Contacts of the helix formed by residues 211 - 225 (chain A) in PDB entry 3H90
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 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A ALA 4.6 1.1 - - - +
210A LEU* 1.4 87.2 - - + +
212A ASP* 1.3 55.9 + - - +
213A GLU* 4.5 7.0 - - + +
214A GLU* 2.8 57.1 + - + +
215A ARG 3.1 8.0 + - - -
238A GLN* 4.8 3.6 - - - +
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Residues in contact with ASP 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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210A LEU 3.5 2.8 + - - -
211A PRO* 1.3 69.4 - - - +
213A GLU* 1.3 56.1 + - - +
215A ARG* 3.3 29.7 + - - +
216A GLN* 2.9 30.9 + - - +
69C ASP* 5.4 4.4 - - - +
70C ASN* 5.9 1.2 + - - -
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Residues in contact with GLU 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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211A PRO* 2.9 7.3 + - + +
212A ASP* 1.3 76.1 - - - +
214A GLU* 1.3 67.7 + - + +
216A GLN* 3.1 8.7 + - - +
217A GLU* 3.1 44.4 + - - +
287D CYS* 4.0 21.9 - - - +
289D VAL 5.2 5.1 - - - +
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Residues in contact with GLU 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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210A LEU* 4.1 16.7 - - + +
211A PRO* 2.8 40.8 + - + +
213A GLU* 1.3 82.6 - - + +
215A ARG* 1.3 61.5 + - - +
217A GLU* 3.4 5.5 + - - +
218A ILE* 3.3 23.1 + - - +
238A GLN* 4.1 1.9 - - - +
243A ARG* 2.9 39.5 + - - -
275A PHE* 3.1 41.0 - - + -
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Residues in contact with ARG 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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209A ALA* 3.3 29.9 - - - +
210A LEU* 3.4 20.3 + - + +
211A PRO 3.1 8.1 + - - +
212A ASP* 3.5 31.7 + - - +
214A GLU* 1.3 79.5 - - - +
216A GLN* 1.3 60.0 + - - +
218A ILE* 3.6 11.2 + - - +
219A ILE* 3.2 33.4 + - + +
234A LEU* 3.7 26.0 - - + +
236A THR* 4.4 11.1 + - + +
69C ASP* 3.2 39.6 + - - -
70C ASN* 4.1 10.9 - - - +
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Residues in contact with GLN 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 ASP 2.9 16.8 + - - +
213A GLU* 3.1 8.3 + - - +
215A ARG* 1.3 75.6 - - - +
217A GLU* 1.3 54.6 + - + +
219A ILE* 3.0 27.5 + - - +
220A ASP* 2.8 66.4 + - - +
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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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213A GLU* 3.1 41.4 + - - +
214A GLU* 3.6 10.5 - - - +
216A GLN* 1.3 75.9 - - - +
218A ILE* 1.3 52.4 + - - +
220A ASP* 3.6 7.6 - - - +
221A ILE* 2.8 41.7 + - - +
274A ARG* 2.7 45.6 + - - +
275A PHE* 3.9 21.3 - - + -
287D CYS 4.7 4.3 - - - +
288D SER* 3.8 18.5 - - - -
289D VAL 4.6 3.3 + - - +
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Residues in contact with ILE 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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210A LEU* 4.1 16.8 - - + -
214A GLU 3.3 16.9 + - - +
215A ARG* 3.6 8.1 - - - +
217A GLU* 1.3 76.9 - - - +
219A ILE* 1.3 62.0 + - - +
221A ILE* 3.3 8.2 + - - +
222A VAL* 3.0 40.3 + - + +
234A LEU* 3.9 25.8 - - + -
236A THR* 4.1 9.9 - - + -
245A ILE* 3.8 35.2 - - + -
247A ILE* 4.9 2.0 - - + -
271A ILE* 4.4 14.6 - - + -
275A PHE* 3.6 17.0 - - + -
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Residues in contact with ILE 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 ARG* 3.2 25.3 + - + +
216A GLN* 3.0 34.3 + - - +
218A ILE* 1.3 77.1 - - - +
220A ASP* 1.3 60.2 + - - +
222A VAL* 3.4 4.1 + - - +
223A THR* 3.0 47.7 + - + +
234A LEU* 4.8 14.4 - - + -
247A ILE* 5.9 2.7 - - + -
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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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216A GLN* 2.8 50.6 + - - +
217A GLU* 3.6 7.8 - - - +
219A ILE* 1.3 72.0 - - - +
221A ILE* 1.3 67.2 + - + +
222A VAL 3.1 1.0 + - - -
223A THR* 3.7 5.5 + - - -
224A SER* 3.1 27.9 + - - -
274A ARG* 5.5 2.7 - - - +
258B VAL* 4.3 25.5 - - + +
262B MET* 4.5 9.0 - - + -
253D ASP* 5.0 3.1 - - - +
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Residues in contact with ILE 221 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A GLU 2.8 28.8 + - - +
218A ILE* 3.6 9.6 - - - +
220A ASP* 1.3 71.5 - - - +
222A VAL* 1.3 61.4 + - + +
224A SER* 2.9 15.6 + - - -
225A TRP* 3.7 15.7 - - + -
267A VAL* 4.6 1.3 - - + +
270A ALA* 3.7 29.8 - - + +
271A ILE* 4.1 25.8 - - + +
274A ARG* 3.8 52.7 - - + +
275A PHE* 4.6 4.0 - - + -
262B MET* 3.6 16.8 - - + -
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Residues in contact with VAL 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 ILE* 3.0 23.2 + - + +
219A ILE* 3.9 3.8 - - - +
220A ASP 3.1 0.2 - - - -
221A ILE* 1.3 75.6 - - - +
223A THR* 1.3 63.6 + - + +
225A TRP* 3.1 21.0 + - - +
228A VAL* 3.2 20.3 - - + +
231A ALA* 3.6 21.3 - - + -
247A ILE* 4.1 18.8 - - + -
249A LEU* 3.6 27.1 - - + -
267A VAL* 3.6 24.9 - - + -
271A ILE* 4.0 13.7 - - + -
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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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219A ILE* 3.0 34.4 + - + +
220A ASP* 3.7 6.4 + - - -
222A VAL* 1.3 79.6 - - + +
224A SER* 1.3 63.2 + - - +
225A TRP 3.4 5.0 + - - +
228A VAL* 4.2 12.4 - - - +
229A SER 5.7 0.3 - - - +
230A GLY* 6.1 1.1 - - - -
231A ALA* 5.1 12.3 - - + +
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Residues in contact with SER 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 ASP 3.1 11.1 + - - -
221A ILE 2.9 15.1 + - - -
223A THR* 1.3 84.2 + - - +
225A TRP* 1.3 65.6 + - - +
226A PRO* 3.5 2.6 - - - +
259B GLN* 6.1 3.6 - - - -
262B MET* 3.6 23.1 - - - -
266B GLN* 3.3 20.3 + - - +
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Residues in contact with TRP 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 ILE* 3.7 18.4 - - + +
222A VAL 3.1 16.0 + - - +
223A THR 4.0 1.6 - - - +
224A SER* 1.3 81.4 + - - +
226A PRO* 1.3 96.1 - - + +
227A GLY 3.6 10.8 + - - -
228A VAL* 3.7 17.5 + - + +
263A VAL* 4.6 4.5 - - + -
266A GLN* 2.7 47.0 + - + +
267A VAL* 3.6 26.2 - - + -
270A ALA* 3.4 26.0 - - + -
225B TRP* 4.4 9.1 - + - -
262B MET* 5.2 7.0 - - + -
265B ASP* 5.4 0.9 - - + -
266B GLN* 3.5 38.6 - - + +
269B GLN* 3.8 25.1 - - - -
273B ARG* 4.7 2.9 - - - -
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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