Contacts of the helix formed by residues 207 - 222 (chain A) in PDB entry 1QAG
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 PRO 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A THR 4.1 5.8 - - - +
181A ASP* 3.3 39.0 - - + +
205A MSE 4.6 0.4 - - - +
206A SER* 1.3 88.3 - - - +
208A ILE* 1.3 61.2 + - + +
210A ARG* 3.5 11.1 - - + +
211A LEU* 3.0 34.6 + - + +
234A ALA* 5.2 6.1 - - + -
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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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206A SER* 3.1 6.8 + - - +
207A PRO* 1.3 78.7 - - + +
209A GLU* 1.3 70.8 + - + +
211A LEU* 3.3 3.1 + - + +
212A GLU* 2.9 51.8 + - - +
230A PRO* 3.3 36.7 - - + +
231A GLU* 4.2 9.6 - - + +
234A ALA* 4.6 13.0 - - + -
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Residues in contact with GLU 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 MSE 2.9 44.9 - - + +
206A SER* 2.8 28.9 + - - +
208A ILE* 1.3 79.6 - - + +
210A ARG* 1.3 65.3 + - - +
211A LEU 2.9 0.2 + - - -
212A GLU* 3.1 12.8 + - - +
213A HIS* 2.8 27.9 + - - +
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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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181A ASP* 3.3 32.0 + - - +
182A GLY 3.9 6.5 - - - +
183A LEU* 2.9 52.5 - - - +
186A ASN* 2.7 25.2 + - - +
202A VAL* 3.7 23.5 + - + +
203A VAL* 3.6 15.7 + - - +
204A LYS 5.3 0.2 + - - -
205A MSE 2.8 33.1 + - + +
206A SER 2.6 18.7 + - - +
207A PRO* 3.5 18.3 - - - +
209A GLU* 1.3 72.7 - - - +
211A LEU* 1.3 59.1 + - - +
213A HIS* 3.8 0.7 - - - +
214A ALA* 3.4 10.7 + - - +
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Residues in contact with LEU 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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179A TRP 4.2 0.2 - - - +
180A THR 4.1 15.0 - - - +
182A GLY* 3.5 24.0 - - - +
185A PHE* 3.6 26.5 - - + -
207A PRO 3.0 24.0 + - - +
208A ILE* 3.9 2.0 - - - +
209A GLU 3.0 0.4 - - - -
210A ARG* 1.3 74.8 - - - +
212A GLU* 1.3 68.7 + - - +
213A HIS 2.7 2.7 + - - -
214A ALA* 3.0 4.0 + - - +
215A PHE* 2.9 46.0 + - + -
230A PRO* 4.2 24.0 - - + +
233A VAL* 4.1 14.4 - - + -
234A ALA* 4.4 11.4 - - + -
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Residues in contact with GLU 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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208A ILE* 2.9 41.9 + - - +
209A GLU* 3.7 10.1 - - - +
211A LEU* 1.3 75.8 - - - +
213A HIS* 1.3 56.7 + - - +
215A PHE* 4.1 5.3 - - - +
216A SER* 3.1 29.5 + - - -
226A LYS* 5.0 1.9 - - - -
230A PRO* 3.7 20.4 - - + +
231A GLU* 5.5 0.9 - - - +
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Residues in contact with HIS 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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186A ASN* 3.0 22.1 + - - -
197A PHE* 3.4 36.6 - + - +
201A LYS* 5.3 9.9 - - - -
202A VAL* 4.2 0.2 - - + -
205A MSE 3.6 26.6 - - + +
209A GLU 2.8 17.5 + - - +
210A ARG 3.8 3.8 - - - +
211A LEU 2.7 0.4 + - - -
212A GLU* 1.3 74.1 - - - +
214A ALA* 1.3 53.5 + - - +
216A SER* 2.7 12.5 + - - -
217A LYS* 2.6 71.4 + - + +
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Residues in contact with ALA 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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185A PHE* 4.3 20.9 - - + +
186A ASN* 3.1 30.5 - - - +
189A LEU* 3.8 6.1 - - + +
210A ARG 3.4 9.6 + - - +
211A LEU* 3.0 4.6 + - - +
213A HIS* 1.3 80.9 + - - +
215A PHE* 1.3 63.0 + - + +
217A LYS* 3.5 6.1 - - - +
218A ALA* 2.8 35.2 + - - +
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Residues in contact with PHE 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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185A PHE* 3.6 31.4 - + + -
211A LEU* 2.9 50.6 + - + +
212A GLU* 4.1 3.8 - - - +
214A ALA* 1.3 77.4 - - + +
216A SER* 1.3 62.2 + - - +
218A ALA* 4.0 1.0 - - - +
219A GLN* 3.0 25.1 + - - +
224A ILE 5.0 0.2 - - - +
226A LYS* 3.8 23.9 - - + +
228A LEU* 3.8 37.7 - - + -
229A ASP 4.1 0.7 - - - -
230A PRO* 4.0 22.0 - - + -
233A VAL* 4.0 2.7 - - + -
246A TYR* 3.6 34.3 + + - +
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Residues in contact with SER 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 GLU 3.1 17.1 + - - -
213A HIS* 2.7 17.0 + - - -
215A PHE* 1.3 68.5 - - - +
217A LYS* 1.3 71.7 + - - +
219A GLN* 3.2 3.3 + - - +
220A THR* 2.8 27.1 + - - -
226A LYS* 3.6 23.0 + - - +
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Residues in contact with LYS 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* 3.6 14.8 - - + -
196A LEU* 3.8 27.3 + - + -
197A PHE* 4.3 8.5 - - + +
213A HIS* 2.6 54.6 + - + +
214A ALA 3.5 7.2 - - - +
216A SER* 1.3 75.4 - - - +
218A ALA* 1.3 66.0 + - - +
219A GLN 2.7 2.6 + - - -
220A THR* 2.9 9.9 + - - -
221A TYR* 3.0 53.7 + - + -
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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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189A LEU* 3.6 12.1 - - + +
214A ALA 2.8 19.8 + - - +
217A LYS* 1.3 73.0 - - - +
219A GLN* 1.3 55.8 + - - +
221A TYR* 5.5 0.2 - - - -
222A LEU* 2.8 42.5 + - + +
223A GLY 3.4 1.4 + - - -
224A ILE* 3.6 7.0 + - + -
246A TYR* 3.8 15.0 - - + +
250A LEU* 3.4 31.6 - - + -
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Residues in contact with GLN 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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215A PHE 3.0 19.2 + - - +
216A SER* 3.2 8.5 - - - +
217A LYS 2.7 4.2 + - - -
218A ALA* 1.3 74.2 - - - +
220A THR* 1.3 65.1 + - - +
223A GLY* 2.9 27.9 + - - -
224A ILE 3.1 22.4 + - - +
225A GLU* 4.5 10.5 + - - -
226A LYS* 3.9 35.2 - - + +
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Residues in contact with THR 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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216A SER* 2.8 18.3 + - - -
217A LYS* 2.9 7.4 + - - -
219A GLN* 1.3 81.4 + - - +
221A TYR* 1.3 80.3 + - + -
223A GLY* 4.5 1.6 + - - -
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Residues in contact with TYR 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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196A LEU* 3.2 45.9 + - + +
217A LYS* 3.0 50.9 + - + +
220A THR* 1.3 95.5 - - + +
222A LEU* 1.3 72.0 + - + +
223A GLY 3.9 0.2 - - - -
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Residues in contact with LEU 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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189A LEU* 3.7 22.2 - - + -
218A ALA* 2.8 18.4 + - - +
221A TYR* 1.3 86.7 - - + +
223A GLY* 1.3 60.5 + - - +
224A ILE* 2.9 14.0 + - + +
250A LEU* 4.0 11.4 - - + -
253A VAL* 3.6 56.6 - - + +
254A LEU* 3.4 30.1 - - + -
255A PRO* 4.9 5.6 - - + -
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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