Contacts of the helix formed by residues 195 - 201 (chain A) in PDB entry 4IZ5
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 ALA 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A TYR 3.8 1.0 + - - -
194A ARG* 1.3 76.3 - - - +
196A PRO* 1.3 72.6 - - + +
197A GLU* 3.4 26.5 - - - +
198A ILE* 3.0 28.1 + - + +
199A MET* 3.2 10.9 + - - +
209A ILE* 4.0 12.2 + - + +
212A TRP* 3.3 24.8 - - + -
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Residues in contact with PRO 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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194A ARG 3.6 0.4 - - - -
195A ALA* 1.3 85.3 - - + +
197A GLU* 1.3 68.9 + - - +
199A MET* 3.2 21.8 + - + +
200A LEU* 3.2 27.8 + - + +
212A TRP* 3.5 38.4 - - + -
237A LEU* 5.2 2.2 - - + -
240A ILE* 4.3 11.7 - - + -
296A PHE* 3.9 46.0 - - + +
301A ARG* 4.3 0.2 - - - +
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Residues in contact with GLU 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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195A ALA* 3.4 12.7 - - - +
196A PRO* 1.3 73.6 - - + +
198A ILE* 1.3 66.9 + - - +
199A MET 3.1 2.0 - - - -
200A LEU* 3.9 9.0 - - + -
201A ASN* 3.1 46.3 + - + +
204A GLY 5.5 2.9 - - - +
205A TYR* 3.7 10.7 - - + -
206A THR* 5.1 1.3 + - - +
208A SER* 4.0 1.9 + - - -
209A ILE* 3.4 21.6 - - + +
254A CYS* 5.6 2.0 - - + +
296A PHE* 4.2 2.0 - - - +
298A PRO* 3.5 29.1 - - + +
301A ARG* 2.6 39.3 + - - -
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Residues in contact with ILE 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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148A ARG* 5.5 6.3 - - + +
180A HIS* 5.9 1.5 - - + +
184A LEU* 3.8 24.2 - - + -
185A GLU* 5.6 2.9 - - - +
194A ARG* 3.7 23.6 - - + +
195A ALA* 3.0 23.4 + - + +
197A GLU* 1.3 79.9 - - - +
199A MET* 1.3 62.6 + - - +
200A LEU 3.4 0.5 + - - -
201A ASN 4.1 2.3 + - - -
202A SER 4.7 0.2 + - - -
205A TYR* 3.0 44.7 + - + +
209A ILE* 3.6 50.5 - - + +
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Residues in contact with MET 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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191A ARG* 3.9 22.7 - - - -
194A ARG* 3.7 30.7 - - + +
195A ALA 3.2 4.9 + - - +
196A PRO* 3.2 8.7 + - + +
197A GLU 3.1 0.8 - - - -
198A ILE* 1.3 82.6 - - - +
200A LEU* 1.3 54.1 + - - +
233A TYR* 2.6 56.0 + - + -
236A GLN* 3.6 35.4 - - + -
237A LEU* 4.1 15.5 - - + -
240A ILE* 3.8 15.9 - - + -
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Residues in contact with LEU 200 (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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196A PRO* 3.2 37.3 + - + +
197A GLU* 3.9 11.4 - - + -
198A ILE 3.3 0.2 - - - -
199A MET* 1.3 78.4 - - - +
201A ASN* 1.3 61.2 + - - +
233A TYR* 4.3 6.7 - - - +
237A LEU* 3.6 31.2 - - + -
255A ILE* 3.8 30.7 - - + +
257A ASN* 3.4 23.7 - - - +
260A ALA* 3.6 23.3 - - + +
264A LEU* 4.3 21.3 - - + -
296A PHE* 5.2 4.7 - - + -
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Residues in contact with ASN 201 (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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197A GLU* 3.1 38.4 + - - +
198A ILE 4.1 0.6 + - - -
199A MET 3.9 0.8 - - - -
200A LEU* 1.3 83.2 - - - +
202A SER* 1.3 69.2 + - - +
203A LYS* 3.3 25.5 + - - +
205A TYR* 4.4 1.1 - - + -
254A CYS 3.4 18.7 + - - -
255A ILE* 3.5 6.5 - - - +
256A ILE* 2.7 44.5 + - + +
257A ASN* 3.6 16.6 + - - +
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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