3.2 17.4 + - - +
112H CYS 3.4 0.6 - - - -
113H GLY* 1.3 74.7 - - - +
115H PRO* 1.3 66.0 - - + +
117H LEU* 3.0 12.0 + - - -
118H LEU* 2.8 43.3 + - + +
161H MET* 5.7 0.7 - - - -
164H VAL* 3.6 36.1 - - + +
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Residues in contact with PRO 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E SER* 4.5 1.6 + - - -
446F TYR* 3.3 50.7 - - + +
61H PRO* 3.9 27.4 - - + +
62H LEU* 3.9 21.3 - - + +
65H ALA* 4.5 1.1 - - + -
112H CYS 4.2 6.1 - - - +
113H GLY* 3.4 6.5 - - - -
114H ALA* 1.3 96.1 - - + +
116H GLU* 1.3 58.6 + - - +
118H LEU* 3.8 3.6 + - + +
119H LYS* 3.5 21.1 + - - +
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Residues in contact with GLU 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E GLU* 4.7 4.7 - - - +
110F TYR* 3.3 23.4 + - + -
116F GLU* 4.1 21.8 - - + +
117F LEU* 3.8 27.7 - - + +
446F TYR* 4.6 2.1 - - - -
465F PRO* 5.7 0.9 - - - +
113H GLY* 3.2 13.4 + - - +
115H PRO* 1.3 76.1 - - - +
117H LEU* 1.3 65.5 + - + +
118H LEU 3.2 0.2 - - - -
119H LYS* 2.7 56.2 + - - +
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Residues in contact with LEU 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F GLU* 3.5 31.4 - - + +
110H TYR* 3.1 61.5 - - + +
111H ALA* 5.1 0.2 - - - -
113H GLY* 3.5 13.7 - - - +
114H ALA* 3.0 8.4 + - - +
116H GLU* 1.3 77.7 - - + +
118H LEU* 1.3 60.6 + - + +
119H LYS 3.3 5.6 + - - +
136H PHE* 5.2 2.9 - - - -
161H MET* 3.7 19.1 - - + -
465H PRO* 5.9 0.4 - - + -
468H VAL* 3.6 27.6 - - + +
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Residues in contact with LEU 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E HIS 4.4 1.2 - - - +
123E SER* 5.9 1.1 - - - -
124E ARG* 5.4 4.7 + - - +
61H PRO* 4.1 19.5 - - + -
64H ARG* 3.6 26.9 - - - +
114H ALA* 2.8 23.5 + - + +
115H PRO* 4.2 7.0 - - + +
116H GLU 3.2 0.2 - - - -
117H LEU* 1.3 77.8 - - + +
119H LYS* 1.3 64.3 + - - +
120H GLY 3.2 3.8 + - - -
136H PHE* 4.1 26.7 + - + +
164H VAL 4.1 9.9 - - - +
165H CYS* 4.0 17.7 - - + +
468H VAL* 4.2 8.3 - - + -
472H THR* 3.9 28.0 - - + -
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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