Contacts of the helix formed by residues 214 - 228 (chain A) in PDB entry 1QZZ
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 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A TRP* 3.6 37.0 - - + +
147A GLU* 4.0 17.0 - - + +
150A SER* 3.5 15.5 - - - +
213A GLU* 1.3 87.5 + - - +
215A ALA* 1.3 66.8 + - - +
216A GLY 3.3 1.0 + - - -
217A PRO* 3.4 2.8 - - + +
218A ALA* 3.1 16.9 + - - +
238A GLU* 5.1 0.7 - - - -
239A GLY 3.9 7.6 - - - +
240A ASP* 5.0 3.1 - - + -
635A SAM 3.6 53.1 + - + +
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Residues in contact with ALA 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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150A SER* 3.5 6.0 + - - +
214A LEU* 1.3 73.1 - - - +
216A GLY* 1.3 64.4 + - - +
218A ALA* 3.2 2.0 + - - +
219A GLU* 3.0 25.3 + - - +
238A GLU* 3.8 34.1 + - - +
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Residues in contact with GLY 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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149A LEU 5.5 0.2 - - - -
150A SER* 3.0 33.5 + - - -
156A ALA* 6.3 0.2 - - - -
215A ALA* 1.3 75.7 - - - +
217A PRO* 1.3 67.6 - - - +
219A GLU* 3.3 16.5 + - - +
220A ARG* 3.3 21.5 + - - +
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Residues in contact with PRO 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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146A TRP* 6.2 0.4 - - + -
150A SER* 3.9 10.5 - - - +
192A GLY* 3.5 19.9 - - - +
193A ASN* 4.0 0.6 - - - +
213A GLU* 3.3 28.5 - - - +
214A LEU* 3.4 14.1 - - + +
216A GLY* 1.3 90.4 - - - +
218A ALA* 1.3 55.5 + - - +
220A ARG* 3.1 28.8 + - + +
221A ALA* 2.8 30.5 + - - +
635A SAM 3.6 16.6 - - - +
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Residues in contact with ALA 218 (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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213A GLU* 4.0 13.1 - - + +
214A LEU 3.1 20.5 + - - +
215A ALA 3.5 4.0 - - - +
217A PRO* 1.3 76.6 - - - +
219A GLU* 1.3 57.0 + - - +
221A ALA* 3.2 3.7 + - - +
222A ARG* 2.9 37.9 + - - +
236A VAL* 3.5 25.3 - - + +
238A GLU* 4.0 20.4 - - + -
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Residues in contact with GLU 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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153A VAL* 5.4 8.7 - - - +
215A ALA 3.0 12.0 + - - +
216A GLY* 3.6 13.1 - - - +
217A PRO 3.3 0.2 - - - -
218A ALA* 1.3 77.0 - - - +
220A ARG* 1.3 67.9 + - - +
222A ARG* 3.3 30.5 + - - +
223A ARG* 3.3 12.8 + - - +
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Residues in contact with ARG 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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149A LEU* 5.0 1.4 + - - +
150A SER* 5.5 0.2 - - - +
153A VAL* 5.6 7.2 - - + +
156A ALA* 3.5 26.8 + - - +
157A ASP* 3.4 25.2 + - - -
160A ASP* 2.7 29.4 + - - -
193A ASN* 3.8 21.4 + - + +
216A GLY* 3.3 14.1 + - - +
217A PRO* 3.1 41.7 + - - +
219A GLU* 1.3 81.5 - - - +
221A ALA* 1.3 64.4 + - - +
223A ARG* 3.5 8.0 + - - +
224A ARG* 3.2 21.1 + - - +
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Residues in contact with ALA 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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192A GLY 3.6 7.0 - - - +
193A ASN* 3.2 30.5 - - - +
211A LEU* 4.0 16.2 - - + -
217A PRO 2.8 18.7 + - - +
218A ALA 3.7 4.0 - - - +
220A ARG* 1.3 70.5 - - - +
222A ARG* 1.3 68.3 + - - +
224A ARG* 3.1 1.2 + - - +
225A PHE* 2.9 37.9 + - + -
236A VAL* 4.1 4.5 - - + -
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Residues in contact with ARG 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 ALA 2.9 14.9 + - - +
219A GLU* 3.5 38.6 - - - +
221A ALA* 1.3 78.1 - - - +
223A ARG* 1.3 61.8 + - - +
225A PHE* 3.4 4.6 + - - +
226A ALA* 3.0 23.8 + - - +
231A ALA* 5.8 0.7 - - - +
236A VAL* 3.6 39.5 + - + +
238A GLU* 3.2 41.0 + - - +
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Residues in contact with ARG 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 GLU 3.3 9.1 + - - +
220A ARG* 3.7 10.1 - - - +
221A ALA 3.2 0.6 - - - -
222A ARG* 1.3 76.9 - - - +
224A ARG* 1.3 59.5 + - - +
226A ALA* 3.3 5.3 + - - +
227A ASP* 2.8 56.2 + - - +
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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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165A CYS 5.6 0.6 + - - -
166A ASP* 4.8 15.6 + - - +
167A GLU 5.0 7.3 + - - -
168A ASP* 5.6 3.8 + - - +
171A TYR* 5.5 4.2 - - - -
193A ASN* 2.7 56.7 + - - +
194A GLY* 3.6 15.5 - - - -
195A GLY* 3.5 17.0 - - - -
198A ALA* 4.3 12.9 - - + +
220A ARG 3.2 9.9 + - - +
221A ALA 3.1 8.2 + - - +
223A ARG* 1.3 76.0 - - - +
225A PHE* 1.3 65.5 + - + +
227A ASP* 3.3 8.4 + - - +
228A ALA* 3.1 23.8 + - + +
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Residues in contact with PHE 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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193A ASN 4.7 0.9 - - - -
194A GLY* 3.5 40.6 - - - -
197A LEU* 3.9 11.7 - - + -
198A ALA* 4.1 12.8 - - + -
211A LEU* 4.0 9.6 - - + -
221A ALA* 2.9 24.6 + - + +
222A ARG* 3.9 4.9 - - - +
224A ARG* 1.3 80.7 - - - +
226A ALA* 1.3 60.1 + - - +
228A ALA* 3.3 2.3 + - - +
229A GLY 3.2 3.5 + - - -
230A LEU* 2.8 49.7 + - + +
231A ALA* 4.2 9.2 - - + +
234A VAL* 3.5 40.4 - - + +
235A THR 4.9 0.2 - - - -
236A VAL* 3.8 26.9 - - + -
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Residues in contact with ALA 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 ARG 3.0 16.6 + - - +
223A ARG* 3.6 7.6 - - + +
225A PHE* 1.3 72.3 - - - +
227A ASP* 1.3 69.6 + - - +
229A GLY* 3.0 14.5 + - - +
230A LEU 4.9 0.2 - - - +
231A ALA* 4.6 15.4 - - + +
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Residues in contact with ASP 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 ARG* 2.8 47.5 + - - +
224A ARG* 3.6 8.3 - - - +
226A ALA* 1.3 79.3 - - - +
228A ALA* 1.3 59.3 + - - +
229A GLY 3.6 0.3 + - - -
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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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198A ALA* 5.3 4.3 - - + -
202A LEU* 4.3 22.8 - - + +
224A ARG* 3.1 16.7 + - + +
225A PHE 3.3 0.6 + - - +
226A ALA 3.1 0.4 - - - -
227A ASP* 1.3 77.9 - - - +
229A GLY* 1.3 60.2 + - - +
230A LEU* 3.3 28.5 - - + +
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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