Contacts of the helix formed by residues 106 - 111 (chain A) in PDB entry 3ZG2
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 MET 106 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A TYR* 3.4 15.3 - - + +
104A THR 2.7 0.6 + - - -
105A ILE* 1.3 96.8 - - - +
107A THR* 1.3 66.3 + - - +
108A PRO* 3.1 4.3 - - - -
109A VAL* 3.0 22.8 + - + +
110A PHE* 3.1 49.0 + - + -
116A TYR* 5.0 8.1 - - + -
208A LEU* 4.0 22.2 - - + -
290A PHE* 3.1 43.3 - - + -
460A MET* 4.9 1.8 - - - -
1490A UDO 3.7 24.7 - - - +
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Residues in contact with THR 107 (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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103A TYR 4.4 2.9 - - - +
104A THR* 3.0 30.4 + - + +
106A MET* 1.3 78.6 - - - +
108A PRO* 1.3 61.9 - - - +
110A PHE* 4.5 2.9 - - - +
111A GLY* 2.5 41.0 + - - +
112A GLU* 3.9 18.7 + - - +
114A VAL 5.7 0.7 - - - -
116A TYR* 5.9 1.3 - - + -
117A ALA* 4.1 30.5 - - + +
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Residues in contact with PRO 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A THR 4.1 4.0 - - - +
105A ILE* 4.2 4.3 - - - +
106A MET* 3.1 12.3 - - - +
107A THR* 1.3 98.8 - - - +
109A VAL* 1.3 65.2 + - + +
111A GLY* 4.3 2.6 + - - +
207A SER* 5.2 7.4 - - - +
226A SER* 5.7 8.1 - - - +
229A CYS* 3.8 14.1 - - + -
230A ARG* 5.6 0.9 + - - -
233A ARG* 3.3 20.3 - - - -
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Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ILE 4.6 0.7 - - - +
106A MET* 3.0 19.2 + - + +
108A PRO* 1.3 89.0 - - + +
110A PHE* 1.3 77.1 + - + +
201A LEU* 6.5 0.2 - - + -
204A MET* 3.9 30.5 - - + +
205A GLU* 4.8 5.8 - - + -
207A SER* 4.5 2.5 - - - +
208A LEU* 4.4 23.1 - - + -
229A CYS* 4.3 5.2 - - - -
233A ARG* 3.1 20.7 + - - +
286A VAL* 3.5 20.8 - - + +
290A PHE* 5.4 6.1 - - + -
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Residues in contact with PHE 110 (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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106A MET* 3.1 40.5 + - + +
107A THR* 4.2 1.6 - - - +
109A VAL* 1.3 108.3 - - + +
111A GLY* 1.3 59.3 - - - +
114A VAL* 3.5 28.6 - - + +
115A ALA* 3.6 26.2 - - + -
116A TYR* 5.4 2.0 - + - -
233A ARG* 3.4 8.2 + - - -
279A HIS* 4.3 1.0 + - - +
283A GLY* 3.4 23.4 - - - +
286A VAL* 4.3 1.8 - - + -
287A ALA* 3.7 41.1 - - + -
290A PHE* 4.2 16.6 - + - -
1490A UDO 4.4 18.2 - + - -
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Residues in contact with GLY 111 (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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107A THR* 2.5 21.0 + - - +
108A PRO* 4.3 3.6 + - - -
109A VAL 3.8 0.6 - - - -
110A PHE* 1.3 73.6 - - - +
112A GLU* 1.3 69.2 + - - -
113A GLY 3.3 0.2 + - - -
114A VAL* 3.0 25.1 + - - +
117A ALA* 3.9 2.1 - - - +
233A ARG* 4.6 1.1 - - - -
279A HIS* 3.6 23.6 - - - -
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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