Contacts of the helix formed by residues 113 - 118 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A GLU 6.0 1.8 - - - -
113A GLY* 5.7 11.0 - - - -
109C GLU 4.0 1.2 + - - -
110C TYR 3.3 9.0 + - - -
111C ALA 2.9 2.5 + - - -
112C CYS* 1.3 77.0 - - - +
114C ALA* 1.3 62.4 + - - +
115C PRO* 3.2 5.8 - - - -
116C GLU* 3.2 18.3 + - - +
117C LEU* 3.3 20.0 + - - +
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Residues in contact with ALA 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C PRO* 4.8 2.7 - - + +
65C ALA* 4.5 1.8 - - + -
111C ALA 3.0 7.0 + - - +
112C CYS 3.3 0.6 - - - -
113C GLY* 1.3 77.3 - - - +
115C PRO* 1.3 67.3 - - + +
117C LEU* 3.2 10.4 + - - -
118C LEU* 2.8 43.0 + - + +
161C MET* 5.9 0.2 - - - -
164C VAL* 3.5 47.6 - - + +
165C CYS* 6.1 0.2 - - - -
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Residues in contact with PRO 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A TYR* 3.4 49.4 - - + +
123B SER* 4.7 0.9 + - - -
61C PRO* 3.9 22.0 - - + -
62C LEU* 3.9 20.4 - - + +
65C ALA* 4.2 10.8 - - + -
112C CYS 4.3 1.8 - - - +
113C GLY* 3.4 6.5 - - - -
114C ALA* 1.3 95.3 - - + +
116C GLU* 1.3 60.0 + - - +
118C LEU* 3.6 7.4 + - + +
119C LYS* 3.5 17.0 + - - +
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Residues in contact with GLU 116 (chain C).
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* 2.7 42.1 + - + -
116A GLU* 4.3 21.9 - - + +
117A LEU* 3.7 19.2 - - + +
446A TYR* 4.5 3.0 - - - +
121B GLU* 4.2 8.0 - - - +
113C GLY* 3.2 12.0 + - - +
115C PRO* 1.3 77.2 - - - +
117C LEU* 1.3 62.8 + - + +
119C LYS* 2.9 46.7 + - - +
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Residues in contact with LEU 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A GLU* 3.6 29.4 - - + +
110C TYR* 3.2 65.5 - - + +
111C ALA* 5.0 0.2 - - - -
113C GLY 3.3 15.9 - - - +
114C ALA* 3.2 11.1 + - - +
116C GLU* 1.3 77.7 - - + +
118C LEU* 1.3 60.9 + - + +
119C LYS 3.4 4.9 + - - +
136C PHE* 5.4 2.3 - - - -
161C MET* 3.8 15.0 - - + -
468C VAL* 3.6 28.5 - - + +
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Residues in contact with LEU 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B HIS 4.2 1.4 - - - +
123B SER* 5.3 2.8 - - - -
124B ARG* 5.4 2.9 + - - +
61C PRO* 4.1 14.4 - - + -
64C ARG* 3.7 26.0 - - - +
114C ALA* 2.8 28.2 + - + +
115C PRO* 3.6 5.8 + - + +
116C GLU 3.3 0.4 - - - -
117C LEU* 1.3 79.1 - - + +
119C LYS* 1.3 63.2 + - - +
120C GLY* 3.2 3.6 + - - -
135C GLU* 6.0 0.2 - - - -
136C PHE* 4.2 27.1 + - + +
164C VAL 3.9 12.3 - - - +
165C CYS* 4.1 25.8 - - + +
468C VAL* 4.4 7.6 - - + -
472C THR* 4.2 17.7 - - + -
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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