Contacts of the helix formed by residues 193 - 198 (chain E) in PDB entry 4SKN
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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127E THR* 5.8 0.7 - - - +
131E MET* 3.2 28.2 - - - +
154E HIS* 4.8 3.8 - - - -
156E LEU* 4.0 10.1 - - - +
191E ASP* 2.9 22.3 + - - -
192E LEU* 1.3 76.8 - - - +
194E GLY* 1.3 62.4 + - - +
196E ALA* 3.3 5.3 + - - +
197E LYS* 2.9 36.0 + - - +
304E LEU* 5.6 1.3 - - - -
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Residues in contact with GLY 194 (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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192E LEU 2.8 4.0 + - - -
193E SER* 1.3 80.0 - - - +
195E TRP* 1.3 60.9 + - - -
197E LYS* 3.4 8.3 + - - +
198E GLN* 3.1 23.8 + - - +
303E GLU* 3.4 24.7 - - - +
304E LEU* 3.6 19.0 + - - +
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Residues in contact with TRP 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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141E ILE* 4.4 15.3 - - + -
158E PHE* 6.6 0.2 - + - -
170E LEU* 5.0 1.8 - - + -
173E ILE* 4.1 19.7 - - + -
174E TYR* 4.8 2.9 - + - -
177E LEU* 3.6 31.6 - - + -
192E LEU* 3.0 34.7 + - + +
194E GLY* 1.3 75.2 - - - +
196E ALA* 1.3 57.1 + - - +
198E GLN* 2.7 36.7 + - - +
199E GLY 3.3 0.5 + - - -
200E VAL* 3.2 29.0 - - + +
202E LEU* 4.2 18.6 - - + -
245E TRP* 5.7 1.6 - + - -
284E PHE* 4.7 2.7 - + - -
299E ILE* 5.2 0.9 - - + -
301E TRP* 3.2 47.0 + + + -
303E GLU 4.4 3.6 - - - -
304E LEU* 3.0 40.1 - - + +
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Residues in contact with ALA 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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131E MET* 3.5 32.3 - - + +
132E CYS* 3.8 12.6 - - - +
156E LEU* 3.7 19.1 - - + -
192E LEU 3.3 3.2 + - - +
193E SER 3.3 9.6 + - - +
195E TRP* 1.3 79.5 - - - +
197E LYS* 1.3 60.9 + - - +
199E GLY* 3.1 13.2 + - - -
200E VAL 3.4 21.0 + - - +
202E LEU* 4.4 5.8 - - + +
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Residues in contact with LYS 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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131E MET* 3.5 39.9 + - + +
132E CYS* 4.3 8.6 - - - +
193E SER* 2.9 28.1 + - - +
194E GLY* 3.8 7.2 - - - +
195E TRP 3.3 0.2 - - - -
196E ALA* 1.3 71.8 - - - +
198E GLN* 1.3 60.9 + - + +
199E GLY 3.6 0.3 + - - -
303E GLU* 6.2 0.2 - - - +
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Residues in contact with GLN 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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136E ASP 4.6 2.0 - - - +
138E LYS* 3.1 27.0 + - - +
194E GLY 3.1 14.3 + - - +
195E TRP* 2.7 15.3 + - - +
197E LYS* 1.3 78.8 - - + +
199E GLY* 1.3 55.0 + - - -
298E PRO 4.6 1.9 - - - +
299E ILE* 3.5 24.3 - - + +
300E ASP* 3.0 48.9 + - - +
303E GLU* 3.4 39.5 + - - +
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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