Contacts of the helix formed by residues 207 - 224 (chain A) in PDB entry 2QUH
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 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A TYR* 3.8 4.9 - - - -
206A LEU* 1.3 77.8 - - - +
208A LEU* 1.3 67.1 + - - +
209A ASP* 3.7 11.2 + - - +
210A GLN* 2.8 45.0 + - - +
211A ALA* 3.0 10.0 + - - +
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Residues in contact with LEU 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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201A TYR* 3.4 42.6 - - + -
207A THR* 1.3 70.8 - - - +
209A ASP* 1.3 66.3 + - - +
211A ALA* 3.5 3.0 + - - +
212A TYR* 3.0 24.7 + - - +
238A LEU* 3.8 34.3 - - + +
249B LYS* 3.6 48.9 - - + +
252B VAL* 4.4 4.7 - - + -
253B LYS* 3.7 28.0 - - + +
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Residues in contact with ASP 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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207A THR* 3.0 10.8 + - - +
208A LEU* 1.3 79.1 - - - +
210A GLN* 1.3 58.2 + - + +
212A TYR* 3.3 8.9 + - - +
213A SER* 2.8 30.6 + - - -
249B LYS* 5.8 2.1 + - - -
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Residues in contact with GLN 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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205A ASP 4.3 1.7 - - - +
206A LEU* 3.3 18.8 - - + +
207A THR* 2.8 46.3 + - - +
209A ASP* 1.3 69.6 - - + +
211A ALA* 1.3 68.1 + - - +
213A SER* 2.5 24.4 + - - -
214A TYR* 2.8 40.1 + - + +
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Residues in contact with ALA 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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164A PRO* 4.3 4.2 - - - +
197A ASP* 3.4 37.5 - - + +
200A LYS* 4.7 1.6 - - + -
201A TYR* 4.1 19.3 - - + +
206A LEU* 4.5 10.3 - - + +
207A THR 3.0 7.7 + - - +
208A LEU* 3.7 7.6 - - - +
210A GLN* 1.3 79.6 - - - +
212A TYR* 1.3 63.8 + - - +
214A TYR* 3.2 13.4 + - - +
215A ALA 3.1 15.2 + - - -
238A LEU* 4.9 0.7 - - + -
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Residues in contact with TYR 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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197A ASP* 3.4 23.5 - - - +
208A LEU 3.0 18.5 + - - +
209A ASP* 3.5 8.7 - - - +
211A ALA* 1.3 77.1 - - - +
213A SER* 1.3 66.4 + - - +
215A ALA* 2.9 15.1 + - - +
216A VAL* 3.1 34.6 + - + +
236A SER* 3.5 16.8 - - - -
238A LEU* 4.4 9.4 - - + -
239A ASP* 2.8 32.3 + - - -
461A MET* 4.7 8.1 - - - +
249B LYS* 6.0 8.3 - - - +
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Residues in contact with SER 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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209A ASP 2.8 19.1 + - - -
210A GLN* 2.5 26.3 + - - -
212A TYR* 1.3 78.8 - - - +
214A TYR* 1.3 70.0 + - - +
216A VAL* 3.1 10.0 + - - +
217A GLU* 3.0 27.8 + - - +
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Residues in contact with TYR 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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164A PRO* 3.3 29.4 - - + +
165A SER 3.7 17.7 - - - -
166A SER* 4.0 14.6 - - - +
167A GLU* 4.4 28.0 - - + -
206A LEU* 3.7 29.8 - - + +
210A GLN* 2.8 44.4 + - + -
211A ALA* 3.4 7.2 - - - +
213A SER* 1.3 79.5 + - - +
215A ALA* 1.3 58.8 + - - +
217A GLU* 3.3 4.8 + - - +
218A ASN* 2.8 36.9 + - - +
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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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164A PRO* 3.6 23.7 - - + +
195A MET* 3.2 27.4 - - + +
197A ASP* 4.0 14.1 - - + +
211A ALA 3.1 11.1 + - - +
212A TYR* 2.9 14.2 + - + +
214A TYR* 1.3 78.4 - - - +
216A VAL* 1.3 56.0 + - + +
219A ALA* 3.0 25.8 + - - +
236A SER* 4.8 6.1 - - - -
461A MET* 4.9 2.4 - - - +
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Residues in contact with VAL 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 TYR* 3.1 40.8 + - + +
213A SER* 3.1 9.3 + - - +
215A ALA* 1.3 76.0 - - - +
217A GLU* 1.3 74.3 + - - +
219A ALA* 3.2 18.9 - - - +
220A LYS* 3.3 13.5 + - - +
454A ASP* 5.9 2.7 - - - +
457A VAL* 3.9 9.6 - - + +
461A MET* 3.6 29.8 - - + -
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Residues in contact with GLU 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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167A GLU* 3.9 40.5 - - + +
213A SER* 3.0 19.3 + - - +
214A TYR* 3.8 5.2 - - - +
216A VAL* 1.3 84.2 - - - +
218A ASN* 1.3 56.2 + - - +
220A LYS* 2.7 55.6 + - - +
221A ASP* 3.5 2.5 - - - +
449A ARG* 2.8 34.5 + - - +
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Residues in contact with ASN 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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162A ARG* 2.8 34.7 + - + +
164A PRO* 3.3 9.9 - - - +
166A SER 3.2 19.7 + - - +
167A GLU* 3.9 13.9 + - - +
169A MET* 3.1 32.4 - - + +
195A MET* 3.7 17.7 - - + -
214A TYR 2.8 23.9 + - - +
215A ALA* 4.6 0.2 - - - -
217A GLU* 1.3 72.2 - - - +
219A ALA* 1.3 62.2 + - - +
221A ASP* 3.1 3.0 + - - -
222A ILE* 3.0 22.2 + - - +
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Residues in contact with ALA 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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195A MET* 3.8 8.9 - - + +
215A ALA 3.0 17.0 + - - +
216A VAL* 3.2 17.0 - - - +
217A GLU 3.0 0.4 - - - -
218A ASN* 1.3 76.6 - - - +
220A LYS* 1.3 56.2 + - - +
222A ILE* 3.6 7.9 - - - +
223A ILE* 2.9 39.8 + - + +
234A ILE* 4.4 12.1 - - + -
457A VAL* 4.3 7.6 - - + -
461A MET* 4.3 15.9 - - + -
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Residues in contact with LYS 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 VAL* 3.7 12.1 - - - +
217A GLU* 2.7 34.7 + - - +
219A ALA* 1.3 78.2 - - - +
221A ASP* 1.3 56.8 + - - +
223A ILE* 3.2 4.2 + - - +
224A ALA* 2.9 27.5 + - - +
449A ARG* 3.7 39.8 - - + +
452A VAL* 3.8 32.1 + - + +
454A ASP* 4.2 18.3 + - - +
457A VAL* 3.8 26.0 - - + -
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Residues in contact with ASP 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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167A GLU 5.3 3.5 - - - +
169A MET* 3.0 36.2 - - + +
174A LEU* 5.2 2.5 - - + -
217A GLU 3.5 2.4 - - - +
218A ASN* 3.1 1.1 + - - -
220A LYS* 1.3 76.0 - - - +
222A ILE* 1.3 61.9 + - - +
224A ALA* 3.1 17.6 + - - +
225A CYS* 3.4 8.8 + - - -
361A LEU* 3.5 14.4 - - + +
362A THR* 6.1 0.7 - - - +
445A HIS* 2.9 38.5 + - - +
449A ARG* 2.7 36.4 + - - +
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Residues in contact with ILE 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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162A ARG* 3.9 9.0 - - + -
169A MET* 5.1 6.5 - - + -
174A LEU* 5.8 0.9 - - + -
177A PHE* 3.4 49.6 - - + -
193A ILE* 3.8 13.7 - - + -
195A MET* 3.7 31.4 - - + -
218A ASN 3.0 17.1 + - - +
219A ALA* 3.6 8.1 - - - +
221A ASP* 1.3 76.1 - - - +
223A ILE* 1.3 62.7 + - - +
225A CYS* 3.1 13.8 + - - +
227A PHE* 3.1 35.6 - - + -
234A ILE* 4.1 9.4 - - + -
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Residues in contact with ILE 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 ALA* 2.9 26.6 + - + +
220A LYS 3.2 4.5 + - - +
222A ILE* 1.3 76.1 - - - +
224A ALA* 1.3 52.8 + - - +
225A CYS 3.0 0.2 - - - -
226A GLY* 2.8 27.5 + - - -
227A PHE* 3.7 9.4 + - - +
234A ILE* 3.6 17.9 - - + -
452A VAL* 4.0 24.0 - - + -
456A ILE* 4.4 6.7 - - + -
457A VAL* 3.9 20.9 - - + +
460A PHE* 3.5 51.6 - - + -
461A MET* 6.1 0.2 - - + -
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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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220A LYS 2.9 14.3 + - - +
221A ASP* 3.1 15.2 + - - +
223A ILE* 1.3 72.0 - - - +
225A CYS* 1.3 55.4 + - - +
226A GLY* 2.9 10.4 + - - -
445A HIS* 3.9 18.8 - - + +
448A ARG* 3.4 33.5 + - - -
449A ARG* 3.9 27.6 - - - +
452A VAL* 4.6 4.5 - - - -
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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