Contacts of the helix formed by residues 202 - 217 (chain A) in PDB entry 1P8Z
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 THR 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A PHE 4.7 0.2 - - - -
201A VAL* 1.3 86.7 - - + +
203A THR* 1.3 65.6 + - - +
204A ALA* 3.6 8.7 + - - +
205A GLU* 3.3 34.5 + - - +
206A ARG* 3.4 17.8 + - - +
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Residues in contact with THR 203 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ARG* 3.7 41.6 + - - +
202A THR* 1.3 72.2 - - - +
204A ALA* 1.3 67.3 + - - +
206A ARG* 3.2 19.3 + - - +
207A GLU* 3.4 12.2 - - - +
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Residues in contact with ALA 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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62A ARG* 6.4 0.4 - - - +
202A THR* 3.3 8.7 + - - +
203A THR* 1.3 84.8 + - - +
205A GLU* 1.3 59.5 - - + +
207A GLU* 2.8 38.3 - - - +
208A ILE* 4.3 6.6 + - - +
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Residues in contact with GLU 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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199A SER 2.6 28.8 - - - +
200A PHE* 2.9 32.8 - - + +
201A VAL 3.6 4.2 + - - -
202A THR* 3.3 26.0 + - - +
203A THR 3.2 0.8 - - - -
204A ALA* 1.3 78.9 - - + +
206A ARG* 1.3 59.5 + - - +
207A GLU 3.0 2.9 - - - -
208A ILE* 2.8 44.7 + - + +
209A VAL* 3.4 3.6 + - - +
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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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183A ARG* 3.1 43.4 + - - +
186A THR* 3.6 17.7 - - + +
187A ASP* 2.5 33.3 + - - -
190A MET* 3.5 31.2 - - + +
200A PHE* 4.8 0.4 - - - +
202A THR 3.4 9.6 + - - +
203A THR* 3.2 14.4 + - - +
205A GLU* 1.3 78.3 - - - +
207A GLU* 1.3 61.2 + - - +
209A VAL* 3.3 5.6 + - - +
210A ARG* 3.1 28.2 + - - +
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Residues in contact with GLU 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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62A ARG* 4.7 12.0 + - - -
203A THR 3.4 7.9 - - - +
204A ALA* 2.8 39.2 + - - +
206A ARG* 1.3 73.2 - - - +
208A ILE* 1.3 63.1 + - + +
210A ARG* 3.4 24.2 + - - +
211A ASP* 3.2 21.8 + - - +
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Residues in contact with ILE 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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200A PHE* 3.5 26.9 - - + -
204A ALA 4.3 4.5 - - - +
205A GLU* 2.8 39.0 + - + +
207A GLU* 1.3 76.6 - - + +
209A VAL* 1.3 63.3 + - - +
211A ASP* 3.1 8.7 + - - +
212A ILE* 3.0 23.9 + - + +
240A TYR* 3.9 25.6 - - + +
242A LEU* 4.0 21.8 - - + -
243A PRO* 4.9 13.5 - - + -
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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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186A THR* 3.7 17.9 - - + +
189A LEU* 3.5 29.1 - - + +
190A MET* 3.7 24.7 - - + +
193A LEU* 4.2 4.3 - - + -
200A PHE* 3.6 42.2 - - + -
205A GLU 4.0 2.9 - - - +
206A ARG* 3.3 9.8 + - - +
208A ILE* 1.3 75.6 - - - +
210A ARG* 1.3 58.4 + - - +
212A ILE* 3.1 8.9 + - - +
213A LYS* 2.9 27.1 + - - +
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Residues in contact with ARG 210 (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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59A GLN* 5.2 7.5 + - - -
69A TYR* 5.7 2.6 + - - -
186A THR* 4.3 19.5 + - + +
206A ARG* 3.1 20.0 + - + +
207A GLU* 3.7 24.1 - - - +
208A ILE 3.2 0.4 - - - -
209A VAL* 1.3 77.3 - - - +
211A ASP* 1.3 57.7 + - - +
213A LYS* 3.3 7.0 + - - +
214A GLU* 3.0 60.2 + - - +
380A ATP 3.9 15.0 - - - +
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Residues in contact with ASP 211 (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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207A GLU 3.2 12.3 + - - +
208A ILE* 3.1 7.5 + - - +
210A ARG* 1.3 75.0 - - - +
212A ILE* 1.3 60.8 + - - +
214A GLU* 3.8 5.5 - - - +
215A LYS* 2.4 71.2 + - - +
240A TYR* 2.4 32.0 + - - +
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Residues in contact with ILE 212 (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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189A LEU* 3.9 17.3 - - + -
193A LEU* 4.3 14.1 - - + -
200A PHE* 4.5 1.1 - - + -
208A ILE* 3.0 24.9 + - + +
209A VAL* 3.1 7.8 + - - +
211A ASP* 1.3 74.1 - - - +
213A LYS* 1.3 62.2 + - - +
216A LEU* 2.8 39.5 + - + -
217A CYS* 3.5 5.7 + - - -
240A TYR* 3.6 42.0 - - + -
248A ILE* 3.8 22.4 - - + -
250A ILE* 4.2 23.8 - - + -
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Residues in contact with LYS 213 (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 GLY* 2.8 36.0 + - - -
185A LEU* 4.0 5.2 - - + -
186A THR* 2.9 21.2 + - - +
189A LEU* 3.8 7.6 - - + -
209A VAL* 2.9 16.6 + - + +
210A ARG* 3.5 4.7 - - - +
212A ILE* 1.3 77.6 - - - +
214A GLU* 1.3 64.1 + - - +
217A CYS* 3.1 34.1 + - - +
257A CYS* 3.9 21.5 - - - -
306A TYR* 3.1 35.8 + - + +
380A ATP 3.2 36.0 + - - -
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Residues in contact with GLU 214 (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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210A ARG* 3.0 46.0 + - + +
211A ASP* 4.1 6.7 - - - +
213A LYS* 1.3 79.6 - - - +
215A LYS* 1.3 62.3 + - + +
217A CYS 5.9 0.4 - - - -
336A LYS* 5.6 0.5 + - - -
380A ATP 3.2 76.0 + - + +
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Residues in contact with LYS 215 (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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211A ASP* 2.4 58.5 + - - +
212A ILE 4.2 0.2 - - - +
214A GLU* 1.3 83.7 - - + +
216A LEU* 1.3 78.6 + - + +
217A CYS 5.1 1.3 - - - +
240A TYR* 4.8 8.7 - - + -
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Residues in contact with LEU 216 (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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212A ILE* 2.8 29.9 + - + +
215A LYS* 1.3 92.9 - - + +
217A CYS* 1.3 66.6 + - - +
218A TYR* 3.7 0.3 - - - -
238A LYS* 4.0 36.1 - - + +
239A SER 4.7 6.1 - - - +
240A TYR* 3.7 39.9 - - + -
250A ILE* 5.1 5.8 - - + -
254A ARG* 3.0 44.8 + - + +
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Residues in contact with CYS 217 (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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189A LEU* 4.1 10.1 - - - -
212A ILE* 4.2 4.3 - - - -
213A LYS* 3.1 36.7 + - - +
214A GLU 5.9 0.3 - - - -
215A LYS 5.1 1.4 - - - +
216A LEU* 1.3 81.5 - - - +
218A TYR* 1.3 64.1 + - - +
250A ILE* 6.1 0.4 - - - -
253A GLU 3.9 6.5 - - - -
254A ARG* 3.0 19.7 - - - +
257A CYS* 3.6 23.8 - - - -
258A PRO* 4.0 1.6 - - + -
306A TYR* 3.8 17.5 - - + -
307A PRO* 3.7 15.4 - - - +
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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