Contacts of the helix formed by residues 218 - 232 (chain A) in PDB entry 1QS0
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 GLU 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A LEU* 3.8 13.5 - - + +
185A ALA* 3.4 24.9 - - + -
215A ALA* 2.7 22.2 + - + +
216A THR 3.5 0.7 - - - +
217A ALA* 1.3 80.8 - - - +
219A SER* 1.3 78.8 + - - +
220A ASP* 4.4 5.4 - - - +
221A PHE* 3.0 21.1 + - - +
222A HIS* 4.1 1.4 + - - +
500A TPP 3.7 28.1 + - - +
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Residues in contact with SER 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 ALA 3.7 2.4 + - - -
218A GLU* 1.3 83.3 + - - +
220A ASP* 1.3 72.5 + - - +
221A PHE 3.1 1.6 + - - -
222A HIS* 3.2 11.3 + - - +
223A THR* 3.2 22.5 + - - -
63B SER* 5.0 6.3 + - - -
91B PRO 5.7 0.3 + - - -
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Residues in contact with ASP 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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184A LEU 4.9 1.6 - - - +
185A ALA* 3.7 24.0 - - + +
186A THR* 3.6 15.8 + - - +
188A PHE* 4.3 0.2 - - - +
189A VAL* 2.8 42.4 + - + +
218A GLU* 3.1 4.5 + - - +
219A SER* 1.3 83.9 + - - +
221A PHE* 1.3 64.6 + - - +
223A THR* 3.8 3.3 + - - -
224A ALA* 3.0 8.8 + - - +
63B SER* 3.7 27.3 + - - +
94B ASP* 4.5 5.4 - - - +
95B GLN* 3.6 23.7 + - - +
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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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185A ALA* 4.5 2.8 - - - +
188A PHE* 3.4 35.2 - + - -
211A ILE* 4.1 15.0 - - + -
216A THR* 3.2 44.2 - - + +
218A GLU 3.0 6.6 + - - +
220A ASP* 1.3 76.0 - - - +
222A HIS* 1.3 69.2 - - + +
224A ALA* 3.2 13.3 + - - +
225A LEU* 3.2 44.0 + - + +
239A VAL* 3.8 24.2 - - + -
260A PHE* 4.9 2.9 - - + -
263A ARG* 4.3 27.4 - - + -
301A LEU* 4.6 5.8 - - + -
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Residues in contact with HIS 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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218A GLU 5.1 0.7 - - - +
219A SER* 3.2 10.8 + - - +
221A PHE* 1.3 86.2 - - + +
223A THR* 1.3 69.0 + - - +
225A LEU* 3.2 6.7 + - + +
226A THR* 2.9 41.7 + - - -
267A CYS* 4.7 17.6 - - - -
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Residues in contact with THR 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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189A VAL* 3.6 22.0 - - + -
219A SER* 3.2 12.2 + - - -
220A ASP* 3.8 3.9 - - - -
221A PHE 3.3 0.2 - - - -
222A HIS* 1.3 82.4 + - - +
224A ALA* 1.3 62.3 + - - +
226A THR* 3.4 5.9 + - - -
227A PHE* 3.0 30.6 + - + +
61B SER* 3.5 15.8 + - - +
63B SER* 3.5 10.1 + - - +
64B GLY* 3.0 37.9 - - - +
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Residues in contact with ALA 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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188A PHE* 3.4 43.1 - - + +
189A VAL* 3.7 6.0 - - - +
192A VAL* 3.7 14.0 - - + +
220A ASP 3.0 18.2 + - - +
221A PHE 3.2 6.7 + - - +
223A THR* 1.3 74.9 - - - +
225A LEU* 1.3 60.9 + - - +
227A PHE* 5.1 0.2 - - - -
228A ALA* 2.8 33.1 + - - +
237A LEU* 4.6 1.8 - - + -
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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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188A PHE* 4.4 2.9 - - + -
221A PHE* 3.2 45.2 + - + +
222A HIS* 3.2 8.5 + - + +
224A ALA* 1.3 75.6 - - - +
226A THR* 1.3 64.3 + - - +
228A ALA* 3.6 1.3 - - - +
229A HIS* 2.9 27.3 + - - +
237A LEU* 3.4 26.2 - - + -
263A ARG* 3.8 27.8 - - + +
264A GLY* 4.4 3.4 - - - +
267A CYS* 4.2 18.6 - - + -
269A ILE* 3.6 17.6 - - + +
301A LEU* 4.1 14.8 - - + -
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Residues in contact with THR 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 HIS* 2.9 38.8 + - - -
223A THR* 3.6 7.0 - - - -
225A LEU* 1.3 78.1 - - - +
227A PHE* 1.3 61.7 + - + +
229A HIS* 3.7 3.6 - - - +
230A VAL* 2.9 37.8 + - + +
267A CYS* 5.2 5.8 - - - -
59B PRO* 4.3 26.9 - - + -
61B SER* 6.1 1.8 - - - -
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Residues in contact with PHE 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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192A VAL* 3.9 18.8 - - + +
196A MSE 4.3 3.6 - - + -
223A THR* 3.0 26.7 + - + +
224A ALA* 4.2 0.4 - - - +
226A THR* 1.3 77.9 - - + +
228A ALA* 1.3 65.4 + - - +
230A VAL* 4.5 1.3 - - - -
231A TYR* 3.1 51.8 + + + +
233A ALA* 4.7 0.2 - - - +
29B TYR* 5.0 4.3 - + - -
58B ALA* 4.7 2.7 - - + -
59B PRO* 3.7 30.5 - - + -
61B SER* 3.7 22.0 - - - -
64B GLY* 3.4 37.7 - - - -
65B ILE* 3.7 11.9 - - + -
68B THR* 3.6 23.3 - - + -
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Residues in contact with ALA 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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192A VAL* 3.8 17.4 - - + +
224A ALA 2.8 23.3 + - - +
225A LEU 3.6 3.8 - - - +
227A PHE* 1.3 73.1 - - - +
229A HIS* 1.3 58.5 + - - +
232A ARG* 2.9 25.5 + - - -
233A ALA* 3.0 15.0 + - + -
235A VAL* 5.6 0.9 - - + -
237A LEU* 4.0 22.9 - - + -
269A ILE* 4.4 1.1 - - + -
299A PRO* 3.8 19.9 - - + +
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Residues in contact with HIS 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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225A LEU 2.9 14.8 + - - +
226A THR* 3.7 3.6 - - - +
228A ALA* 1.3 75.4 - - - +
230A VAL* 1.3 74.1 + - + +
232A ARG* 3.1 24.7 + - - +
267A CYS 3.1 27.1 + - - +
268A GLY* 3.5 26.6 + - - -
269A ILE* 4.2 8.3 - - + +
299A PRO* 4.6 3.1 - - - +
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Residues in contact with VAL 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 THR* 2.9 30.0 + - + +
227A PHE* 4.5 0.4 - - - -
229A HIS* 1.3 83.2 - - + +
231A TYR* 1.3 91.2 + - + +
232A ARG* 5.3 0.5 - - - +
57B ASP 5.9 0.2 - - - +
59B PRO* 4.2 19.1 - - + -
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Residues in contact with TYR 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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196A MSE 3.6 34.5 - - + -
227A PHE* 3.1 42.5 + + - +
230A VAL* 1.3 96.3 - - + +
232A ARG* 1.3 73.5 + - - +
233A ALA* 3.3 2.2 + - - +
56B PHE* 3.6 31.9 - + + -
57B ASP 2.8 23.4 + - - -
58B ALA* 3.2 18.9 - - - +
59B PRO* 3.4 5.6 - - + +
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Residues in contact with ARG 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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228A ALA 2.9 10.1 + - - -
229A HIS* 3.1 19.6 + - - +
230A VAL 5.3 0.4 - - - +
231A TYR* 1.3 81.5 - - - +
233A ALA* 1.3 62.3 + - - +
234A PRO* 3.8 4.9 - - - +
296A GLY* 4.4 15.1 - - - +
297A LEU 4.7 3.8 - - - -
298A GLY* 3.6 24.3 + - - +
299A PRO* 3.9 7.2 - - + -
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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