Contacts of the helix formed by residues 113 - 118 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A GLU 3.8 2.0 + - - -
110A TYR 3.1 10.1 + - - -
111A ALA 3.0 2.0 - - - -
112A CYS* 1.3 75.7 - - - +
114A ALA* 1.3 63.7 + - - -
115A PRO* 3.0 7.4 - - - -
116A GLU* 3.1 17.5 + - - +
117A LEU* 3.2 18.8 + - - +
109C GLU 5.9 2.7 - - - -
113C GLY* 5.7 9.8 - - - -
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Residues in contact with ALA 114 (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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61A PRO* 4.5 6.5 - - + +
65A ALA* 4.6 0.4 - - + -
111A ALA 3.1 17.2 + - - +
112A CYS 3.2 0.6 - - - -
113A GLY* 1.3 73.8 - - - +
115A PRO* 1.3 66.7 - - + +
117A LEU* 3.2 11.2 + - - +
118A LEU* 2.9 47.8 + - + +
161A MET* 5.9 0.4 - - - -
164A VAL* 3.6 31.0 - - + +
165A CYS* 5.9 0.2 - - - -
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Residues in contact with PRO 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PRO* 4.1 25.1 - - + +
62A LEU* 4.2 18.8 - - + +
65A ALA* 4.5 1.3 - - + -
112A CYS 3.8 8.7 - - - +
113A GLY* 3.2 6.3 - - - -
114A ALA* 1.3 95.8 - - + +
116A GLU* 1.3 61.7 + - - +
118A LEU* 3.6 8.5 + - + +
119A LYS* 3.7 13.7 + - - +
446C TYR* 3.5 50.9 - - + +
123D SER* 4.7 1.2 + - - -
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Residues in contact with GLU 116 (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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113A GLY* 3.1 10.6 + - - +
115A PRO* 1.3 77.2 - - - +
117A LEU* 1.3 65.6 + - + +
118A LEU 3.1 1.6 + - - -
119A LYS* 2.8 60.3 + - - +
110C TYR* 2.9 27.1 + - + -
116C GLU* 4.3 20.4 - - + +
117C LEU* 3.6 28.2 - - + +
446C TYR* 4.6 2.1 - - - +
465C PRO* 5.7 0.9 - - - +
121D GLU* 4.4 4.7 - - - +
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Residues in contact with LEU 117 (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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110A TYR* 3.2 50.0 - - + +
111A ALA* 5.2 0.2 - - - -
113A GLY* 3.4 14.4 - - - +
114A ALA* 3.2 10.0 + - - +
116A GLU* 1.3 78.3 - - + +
118A LEU* 1.3 59.3 + - + +
119A LYS 3.4 4.8 + - - +
136A PHE* 5.5 1.7 - - - -
161A MET* 3.6 32.5 - - + -
165A CYS* 6.4 0.2 - - - -
465A PRO* 5.9 0.4 - - + -
468A VAL* 3.4 30.4 - - + +
116C GLU* 3.7 25.8 - - + +
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Residues in contact with LEU 118 (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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61A PRO* 4.2 14.4 - - + -
64A ARG* 3.7 25.4 - - - +
114A ALA* 2.9 35.4 + - + +
115A PRO* 4.1 5.2 - - + +
116A GLU 3.2 0.4 - - - -
117A LEU* 1.3 75.4 - - + +
119A LYS* 1.3 65.3 + - - +
120A GLY 3.3 2.8 + - - -
136A PHE* 4.0 36.4 + - + +
164A VAL 4.2 3.8 - - - +
165A CYS* 4.0 25.1 - - + +
468A VAL* 4.2 8.5 - - + -
472A THR* 4.0 9.6 - - + -
122D HIS 4.3 1.4 - - - +
123D SER* 6.0 0.4 - - - -
124D ARG* 5.5 5.0 + - - +
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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