Contacts of the helix formed by residues 201 - 209 (chain A) in PDB entry 1PHP
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 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A ILE* 4.0 10.3 - - + -
194A GLY 3.4 16.7 + - - -
195A GLY* 4.6 1.3 - - - -
197A LYS 3.7 5.8 - - - +
198A VAL 2.8 5.0 + - - +
200A ASP* 1.3 90.6 - - - +
202A ILE* 1.3 64.7 - - - +
203A GLY 3.3 3.3 + - - -
204A VAL* 3.3 11.5 + - + -
205A ILE* 2.9 33.1 + - + +
221A LEU* 3.4 31.0 - - + -
316A ASN* 2.8 29.6 + - - +
317A GLY* 4.9 0.2 - - - -
377A LEU* 4.0 11.4 - - + +
396A ADP 2.8 42.9 + - - -
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Residues in contact with ILE 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 VAL* 3.1 18.8 + - + +
199A LYS* 3.8 15.9 - - + +
200A ASP 3.7 2.0 - - - -
201A LYS* 1.3 77.0 - - - +
203A GLY* 1.3 59.4 + - - +
205A ILE* 4.9 0.4 - - - -
206A ASP* 2.9 34.8 + - + +
242A LYS* 3.7 22.4 - - + -
245A LEU* 3.5 32.8 - - + -
249A PHE* 3.7 24.3 - - + -
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Residues in contact with GLY 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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200A ASP 5.4 0.4 + - - -
201A LYS 3.3 1.0 - - - -
202A ILE* 1.3 77.6 - - - +
204A VAL* 1.3 60.4 + - - +
206A ASP* 3.8 4.5 - - - +
207A ASN* 3.0 31.5 + - - +
381A GLU* 3.6 29.7 + - - +
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Residues in contact with VAL 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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193A ILE* 4.2 15.7 - - + -
200A ASP 5.1 1.8 - - - +
201A LYS* 3.3 19.7 + - + +
203A GLY* 1.3 75.0 - - - +
205A ILE* 1.4 65.2 + - - +
207A ASN 3.5 0.3 + - - -
208A LEU* 2.9 54.1 + - + +
316A ASN* 5.4 3.6 - - + +
377A LEU* 3.9 26.7 - - + +
380A MET* 4.2 20.2 - - + -
381A GLU* 3.6 27.4 - - + +
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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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193A ILE* 4.1 26.2 - - + -
198A VAL* 5.3 4.5 - - + +
201A LYS* 2.9 34.6 + - + +
202A ILE* 4.0 2.9 - - - +
204A VAL* 1.4 76.4 - - - +
206A ASP* 1.3 65.5 + - - +
208A LEU* 4.0 3.6 - - - +
209A LEU* 3.1 33.8 + - + +
215A LEU* 4.3 17.7 - - + +
217A ILE* 4.5 10.5 - - + -
221A LEU* 4.3 13.7 - - + -
225A PHE* 4.5 10.8 - - + -
249A PHE* 3.9 37.2 - - + -
260A PHE* 5.8 0.2 - - + -
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Residues in contact with ASP 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 ILE* 2.9 21.8 + - + +
203A GLY* 3.8 6.7 - - - +
204A VAL 3.2 0.2 - - - -
205A ILE* 1.3 80.3 - - - +
207A ASN* 1.4 62.8 + - - +
209A LEU* 3.6 7.2 + - - +
210A GLU* 3.8 3.0 - - - +
249A PHE* 3.7 23.5 - - + -
252A LYS* 3.1 44.9 + - - +
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Residues in contact with ASN 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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182A LEU* 4.2 13.9 - - - +
203A GLY 3.0 13.4 + - - +
206A ASP* 1.4 78.6 + - - +
208A LEU* 1.3 61.1 + - - +
210A GLU* 3.2 33.7 + - - +
211A LYS* 3.9 16.7 - - - +
380A MET 3.0 21.1 - - - +
381A GLU 3.3 26.7 + - - +
382A GLY* 3.7 7.7 + - - -
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Residues in contact with LEU 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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182A LEU* 4.4 23.1 - - + -
189A PHE* 4.4 22.2 - - + -
191A ALA* 3.7 24.5 - - + -
193A ILE* 4.2 10.3 - - + -
204A VAL* 2.9 45.5 + - + +
205A ILE* 4.1 3.4 - - - +
207A ASN* 1.3 72.8 - - - +
209A LEU* 1.3 57.0 + - - +
211A LYS* 2.9 7.6 + - + +
212A VAL* 2.8 42.1 + - + +
215A LEU* 5.5 3.8 - - + -
314A VAL* 4.9 13.5 - - + -
380A MET* 4.6 10.8 - - + +
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Residues in contact with LEU 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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205A ILE* 3.1 36.7 + - + +
206A ASP 3.7 6.3 - - - +
207A ASN 3.2 0.2 - - - -
208A LEU* 1.3 77.1 - - - +
210A GLU* 1.3 59.1 + - - +
211A LYS 3.5 0.3 + - - -
212A VAL* 4.4 3.6 + - + +
215A LEU* 4.0 23.3 - - + -
249A PHE* 3.7 31.2 - - + +
252A LYS* 4.0 28.9 - - + -
253A ALA* 4.0 26.2 - - + -
256A LYS* 3.9 18.4 - - - +
258A VAL* 3.9 25.9 - - + +
260A PHE* 5.7 0.2 - - + -
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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