Contacts of the helix formed by residues 218 - 233 (chain A) in PDB entry 1SZU
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 SER 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A PRO* 5.6 0.4 - - - +
180A GLU* 2.5 30.5 + - - -
216A ALA 3.6 3.3 + - - -
217A SER* 1.3 86.2 + - - +
219A PRO* 1.3 74.2 - - - +
220A ALA* 3.4 6.8 + - - +
221A PHE* 3.1 17.5 + - - +
222A MET* 3.0 12.1 + - - +
257A MET* 4.0 0.9 - - - -
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Residues in contact with PRO 219 (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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217A SER 4.4 2.2 - - - +
218A SER* 1.3 88.5 - - - +
220A ALA* 1.3 56.3 + - - +
222A MET* 3.4 0.7 + - + +
223A GLN* 2.8 44.3 + - - +
256A GLN 3.5 20.0 - - - +
257A MET* 3.6 30.2 - - - +
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Residues in contact with ALA 220 (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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180A GLU* 4.2 9.4 - - - +
218A SER* 3.2 7.7 + - - +
219A PRO* 1.3 76.9 - - - +
221A PHE* 1.3 66.1 + - - +
223A GLN* 3.3 15.4 + - - +
224A ARG* 3.0 31.2 + - - +
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Residues in contact with PHE 221 (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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134A PHE* 4.3 14.4 - + - -
172A PRO* 3.8 26.7 - - + -
180A GLU* 3.8 32.9 + - + +
183A ALA* 3.5 25.1 - - + -
184A ILE* 3.6 27.1 - - + -
187A ILE* 5.2 0.4 - - + -
205A ILE* 3.8 25.1 - - + -
217A SER* 3.4 18.2 - - - +
218A SER* 3.1 22.2 + - - +
220A ALA* 1.3 78.0 - - - +
222A MET* 1.3 63.9 + - - +
224A ARG* 2.9 19.1 + - - +
225A LEU* 2.9 25.2 + - + +
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Residues in contact with MET 222 (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* 4.1 18.8 - - + -
207A PRO* 4.1 14.6 - - + -
217A SER* 3.2 31.2 - - - +
218A SER 3.0 12.5 + - - +
219A PRO 3.7 4.5 - - - +
221A PHE* 1.3 81.4 - - - +
223A GLN* 1.3 57.1 + - - +
225A LEU* 3.4 21.6 + - - +
226A ARG* 2.9 28.9 + - - +
236A LEU* 4.6 6.5 - - + -
254A MET* 3.6 42.4 - - + +
257A MET* 3.7 18.2 - - + -
259A VAL* 3.7 9.2 - - + -
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Residues in contact with GLN 223 (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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219A PRO* 2.8 30.0 + - - +
220A ALA* 3.4 14.0 - - - +
221A PHE 3.1 0.2 - - - -
222A MET* 1.3 75.4 - - - +
224A ARG* 1.3 64.8 + - + +
226A ARG* 3.3 3.3 + - - +
227A ALA* 3.1 22.5 + - - +
257A MET 3.0 21.8 + - - +
258A GLY* 4.2 8.1 + - - +
259A VAL* 3.9 25.9 - - + +
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Residues in contact with ARG 224 (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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180A GLU* 3.6 26.0 + - - +
181A ASP* 2.8 32.9 + - - +
184A ILE* 3.7 34.3 - - + +
220A ALA* 3.0 19.4 + - - +
221A PHE* 2.9 12.6 + - - +
223A GLN* 1.3 76.0 - - - +
225A LEU* 1.3 57.0 + - - +
227A ALA* 3.3 7.3 + - - +
228A LEU* 2.9 27.5 + - - +
1001A SO4 2.6 46.1 + - - +
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Residues in contact with LEU 225 (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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134A PHE* 4.5 1.6 - - + -
184A ILE* 4.3 6.4 - - + +
187A ILE* 3.7 29.4 - - + -
203A ILE* 4.0 25.6 - - + -
205A ILE* 3.9 29.6 - - + -
221A PHE* 2.9 23.4 + - + +
222A MET* 3.6 16.8 - - - +
224A ARG* 1.3 72.5 - - - +
226A ARG* 1.3 66.6 + - - +
228A LEU* 3.1 8.7 + - + +
229A CYS* 2.9 28.2 + - - -
236A LEU* 3.8 26.9 - - + -
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Residues in contact with ARG 226 (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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222A MET 2.9 18.1 + - - +
223A GLN 3.5 6.1 - - - +
225A LEU* 1.3 74.3 - - - +
227A ALA* 1.3 63.4 + - - +
229A CYS* 3.3 18.7 + - - +
230A ASP* 3.0 56.7 + - - +
234A ILE 3.9 2.8 + - - -
235A MET* 5.7 0.6 - - - +
236A LEU* 3.6 26.9 - - + +
259A VAL* 3.8 26.9 - - + -
260A ALA 2.9 31.0 + - - +
261A PRO* 3.7 1.6 - - - +
262A ASP* 2.8 39.9 + - - +
282A ARG* 4.5 6.4 - - - +
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Residues in contact with ALA 227 (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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223A GLN 3.1 10.7 + - - +
224A ARG* 3.5 11.2 - - - +
225A LEU 3.2 0.2 - - - -
226A ARG* 1.3 78.6 - - - +
228A LEU* 1.3 63.5 + - - +
230A ASP* 3.3 9.2 + - - +
231A GLU* 2.9 26.4 + - - +
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Residues in contact with LEU 228 (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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184A ILE* 4.5 12.6 - - + -
187A ILE* 4.0 26.2 - - + -
188A HIS* 3.9 31.0 - - + +
191A PHE* 4.0 21.8 - - + -
203A ILE* 3.8 28.0 - - + -
224A ARG 2.9 16.9 + - - +
225A LEU* 3.1 8.5 + - + +
227A ALA* 1.3 76.9 - - - +
229A CYS* 1.3 63.0 + - - +
231A GLU* 3.6 9.7 + - - +
232A HIS* 3.3 34.4 + - + -
234A ILE* 4.7 1.1 - - + -
1001A SO4 5.8 0.2 - - - +
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Residues in contact with CYS 229 (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 ILE* 3.9 26.7 - - - -
225A LEU* 2.9 21.0 + - - +
226A ARG* 3.7 14.8 - - - +
228A LEU* 1.3 74.6 - - - +
230A ASP* 1.3 55.5 + - - +
232A HIS 3.2 0.5 + - - -
233A GLY* 2.7 32.4 + - - -
234A ILE* 2.8 41.2 + - - +
236A LEU* 3.9 28.7 - - - -
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Residues in contact with ASP 230 (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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226A ARG* 3.0 56.4 + - - +
227A ALA* 3.7 8.2 - - - +
229A CYS* 1.3 72.3 - - - +
231A GLU* 1.3 68.3 + - - +
232A HIS 3.2 0.7 + - - -
233A GLY* 3.3 10.3 + - - +
282A ARG* 5.8 0.7 + - - -
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Residues in contact with GLU 231 (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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188A HIS* 5.7 2.4 + - - -
227A ALA 2.9 18.3 + - - +
228A LEU* 3.6 10.3 - - - +
230A ASP* 1.3 79.1 - - - +
232A HIS* 1.3 85.2 + - + +
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Residues in contact with HIS 232 (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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128A ARG* 3.0 28.8 + - - -
188A HIS* 5.1 6.3 + - - -
191A PHE* 4.0 25.4 - + - -
197A PRO* 3.5 31.1 - - + +
228A LEU* 3.3 25.6 + - + +
229A CYS 3.2 2.4 + - - -
230A ASP 3.1 0.4 - - - -
231A GLU* 1.3 109.3 + - + +
233A GLY* 1.3 57.9 + - - +
234A ILE* 3.2 19.1 - - + -
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Residues in contact with GLY 233 (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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126A THR* 3.7 17.7 - - - +
128A ARG* 3.4 16.2 + - - -
229A CYS 2.7 13.2 + - - -
230A ASP* 3.3 10.3 + - - -
231A GLU 3.6 0.2 - - - -
232A HIS* 1.3 75.2 - - - +
234A ILE* 1.3 57.8 + - - -
235A MET* 3.9 8.5 - - - +
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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