Contacts of the helix formed by residues 193 - 203 (chain A) in PDB entry 1K7E
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 LEU 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A PRO* 4.5 11.4 - - + -
176A LEU* 4.1 16.6 - - + -
177A LEU 3.9 15.9 - - - +
178A SER* 3.9 26.5 - - - +
192A PRO* 1.3 86.1 - - + +
194A HIS* 1.3 61.4 + - - +
195A HIS 3.0 3.6 + - - -
196A LEU* 3.0 27.2 + - + +
197A ILE* 2.6 47.0 + - + +
210A GLN* 4.0 28.7 - - + +
226A ALA* 5.8 2.2 - - + -
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Residues in contact with HIS 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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192A PRO* 3.6 10.1 - - + +
193A LEU* 1.3 86.2 + - - +
195A HIS* 1.3 63.2 + - - +
197A ILE* 3.8 8.7 - - - +
198A GLU* 2.9 34.6 + - + +
225A ARG 5.0 1.5 + - - -
226A ALA* 3.6 40.3 - - + +
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Residues in contact with HIS 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 PRO 5.0 3.7 + - - +
193A LEU* 3.0 1.2 - - - +
194A HIS* 1.3 79.2 - - - +
196A LEU* 1.3 81.0 + - + +
197A ILE 3.0 0.3 + - - -
198A GLU* 4.7 5.6 - - + -
199A LYS* 2.9 71.3 + - + +
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Residues in contact with LEU 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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154A CYS* 4.3 8.3 - - - -
155A PRO 3.5 24.5 - - - +
156A PRO* 3.6 24.5 - - + +
158A ALA* 5.4 4.3 - - + +
163A LEU* 4.5 12.3 - - + -
176A LEU* 3.9 27.4 - - + -
192A PRO 4.8 4.0 - - - +
193A LEU* 3.0 20.6 + - + +
195A HIS* 1.3 87.8 - - + +
197A ILE* 1.3 66.9 + - - +
199A LYS* 3.2 5.8 + - - +
200A LEU* 2.8 29.3 + - + +
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Residues in contact with ILE 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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176A LEU* 3.6 27.4 - - + -
193A LEU* 2.6 37.7 + - + +
194A HIS* 3.8 3.8 - - - +
196A LEU* 1.3 72.5 - - - +
198A GLU* 1.3 60.0 + - - +
200A LEU* 3.4 9.4 + - + +
201A LYS* 3.0 37.5 + - + +
208A ALA* 5.3 6.5 - - + -
210A GLN* 6.1 0.4 - - - +
226A ALA* 3.6 29.4 - - + +
227A GLY* 3.6 28.9 - - - +
228A ALA* 3.9 16.6 - - + +
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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 HIS* 2.9 24.4 + - + +
195A HIS* 3.8 8.5 - - + +
197A ILE* 1.3 78.1 - - - +
199A LYS* 1.3 57.0 + - + +
201A LYS* 3.1 20.0 + - - +
202A GLU* 2.6 36.8 + - - +
226A ALA 4.6 10.6 - - - +
227A GLY* 5.4 1.2 - - - -
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Residues in contact with LYS 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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159A ASP* 5.3 1.0 - - - +
160A ASP* 4.2 23.8 + - - +
163A LEU* 3.7 29.5 - - + +
195A HIS* 2.9 58.2 + - + +
196A LEU 3.6 2.5 - - - +
198A GLU* 1.3 79.7 - - + +
200A LEU* 1.4 58.7 + - - +
202A GLU* 2.8 23.2 + - - +
203A TYR* 2.8 48.1 + - + +
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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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154A CYS* 4.2 17.5 - - - -
163A LEU* 3.7 36.8 - - + +
166A VAL* 4.6 6.7 - - + -
167A ALA* 5.0 0.2 - - + -
174A THR* 4.1 24.2 - - + -
176A LEU* 4.5 9.2 - - + -
196A LEU* 2.8 31.0 + - + +
197A ILE* 3.9 4.7 - - - +
199A LYS* 1.4 72.0 - - - +
201A LYS* 1.3 61.4 + - - +
203A TYR* 3.3 3.7 + - - +
204A HIS 3.2 2.4 + - - -
205A ALA* 2.9 47.8 + - + +
206A ALA 5.5 0.9 - - - +
208A ALA* 4.6 14.1 - - + -
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Residues in contact with LYS 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 ILE* 3.0 26.7 + - + +
198A GLU* 3.1 23.5 + - - +
200A LEU* 1.3 75.8 - - - +
202A GLU* 1.3 66.1 + - - +
204A HIS* 2.9 20.1 + - - +
205A ALA 4.9 1.1 - - - +
227A GLY* 3.4 35.4 + - - -
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Residues in contact with GLU 202 (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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198A GLU 2.6 18.6 + - - +
199A LYS* 2.8 28.0 + - - +
201A LYS* 1.3 74.8 - - - +
203A TYR* 1.4 79.9 + - + +
204A HIS* 3.2 19.9 + - - -
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Residues in contact with TYR 203 (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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160A ASP* 2.7 28.0 + - - -
163A LEU* 4.2 19.7 - - + -
164A ARG* 3.0 52.5 + - + -
167A ALA* 3.5 25.7 - - + +
199A LYS* 2.8 39.0 + - + +
200A LEU* 3.3 1.5 + - - +
201A LYS 3.1 0.2 - - - -
202A GLU* 1.4 104.8 + - - +
204A HIS* 1.3 75.2 + - - +
205A ALA 3.2 2.0 + - - -
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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