Contacts of the helix formed by residues 220 - 233 (chain A) in PDB entry 1MVW
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 ASP 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A LYS 5.5 0.5 - - - +
213A LYS* 2.8 65.3 + - + +
214A MET 3.5 4.0 - - - +
217A THR* 2.8 41.1 + - - +
218A LEU 2.9 1.2 - - - -
219A GLU* 1.3 88.6 - - - +
221A GLN* 1.3 50.4 + - - +
222A ILE 3.0 0.7 - - - -
223A ILE* 2.7 7.3 + - - +
224A SER* 2.3 42.2 + - - +
340A ILE* 4.8 1.1 - - + -
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Residues in contact with GLN 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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206A LYS* 4.5 4.0 - - - +
216A GLY* 3.6 6.9 + - - +
217A THR* 2.6 38.0 + - - +
218A LEU* 2.4 47.0 - - + +
220A ASP* 1.3 69.1 - - - +
222A ILE* 1.3 64.0 - - - +
224A SER* 4.2 4.3 - - - -
225A ALA* 2.8 24.1 + - - +
340A ILE* 3.6 20.3 - - + +
341A LEU* 3.4 19.6 - - + +
448A GLN* 4.0 23.8 - - - +
449A LEU* 3.6 15.9 - - + -
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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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193A ILE* 4.0 26.3 - - + +
197A ALA* 5.2 5.6 - - + -
218A LEU* 2.9 37.7 - - + -
219A GLU* 3.5 20.2 - - - +
221A GLN* 1.3 79.5 - - - +
223A ILE* 1.3 69.3 + - + +
225A ALA* 3.3 12.8 - - - +
226A ASN* 4.2 5.5 + - - +
250A ILE* 6.0 1.3 - - + -
252A ILE* 5.0 9.4 - - + -
260A LEU* 5.3 10.5 - - + -
262A SER 5.1 1.1 - - - -
263A ALA* 3.2 31.2 - - + -
449A LEU* 4.7 7.8 - - + +
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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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193A ILE* 5.3 4.5 - - + -
194A GLN* 3.2 49.1 - - - +
197A ALA* 4.9 5.8 - - + -
219A GLU 2.8 25.1 - - - +
220A ASP* 2.7 9.4 + - - +
222A ILE* 1.3 86.0 - - + +
224A SER* 1.3 56.5 + - - +
225A ALA 2.6 16.6 + - - -
226A ASN* 2.9 35.4 + - - +
227A PRO* 3.2 5.9 - - + +
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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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213A LYS 4.2 3.6 + - - -
220A ASP 2.3 33.2 + - - -
221A GLN* 3.7 6.1 - - - -
223A ILE* 1.3 68.5 - - - +
225A ALA* 1.3 63.3 + - - +
226A ASN 3.3 0.2 - - - -
227A PRO* 3.0 22.4 - - - +
228A LEU 3.9 0.2 + - - -
337A ALA* 3.7 16.8 - - - +
340A ILE* 3.8 24.9 - - - +
341A LEU* 3.4 21.0 - - - +
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Residues in contact with ALA 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 GLN 2.8 11.0 + - - +
222A ILE* 3.3 16.4 - - - +
223A ILE 2.6 5.1 + - - -
224A SER* 1.3 73.4 - - - +
226A ASN* 1.3 68.8 + - - +
228A LEU* 3.0 19.9 + - - +
229A LEU* 3.4 11.1 + - + +
265A ILE* 4.1 25.1 - - + -
341A LEU* 3.7 9.9 - - - -
445A ILE* 4.4 14.0 - - + +
449A LEU* 5.2 1.8 - - + -
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Residues in contact with ASN 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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190A MLY 4.1 31.7 - - + +
193A ILE* 5.6 9.5 - - - +
194A GLN* 6.0 0.4 + - - -
222A ILE 4.2 6.1 - - - +
223A ILE* 2.9 31.4 + - - +
225A ALA* 1.3 77.9 - - - +
227A PRO* 1.3 57.6 - - + +
228A LEU 2.8 11.6 + - - -
229A LEU* 3.0 8.4 + - - +
230A GLU* 2.8 33.9 + - + +
248A MLY 2.8 37.2 - - - -
250A ILE* 5.4 1.4 - - - +
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Residues in contact with PRO 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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190A MLY 6.2 1.3 - - - -
223A ILE* 3.2 9.6 - - + +
224A SER* 3.0 22.7 - - - +
226A ASN* 1.3 97.8 - - + +
228A LEU* 1.3 58.3 + - - +
230A GLU* 4.1 12.4 - - + +
231A ALA* 3.7 8.1 + - - +
333A ALA* 4.9 16.4 - - + +
334A THR* 3.8 19.8 + - - -
337A ALA* 4.8 8.7 - - + -
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Residues in contact with LEU 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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224A SER 3.9 5.5 + - - +
225A ALA 3.0 10.0 + - - +
226A ASN 2.8 2.6 + - - -
227A PRO* 1.3 74.6 - - - +
229A LEU* 1.3 71.4 + - + +
230A GLU 3.0 0.7 - - - -
231A ALA* 2.8 14.5 + - - +
232A PHE* 3.2 40.2 - - + -
334A THR* 4.2 9.2 - - + +
337A ALA* 4.6 5.6 - - + -
338A ILE* 3.5 31.2 - - + -
341A LEU* 4.5 9.0 - - + -
343A PHE* 4.1 21.5 - - + -
441A MET* 4.3 14.4 - - - -
445A ILE* 3.9 23.8 - - + -
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Residues in contact with LEU 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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225A ALA* 3.4 13.7 + - + +
226A ASN* 3.0 10.9 + - - +
228A LEU* 1.3 83.0 - - + +
230A GLU* 1.3 53.4 + - + +
232A PHE* 3.1 2.8 + - - +
233A GLY* 2.4 38.8 + - - -
246A PHE* 4.0 20.1 - - + -
248A MLY 5.4 9.6 - - + +
265A ILE* 4.2 30.7 - - + -
267A THR* 5.6 0.4 - - - +
438A PHE* 3.9 23.2 - - + -
441A MET* 5.1 5.8 - - + -
442A VAL* 4.1 22.0 - - + +
445A ILE* 3.9 23.1 - - + -
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Residues in contact with GLU 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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186A THR* 3.6 12.6 - - + +
190A MLY 2.8 47.1 - - - +
226A ASN* 2.8 30.8 + - + +
227A PRO* 4.1 8.7 - - + +
229A LEU* 1.3 76.6 - - + +
231A ALA* 1.3 63.9 + - - +
232A PHE 3.1 0.4 - - - -
234A ASN* 2.9 46.1 + - + +
242A ASN* 2.6 31.5 + - - +
246A PHE* 6.1 0.7 - - + -
248A MLY 5.5 3.8 - - - -
286A HIS* 3.3 9.9 - - + -
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Residues in contact with ALA 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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227A PRO 3.7 5.6 + - - +
228A LEU 2.8 11.5 + - - +
230A GLU* 1.3 80.4 - - - +
232A PHE* 1.3 65.9 - - + +
286A HIS* 3.2 16.9 + - - -
287A ILE* 2.7 38.3 + - + +
290A GLN* 3.5 29.2 - - - +
334A THR* 3.8 9.4 - - + +
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Residues in contact with PHE 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 LEU* 3.2 44.8 + - + -
229A LEU* 3.1 4.3 + - - +
231A ALA* 1.3 79.6 - - + +
233A GLY* 1.3 57.6 + - - +
270A LEU* 5.0 0.3 - - - +
285A TYR* 2.8 21.3 - - - -
287A ILE* 3.0 38.4 - - + -
334A THR* 4.9 1.3 - - + -
338A ILE* 5.6 0.7 - - + -
351A ILE* 3.7 21.5 - - + -
355A THR* 3.8 19.7 - - - -
434A TYR* 2.8 36.3 + + + +
437A MET* 4.0 9.2 - - + -
438A PHE* 3.8 19.7 - - + -
441A MET* 3.8 24.0 - - + -
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Residues in contact with GLY 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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229A LEU 2.4 20.5 + - - -
232A PHE* 1.3 73.4 - - - +
234A ASN* 1.3 60.6 + - - +
245A ARG* 2.9 27.2 + - - -
246A PHE* 3.0 22.9 - - - -
270A LEU* 4.1 3.8 - - - -
285A TYR* 3.3 12.7 - - - -
438A PHE* 3.8 6.4 - - - -
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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