Contacts of the helix formed by residues 193 - 198 (chain E) in PDB entry 2ZHX
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 SER 193 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E SER* 3.6 5.6 - - - -
191E HIS* 2.7 27.5 + - - -
192E PRO* 1.3 70.2 - - - +
194E PRO* 1.3 66.4 - - - +
195E LEU* 3.9 7.4 + - - -
196E SER* 2.9 10.4 + - - -
197E ALA 2.7 32.2 + - - -
20F GLU* 3.2 18.2 + - - -
22F ILE* 4.0 10.1 - - - +
24F MET* 5.1 2.2 - - - -
43F VAL* 4.0 11.9 - - - +
45F THR* 3.4 9.7 + - - -
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Residues in contact with PRO 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E ARG* 3.6 28.5 - - + -
93E SER 4.2 4.9 - - - +
96E ASN* 3.6 20.2 - - - +
192E PRO 3.4 0.6 - - - +
193E SER* 1.3 90.0 - - - +
195E LEU* 1.3 60.8 + - - +
196E SER 3.2 1.0 + - - -
197E ALA* 3.9 6.0 + - + +
198E SER* 4.7 6.2 + - - -
20F GLU* 4.2 0.9 - - - +
45F THR* 3.7 11.0 - - + -
54F ASN* 3.4 31.0 - - + +
56F MET* 3.8 15.5 - - - -
73F GLN* 3.2 25.0 + - - +
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Residues in contact with LEU 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193E SER* 2.9 3.7 + - - +
194E PRO* 1.3 79.9 - - - +
196E SER* 1.3 57.8 + - - +
198E SER* 5.2 2.1 + - - -
199E ARG* 4.3 1.2 - - - +
24F MET* 4.1 13.2 - - + -
28F GLU 5.3 0.4 - - - +
29F VAL* 4.3 17.9 - - + -
32F VAL* 3.4 44.8 - - + +
33F ILE* 4.5 4.7 - - + -
43F VAL* 3.7 33.2 - - + -
56F MET* 3.6 14.3 - - + -
58F LEU* 3.8 32.1 - - + -
71F VAL* 4.4 21.5 - - + -
73F GLN* 4.9 1.8 - - - +
79F ASN* 5.3 1.1 - - - +
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Residues in contact with SER 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E PRO* 3.9 16.4 - - - +
191E HIS* 2.6 28.6 + - - +
193E SER* 2.9 3.0 + - - -
195E LEU* 1.3 78.4 - - - +
197E ALA* 1.3 69.3 + - - +
198E SER 3.2 2.7 - - - -
199E ARG* 2.8 28.7 + - - +
24F MET* 3.3 35.2 - - - +
28F GLU* 5.6 2.9 - - - -
32F VAL* 5.5 1.6 - - - -
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Residues in contact with ALA 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E ASN* 3.5 8.5 - - - +
191E HIS 3.4 7.1 + - - -
192E PRO* 3.4 19.7 - - + +
193E SER 2.7 17.1 + - - +
194E PRO* 3.9 3.2 + - + +
195E LEU 3.8 0.2 - - - -
196E SER* 1.3 77.9 - - - +
198E SER* 1.3 58.6 + - - +
199E ARG 2.9 5.4 + - - -
201E PHE* 3.2 12.5 + - + -
202E PHE* 3.1 49.0 + - + -
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Residues in contact with SER 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E PRO 4.7 8.1 + - - -
195E LEU 5.2 1.4 + - - -
196E SER 4.8 0.3 - - - -
197E ALA* 1.3 77.4 - - - +
199E ARG* 1.3 69.8 + - - +
200E GLY 3.3 4.8 + - - -
202E PHE* 3.6 20.1 - - - +
73F GLN* 5.5 2.9 + - - -
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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