Contacts of the helix formed by residues 199 - 209 (chain A) in PDB entry 2POD
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 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A PHE* 3.7 25.4 - - + -
195A LEU* 3.0 18.2 + - + +
196A LYS* 3.5 27.8 - - + +
197A ARG 3.2 0.4 - - - -
198A ALA* 1.3 76.9 - - - +
200A GLU* 1.3 55.8 + - - +
201A PRO 3.5 0.7 - - - -
202A PHE* 2.9 25.7 + - + +
203A GLU* 3.2 9.8 + - - +
234A ALA* 3.8 35.2 - - + +
235A LEU* 3.8 18.4 - - + -
237A GLU* 6.0 0.2 - - - +
238A TYR* 3.7 26.8 + - + +
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Residues in contact with GLU 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 LYS 3.5 10.2 + - - +
197A ARG* 3.2 38.2 + - - +
199A LEU* 1.3 73.1 - - - +
201A PRO* 1.4 69.3 - - + +
203A GLU* 3.3 10.1 + - + +
204A LYS* 3.1 40.2 + - - +
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Residues in contact with PRO 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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154A PHE* 3.4 24.2 - - + +
155A LEU* 4.9 8.7 - - + +
158A ALA* 4.0 12.6 - - + -
175A ILE* 3.9 23.1 - - + -
177A PRO* 3.9 20.6 - - + -
197A ARG 3.9 5.2 - - - +
198A ALA* 3.4 11.4 - - - +
200A GLU* 1.4 91.0 - - + +
202A PHE* 1.3 58.4 + - - +
204A LYS* 3.6 3.7 + - + +
205A ILE* 3.1 33.1 + - - +
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Residues in contact with PHE 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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175A ILE* 3.7 13.9 - - + -
177A PRO* 3.7 23.6 - - + -
178A PHE* 3.7 18.6 - + - -
198A ALA 3.8 7.6 - - - -
199A LEU* 2.9 20.0 + - - +
201A PRO* 1.3 74.5 - - - +
203A GLU* 1.3 65.0 + - - +
205A ILE* 3.8 6.0 + - - +
206A ARG* 3.3 23.9 + - - +
215A VAL* 3.8 28.7 - - + -
217A VAL* 3.7 34.5 - - + -
235A LEU* 3.8 13.5 - - + -
238A TYR* 3.7 27.3 - - + -
240A THR* 3.9 14.8 - - + -
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Residues in contact with GLU 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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199A LEU 3.2 8.0 + - - +
200A GLU* 3.3 14.1 + - + +
202A PHE* 1.3 76.8 - - - +
204A LYS* 1.3 60.6 + - + +
206A ARG* 2.8 34.8 + - - +
207A ARG* 3.1 51.3 + - - +
237A GLU* 5.5 1.0 - - - +
238A TYR* 3.7 18.4 + - - +
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Residues in contact with LYS 204 (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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156A HIS 3.6 26.2 + - - +
158A ALA* 4.0 15.0 - - + +
159A ASP* 3.5 38.2 - - - +
200A GLU* 3.1 32.3 + - - +
201A PRO* 3.8 5.4 - - + +
202A PHE 3.4 0.2 - - - -
203A GLU* 1.3 78.6 - - + +
205A ILE* 1.3 58.2 + - - +
207A ARG* 3.5 7.0 + - - +
208A ALA* 3.2 26.0 + - - +
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Residues in contact with ILE 205 (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 ALA* 3.4 28.7 - - + +
159A ASP* 4.6 0.4 - - - +
162A ALA* 3.9 12.1 - - + -
173A MSE 4.5 11.2 - - + -
175A ILE* 6.0 3.4 - - + -
201A PRO 3.1 18.4 + - - +
202A PHE* 4.4 7.4 - - - +
204A LYS* 1.3 73.8 - - - +
206A ARG* 1.3 62.6 + - - +
208A ALA* 4.3 5.2 - - - +
209A VAL* 3.0 43.5 + - + -
210A GLY 3.2 10.0 + - - +
213A MSE 3.8 16.2 - - + +
215A VAL* 3.7 32.8 - - + -
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Residues in contact with ARG 206 (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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202A PHE 3.3 17.7 + - - +
203A GLU* 2.8 34.7 + - - +
205A ILE* 1.3 79.5 - - - +
207A ARG* 1.3 61.8 + - - +
210A GLY* 3.4 25.7 - - - -
237A GLU* 2.9 40.9 + - - +
238A TYR* 3.4 33.0 - - - +
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Residues in contact with ARG 207 (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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203A GLU* 3.1 44.1 + - - +
204A LYS* 3.7 10.5 - - - +
205A ILE 3.3 0.2 - - - -
206A ARG* 1.3 78.4 - - - +
208A ALA* 1.3 63.7 + - - +
210A GLY 4.9 0.2 + - - -
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Residues in contact with ALA 208 (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* 3.7 32.8 - - + +
162A ALA* 4.9 0.7 - - + -
163A LEU* 3.8 22.5 - - + +
204A LYS 3.2 15.4 + - - +
205A ILE* 3.3 4.2 + - - +
207A ARG* 1.3 81.0 - - - +
209A VAL* 1.3 65.3 + - + +
212A LYS* 5.4 1.9 + - - -
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Residues in contact with VAL 209 (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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162A ALA* 3.9 12.6 - - + +
163A LEU* 3.8 31.9 - - + +
166A LEU* 3.8 29.2 - - + -
205A ILE* 3.0 31.9 + - + +
207A ARG 5.3 0.2 - - - -
208A ALA* 1.3 79.8 - - - +
210A GLY* 1.3 65.8 + - - +
211A ASP 3.2 3.5 + - - -
212A LYS* 3.4 32.3 + - + +
213A MSE 3.8 17.7 - - + -
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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