Contacts of the helix formed by residues 193 - 201 (chain A) in PDB entry 2D7I
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 LYS 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A SER 3.9 21.6 + - - +
188A ASP* 4.1 8.5 + - - +
189A ARG 3.7 9.9 - - - +
190A GLU* 3.0 45.2 + - - +
191A HIS 3.2 0.8 - - - -
192A LEU* 1.3 84.3 - - + +
194A LYS* 1.3 69.6 + - + +
195A PRO* 3.3 0.9 - - + -
196A LEU 3.3 1.6 + - - -
197A GLU* 3.0 33.2 + - - +
210A ARG* 3.9 8.3 - - - +
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Residues in contact with LYS 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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193A LYS* 1.3 78.8 - - + +
195A PRO* 1.3 72.1 - - + +
197A GLU* 2.9 20.6 + - + +
198A ASP* 2.8 62.2 + - - +
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Residues in contact with PRO 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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158A TRP* 3.9 14.7 - - + -
190A GLU 3.5 19.1 - - - +
191A HIS* 3.6 14.6 - - + +
193A LYS 3.4 4.3 - - - -
194A LYS* 1.3 95.0 - - + +
196A LEU* 1.3 62.9 + - - +
198A ASP* 3.2 7.7 + - + +
199A TYR* 2.9 24.8 + - - +
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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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153A PHE* 3.8 27.4 - - + -
158A TRP* 3.7 13.0 - - + -
161A LEU* 4.0 22.0 - - + -
162A LEU* 4.0 10.3 - - + -
182A LEU* 4.9 2.7 - - + -
191A HIS 3.2 14.4 + - - +
192A LEU* 3.8 20.9 - - + +
193A LYS 3.3 7.5 + - - +
195A PRO* 1.3 78.2 - - - +
197A GLU* 1.3 58.4 + - - +
199A TYR* 3.6 0.7 - - + +
200A MET* 2.8 64.3 + - + +
208A ILE* 3.8 19.7 - - + -
210A ARG* 4.6 0.9 - - - +
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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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193A LYS* 3.0 20.1 + - - +
194A LYS* 2.9 25.4 + - + +
196A LEU* 1.3 76.5 - - - +
198A ASP* 1.3 63.6 + - - +
200A MET* 3.8 0.7 - - - +
201A ALA* 2.9 27.1 + - - +
208A ILE* 3.9 13.9 - - + -
210A ARG* 3.0 35.1 + - - +
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Residues in contact with ASP 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 LYS* 2.8 60.2 + - - +
195A PRO* 3.8 5.3 - - + +
197A GLU* 1.3 74.1 - - - +
199A TYR* 1.3 63.1 + - - +
201A ALA* 3.4 15.8 + - - +
202A LEU* 3.7 13.7 - - - +
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Residues in contact with TYR 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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123A LEU* 4.2 5.6 - - + +
158A TRP* 3.9 20.4 - + + -
162A LEU* 3.5 35.5 - - + +
166A HIS* 2.9 30.1 + + - -
195A PRO 2.9 16.9 + - - +
196A LEU* 3.6 3.8 - - + +
198A ASP* 1.3 78.5 - - - +
200A MET* 1.3 76.4 + - + +
202A LEU* 3.3 24.1 + - + +
203A PHE* 3.4 34.7 - + - -
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Residues in contact with MET 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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161A LEU* 5.2 0.9 - - + -
162A LEU* 3.4 36.8 - - + -
165A VAL* 4.0 23.3 - - + -
166A HIS* 6.2 0.7 - - + -
182A LEU* 4.0 19.5 - - + -
196A LEU* 2.8 35.3 + - + +
197A GLU 4.2 0.7 - - - +
199A TYR* 1.3 78.2 - - + +
201A ALA* 1.3 62.1 + - - +
202A LEU 3.0 6.1 - - - -
203A PHE* 3.0 31.2 + - - +
206A VAL* 3.7 36.9 - - + +
207A ARG* 6.1 0.2 - - - -
208A ILE* 4.1 14.6 - - + -
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Residues in contact with ALA 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 2.9 19.3 + - - +
198A ASP* 3.6 10.3 - - - +
199A TYR 3.2 0.6 - - - -
200A MET* 1.3 77.0 - - - +
202A LEU* 1.3 62.5 + - + +
203A PHE 3.2 4.6 + - - -
204A PRO* 4.7 3.6 - - - +
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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