Contacts of the helix formed by residues 219 - 228 (chain C) in PDB entry 1MPX
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 ASN 219 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208C ASP* 2.7 42.2 + - - +
209C TRP* 3.8 15.9 - - + +
216C ARG* 3.8 20.9 + - - +
217C GLN 3.0 1.8 - - - -
218C VAL* 1.3 87.7 - - - +
220C PHE* 1.3 63.3 + - - +
221C ASP 3.2 2.7 - - - -
222C TYR* 3.1 24.5 + - + +
223C PHE* 3.1 39.3 + - + -
309C GLU* 5.9 2.9 - - - -
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Residues in contact with PHE 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C PHE* 3.6 27.1 - + - -
216C ARG 4.8 0.4 + - - -
217C GLN* 3.2 34.4 + - + +
219C ASN* 1.3 76.6 - - - +
221C ASP* 1.3 63.1 + - - +
223C PHE* 3.2 26.6 + + - +
224C THR* 3.5 3.8 + - - +
236C ILE* 3.4 24.3 - - + +
238C ARG* 5.9 1.1 - - - +
247C PHE* 3.6 28.3 - + + -
253C ALA* 3.6 21.3 - - + -
256C PHE* 3.8 12.8 - + + -
257C ALA* 3.8 4.0 - - + -
262C LEU* 3.3 27.5 - - + +
268C TRP* 3.5 28.0 - + - -
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Residues in contact with ASP 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C GLN 5.7 0.3 - - - +
218C VAL 4.0 8.5 + - - +
219C ASN 3.2 0.4 - - - -
220C PHE* 1.3 74.2 - - - +
222C TYR* 1.3 60.5 + - - +
224C THR* 3.3 8.2 + - - -
225C GLY* 2.9 25.8 + - - -
234C ALA 3.9 2.1 - - - +
235C GLY* 3.8 9.3 - - - -
236C ILE* 3.1 18.5 + - - +
238C ARG* 3.0 44.5 + - - -
459C PHE* 4.2 12.6 - - - +
460C ALA* 5.3 3.5 + - - +
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Residues in contact with TYR 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C TYR* 2.7 36.7 + + - -
129C TYR* 5.1 0.5 + - - -
131C MSE 3.9 27.4 - - + -
175C TYR* 3.5 22.0 - - - -
200C MSE 5.2 2.0 - - + -
209C TRP* 4.0 24.5 - + - -
218C VAL 4.6 1.3 + - - +
219C ASN* 3.1 26.3 + - - +
221C ASP* 1.3 76.2 - - - +
223C PHE* 1.3 61.2 + + - +
225C GLY* 4.4 1.6 - - - +
226C GLN* 2.9 52.8 + - + +
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Residues in contact with PHE 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C MSE 4.1 6.5 - - + -
209C TRP* 3.7 22.4 - + - -
215C PHE* 4.3 9.0 - + - -
219C ASN* 3.1 28.0 + - + -
220C PHE* 3.2 33.1 + + - +
222C TYR* 1.3 80.1 - + - +
224C THR* 1.3 59.6 + - + +
227C LEU* 2.9 41.6 + - + +
262C LEU* 4.6 6.7 - - + -
265C LEU* 4.1 18.6 - - + +
267C TRP* 3.4 28.7 - + + -
268C TRP* 4.3 10.1 - + + -
271C LEU* 3.5 30.3 - - + -
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Residues in contact with THR 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE* 4.1 19.3 - - + -
220C PHE 3.5 1.3 + - - +
221C ASP 3.3 6.8 + - - -
223C PHE* 1.3 74.4 - - - +
225C GLY* 1.3 64.7 + - - +
228C SER* 2.5 37.8 + - - +
233C GLY* 3.8 0.2 - - - -
234C ALA 2.6 26.2 + - - +
235C GLY 3.5 12.9 - - - +
236C ILE* 3.5 19.6 - - + +
262C LEU* 3.5 31.6 - - + -
265C LEU* 4.7 2.5 - - + -
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Residues in contact with GLY 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C TYR* 5.4 0.7 + - - -
221C ASP 2.9 17.7 + - - -
222C TYR* 3.7 2.7 - - - -
223C PHE 3.3 0.4 - - - -
224C THR* 1.3 78.9 - - - +
226C GLN* 1.3 67.3 + - - +
231C GLY 4.3 3.8 - - - +
232C LYS* 4.8 0.5 - - - +
233C GLY* 3.3 22.9 + - - -
234C ALA 3.1 17.6 + - - -
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Residues in contact with GLN 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE* 3.6 9.0 - - - +
81C PRO* 3.0 33.7 + - - +
82C TYR* 3.5 26.8 - - - -
122C LYS* 2.8 38.0 + - - +
123C TYR* 4.7 8.1 + - - -
129C TYR* 4.6 6.1 + - - +
131C MSE 5.6 0.2 - - + -
222C TYR* 2.9 48.5 + - + +
225C GLY* 1.3 87.4 - - - +
227C LEU* 1.3 69.0 + - + +
228C SER 3.7 1.1 - - - -
229C LYS 4.4 0.4 - - - -
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Residues in contact with LEU 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ASP* 3.8 25.2 - - + +
31A ILE* 3.6 18.8 - - - +
32A THR 5.0 0.5 + - - -
36A PHE* 5.0 0.9 - - - +
129C TYR* 3.5 35.4 - - + -
131C MSE 4.0 22.4 - - + -
223C PHE* 2.9 29.1 + - + +
226C GLN* 1.3 80.1 - - + +
228C SER* 1.3 63.6 + - - +
229C LYS 3.4 1.8 - - - -
265C LEU* 3.9 23.3 - - + +
267C TRP* 3.5 34.5 - - + -
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Residues in contact with SER 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE* 5.0 3.0 - - - +
35A PRO* 5.2 2.3 - - - +
36A PHE* 3.7 46.1 + - - +
223C PHE 4.0 0.4 + - - -
224C THR* 2.5 39.6 + - - -
226C GLN 3.7 0.4 - - - -
227C LEU* 1.3 79.8 - - - +
229C LYS* 1.3 78.6 + - - +
233C GLY* 4.4 7.9 - - - -
234C ALA 4.8 1.3 + - - -
265C LEU* 5.1 0.2 - - - -
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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