Contacts of the helix formed by residues 220 - 236 (chain A) in PDB entry 2Q1V
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 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ASN* 3.3 35.4 - - + +
34A ARG* 4.1 15.2 - - + +
37A GLY* 3.8 21.1 - - - -
218A GLU 4.5 0.7 - - - +
219A PHE* 1.3 87.1 - - + +
221A GLU* 1.3 61.1 + - - +
222A MET* 3.1 4.7 - - + +
223A LEU* 2.9 15.4 + - + +
224A VAL* 2.9 22.0 + - - +
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Residues in contact with GLU 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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219A PHE 3.7 12.3 - - - +
220A PRO* 1.3 72.7 - - - +
222A MET* 1.3 61.7 + - - +
223A LEU 3.1 0.7 + - - -
224A VAL* 4.0 20.5 - - - +
225A GLU* 3.1 37.4 + - + +
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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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37A GLY* 3.5 31.9 - - - +
40A MET* 3.8 22.6 - - + +
41A VAL* 4.2 19.1 - - + -
44A VAL* 6.0 4.0 - - + -
220A PRO* 3.1 3.7 - - + +
221A GLU* 1.3 78.3 - - - +
223A LEU* 1.3 58.1 + - - +
225A GLU* 4.1 15.6 - - - +
226A ILE* 3.7 25.5 + - + +
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Residues in contact with LEU 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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33A ASN* 4.1 15.7 - - - +
36A ALA* 3.9 43.3 - - + +
37A GLY* 4.0 3.4 - - - +
40A MET* 3.8 27.4 - - + -
69A TRP* 4.4 13.7 - - + -
205A CYS* 5.6 0.4 - - - -
219A PHE* 3.9 24.2 - - + -
220A PRO* 2.9 17.0 + - + +
222A MET* 1.3 79.4 - - - +
224A VAL* 1.3 64.8 + - - +
225A GLU 3.2 2.0 - - - -
226A ILE* 3.3 4.3 + - + +
227A ILE* 2.9 43.4 + - + +
248A PDN 4.7 0.7 - - - +
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Residues in contact with VAL 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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209A PHE* 4.0 21.4 - - + -
219A PHE* 3.7 28.3 - - + +
220A PRO 2.9 20.4 + - - +
221A GLU* 3.3 23.5 + - - +
223A LEU* 1.3 75.8 - - - +
225A GLU* 1.3 57.8 + - + +
228A SER* 2.6 47.8 + - - +
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Residues in contact with GLU 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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221A GLU* 3.1 25.2 + - + +
222A MET* 4.1 18.4 - - + +
224A VAL* 1.3 81.8 - - + +
226A ILE* 1.3 65.7 + - + +
228A SER* 3.5 6.0 - - - -
229A ASP* 3.5 25.4 + - - +
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Residues in contact with ILE 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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40A MET* 3.3 40.8 - - + -
65A ILE* 5.0 9.2 - - + -
66A GLN* 3.8 27.3 - - + +
69A TRP* 3.9 24.0 - - + +
222A MET* 3.7 20.6 - - + +
223A LEU 3.3 7.0 + - - +
225A GLU* 1.3 76.8 - - + +
227A ILE* 1.3 61.4 + - + +
229A ASP* 3.3 5.7 + - - +
230A GLN* 2.8 31.4 + - - +
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Residues in contact with ILE 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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69A TRP* 4.0 18.8 - - + -
205A CYS* 3.6 25.6 - - - -
206A PHE* 3.8 22.9 - - + -
209A PHE* 3.6 32.5 - - + -
219A PHE* 3.9 25.4 - - + -
223A LEU* 2.9 32.2 + - + +
224A VAL 4.2 1.3 - - - +
226A ILE* 1.3 76.0 - - + +
228A SER* 1.3 62.9 + - - +
230A GLN* 4.1 9.0 - - - +
231A LEU* 2.9 25.8 + - + +
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Residues in contact with SER 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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209A PHE* 3.5 20.9 - - - -
224A VAL* 2.6 33.3 + - - +
225A GLU* 3.5 8.3 - - - -
226A ILE 3.2 0.2 - - - -
227A ILE* 1.3 77.3 - - - +
229A ASP* 1.3 61.6 + - - +
231A LEU* 4.4 0.7 - - - +
232A PRO* 3.1 21.3 - - - +
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Residues in contact with ASP 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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62A MET* 6.0 3.0 - - + +
66A GLN* 4.3 15.7 + - - +
225A GLU* 3.5 12.7 + - - +
226A ILE* 3.3 7.3 + - - +
227A ILE 3.2 0.2 - - - -
228A SER* 1.3 80.4 - - - +
230A GLN* 1.3 62.3 + - - +
232A PRO* 2.9 23.3 - - - +
233A LYS* 3.6 19.5 - - - +
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Residues in contact with GLN 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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66A GLN* 2.9 45.3 + - + +
67A TYR* 4.3 10.2 + - + +
69A TRP* 2.9 26.7 + - - +
70A MET* 5.8 0.4 - - - +
202A LEU* 3.9 26.5 - - - +
206A PHE* 3.8 19.4 - - + -
226A ILE* 2.8 20.7 + - - +
227A ILE* 4.1 8.3 - - - +
229A ASP* 1.3 74.0 - - - +
231A LEU* 1.3 63.9 + - - +
233A LYS* 3.1 6.1 + - - +
234A VAL* 2.9 35.8 + - + +
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Residues in contact with LEU 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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206A PHE* 3.9 43.3 - - + -
209A PHE* 4.0 16.6 - - + -
210A VAL* 3.8 28.9 - - + -
227A ILE 2.9 17.9 + - - +
228A SER* 4.4 1.1 - - - +
230A GLN* 1.3 75.6 - - - +
232A PRO* 1.3 68.7 - - + +
234A VAL* 3.3 1.4 + - - +
235A MET* 2.8 51.1 + - + +
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Residues in contact with PRO 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 SER 3.1 20.4 - - - +
229A ASP* 2.9 28.3 - - - +
231A LEU* 1.3 92.0 - - + +
233A LYS* 1.3 56.3 + - + +
235A MET* 3.8 5.1 - - + +
236A ALA* 2.9 32.8 + - - +
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Residues in contact with LYS 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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62A MET* 4.6 11.1 - - - +
63A THR* 4.5 13.3 + - - +
66A GLN* 2.9 38.8 + - - +
67A TYR* 3.6 25.1 - - + +
229A ASP* 3.6 19.0 - - - +
230A GLN 3.1 7.5 + - - +
232A PRO* 1.3 81.2 - - + +
234A VAL* 1.3 59.7 + - - +
236A ALA 3.5 0.5 + - - -
237A GLY 3.3 3.5 + - - -
238A MET* 3.0 56.1 + - + +
239A ALA 4.5 0.2 + - - -
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Residues in contact with VAL 234 (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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67A TYR* 4.0 20.2 - - + -
202A LEU* 5.0 10.1 - - + -
206A PHE* 4.1 20.4 - - + -
230A GLN* 2.9 41.1 + - + +
231A LEU 3.8 2.9 - - - +
233A LYS* 1.3 72.9 - - - +
235A MET* 1.3 66.5 + - - +
237A GLY* 2.9 20.3 + - - -
238A MET 4.8 1.6 - - - +
239A ALA* 5.3 6.5 - - + +
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Residues in contact with MET 235 (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 PHE* 4.5 19.7 - - - -
231A LEU* 2.8 46.4 + - + +
232A PRO* 3.8 6.5 - - + +
234A VAL* 1.3 79.4 - - - +
236A ALA* 1.3 61.2 + - - +
237A GLY* 3.3 1.2 + - - -
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Residues in contact with ALA 236 (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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232A PRO 2.9 19.3 + - - +
233A LYS 3.8 4.7 - - - +
234A VAL 3.2 0.2 - - - -
235A MET* 1.3 76.4 - - - +
237A GLY* 1.3 62.6 + - - +
238A MET* 4.1 17.1 - - + +
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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