Contacts of the helix formed by residues 193 - 199 (chain A) in PDB entry 1Z29
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 TYR 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A SER 3.3 20.9 - - - +
50A GLY* 4.0 6.7 - - - -
53A TRP* 3.8 23.4 - + - -
128A VAL* 3.7 9.3 - - - +
129A ALA 2.8 9.7 + - - +
130A ARG* 3.4 63.3 + - + -
192A PHE* 1.3 70.9 - - - +
194A GLU* 1.3 67.4 + - + +
196A MET* 3.2 10.5 + - - +
197A LYS* 3.0 38.1 + - + +
259A GLY* 3.4 19.4 + - - -
260A MET 4.0 8.5 - - - -
261A ALA* 4.7 2.7 - - + -
2001A A3P 2.8 36.8 + + - -
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Residues in contact with GLU 194 (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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129A ALA 3.9 1.6 - - - +
130A ARG* 3.5 10.4 - - - +
131A ASN* 3.1 41.8 + - - +
134A ASP* 4.7 0.5 - - - +
192A PHE* 4.1 7.2 - - + +
193A TYR* 1.3 88.2 + - - +
195A ASP* 1.3 61.1 + - - +
197A LYS* 3.0 7.6 + - - +
198A GLU* 2.9 27.9 + - - +
261A ALA* 4.4 7.9 - - + +
291A PHE* 4.8 4.6 - - - -
292A ARG* 3.2 43.1 + - + +
295A LEU* 3.1 28.7 - - - +
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Residues in contact with ASP 195 (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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192A PHE* 2.9 37.7 + - + +
194A GLU* 1.3 74.1 - - - +
196A MET* 1.3 57.9 + - - +
199A ASN 2.9 30.3 + - - -
202A ARG* 3.2 14.9 + - - +
203A GLU* 3.6 26.1 - - - +
206A LYS* 4.9 4.9 + - - -
292A ARG* 2.6 37.2 + - - +
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Residues in contact with MET 196 (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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50A GLY 5.2 1.1 - - - +
53A TRP* 3.3 45.0 - - + -
54A VAL* 4.2 22.4 - - + +
57A ILE* 4.0 22.7 - - + -
128A VAL* 3.9 30.7 - - - -
191A LEU* 4.8 9.6 - - + -
192A PHE 3.1 10.0 + - - +
193A TYR* 3.4 10.1 - - - +
195A ASP* 1.3 76.5 - - - +
197A LYS* 1.3 60.0 + - - +
200A PRO* 3.1 26.4 - - + +
203A GLU* 3.6 26.5 - - + +
207A ILE* 5.2 4.7 - - + -
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Residues in contact with LYS 197 (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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53A TRP* 3.6 7.8 - - + -
193A TYR* 3.0 28.4 + - + +
194A GLU* 3.0 11.0 + - - +
196A MET* 1.3 80.4 - - - +
198A GLU* 1.3 65.0 + - - +
200A PRO* 3.5 6.9 - - - +
229A PHE* 4.5 14.8 - - - +
259A GLY 2.6 30.9 + - - -
260A MET* 4.2 7.5 - - - +
261A ALA* 4.5 10.1 - - + +
295A LEU* 3.6 11.9 - - - +
2001A A3P 4.3 10.2 + - - -
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Residues in contact with GLU 198 (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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194A GLU 2.9 15.5 + - - +
195A ASP 3.7 3.4 - - - +
197A LYS* 1.3 79.1 - - - +
199A ASN* 1.3 60.0 + - + +
200A PRO* 3.8 2.3 - - - +
202A ARG* 3.4 20.9 + - - +
292A ARG* 2.9 40.4 + - - +
295A LEU* 3.7 24.7 + - + +
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Residues in contact with ASN 199 (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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195A ASP 2.9 12.9 + - - -
198A GLU* 1.3 76.5 - - + +
200A PRO* 1.3 65.2 - - - +
201A LYS* 3.5 9.4 + - - +
202A ARG* 3.1 61.9 + - - +
203A GLU* 3.3 13.9 + - - +
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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