Contacts of the helix formed by residues 265 - 274 (chain D) 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 LEU 265 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B ASP 4.3 4.7 - - - +
32B THR* 5.8 2.2 - - + +
36B PHE* 3.8 29.6 - - + -
223D PHE* 4.1 31.6 - - + +
224D THR* 4.6 2.0 - - + +
227D LEU* 3.8 36.6 - - + +
228D SER 4.9 0.4 - - - +
262D LEU* 3.1 34.6 + - + +
264D GLN* 1.3 80.7 - - - +
266D PRO* 1.3 70.9 - - + +
267D TRP 4.3 4.7 - - - +
268D TRP* 3.1 19.4 + - + +
269D HIS* 3.5 13.9 + - - -
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Residues in contact with PRO 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B THR* 4.2 6.8 - - + +
28B THR* 4.0 23.6 - - + -
29B PRO 3.4 19.3 - - - +
30B ASP* 3.7 19.5 - - - +
32B THR* 3.6 19.3 - - + -
264D GLN 3.5 9.4 - - - +
265D LEU* 1.3 83.3 - - - +
267D TRP* 1.3 62.4 + - - +
269D HIS* 3.1 14.1 + - + +
270D LYS* 2.9 31.6 + - - +
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Residues in contact with TRP 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ASP* 3.0 22.6 + - - +
131D MSE 3.6 46.0 - - + +
132D THR* 4.3 5.6 - - - -
209D TRP* 3.5 37.0 - + - -
223D PHE* 3.3 42.2 - + - -
227D LEU* 3.5 24.5 - - + -
265D LEU* 3.1 1.7 - - + -
266D PRO* 1.3 76.6 - - - +
268D TRP* 1.3 62.7 + - - +
270D LYS* 3.2 26.8 + - + +
271D LEU* 3.1 43.6 + - + +
280D PHE* 4.5 11.4 - + - -
281D TRP* 4.0 15.5 - + - -
284D GLN* 5.0 3.8 - - - -
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Residues in contact with TRP 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D PHE* 3.8 16.6 - + - -
220D PHE* 3.5 33.0 - + - -
223D PHE* 4.3 8.3 - + + -
253D ALA 4.3 1.1 - - - -
254D GLY* 4.0 17.2 + - - -
257D ALA* 3.4 26.4 - - + +
262D LEU* 3.3 41.1 - - + +
263D GLU* 4.2 19.3 + - + +
265D LEU* 3.1 8.4 + - + +
267D TRP* 1.3 79.9 - - - +
269D HIS* 1.3 67.1 + + - +
271D LEU* 3.4 16.4 + - + +
272D THR* 3.2 40.4 + - + +
608D PHE* 3.5 27.8 - + - -
609D PHE* 5.2 4.0 - + - -
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Residues in contact with HIS 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B THR* 3.5 19.7 + - + +
263D GLU* 2.8 51.7 + - + +
265D LEU 3.5 17.6 + - - -
266D PRO* 3.1 11.3 + - + +
268D TRP* 1.3 80.3 - + - +
270D LYS* 1.3 64.4 + - - +
272D THR* 3.4 7.6 + - - -
273D GLU* 3.0 40.1 + - - +
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Residues in contact with LYS 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B THR* 4.2 15.7 - - + +
25B SER 3.6 18.6 - - - +
26B PRO* 3.1 18.3 + - + +
28B THR 3.0 18.2 + - - -
30B ASP* 2.9 36.3 + - - +
130D VAL* 4.3 1.8 - - - +
266D PRO* 2.9 20.8 + - - +
267D TRP* 3.2 25.9 + - + +
269D HIS* 1.3 75.8 - - - +
271D LEU* 1.3 62.5 + - - +
273D GLU* 4.6 2.7 - - - -
274D HIS* 3.1 35.0 + - + +
280D PHE* 4.1 31.1 - - + -
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Residues in contact with LEU 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D TRP* 4.1 7.9 - - + -
210D PHE* 3.9 17.6 - - + -
215D PHE* 4.1 7.4 - - + -
223D PHE* 3.5 37.0 - - + -
267D TRP* 3.1 35.0 + - + +
268D TRP* 3.6 26.2 - - + +
269D HIS 3.2 0.2 - - - -
270D LYS* 1.3 77.4 - - - +
272D THR* 1.3 60.4 + - - +
274D HIS 3.3 21.5 - - - +
275D ALA* 3.4 1.7 + - - -
280D PHE* 6.0 0.2 - - + -
281D TRP* 3.7 31.9 - - + -
608D PHE* 3.7 14.6 - - + -
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Residues in contact with THR 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268D TRP* 3.2 51.8 + - + +
269D HIS* 3.4 11.6 + - - -
271D LEU* 1.3 73.9 - - - +
273D GLU* 1.3 64.9 + - - +
274D HIS 3.2 0.2 - - - -
275D ALA* 4.1 4.1 + - - +
606D ASN* 2.8 26.3 + - - -
608D PHE* 3.8 24.2 - - + -
609D PHE* 3.5 30.4 - - + -
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Residues in contact with GLU 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B THR* 2.8 50.9 + - - +
269D HIS* 3.0 34.0 + - - +
270D LYS* 4.8 0.5 - - - -
271D LEU 3.3 0.2 - - - -
272D THR* 1.3 79.5 - - - +
274D HIS* 1.3 82.5 + - + +
275D ALA 3.7 1.1 + - - -
278D ASP* 4.1 3.1 - - - +
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Residues in contact with HIS 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B THR 5.0 7.5 + - - -
26B PRO* 6.1 0.6 - - - +
204D TRP* 4.2 0.9 + - - -
210D PHE* 4.4 1.6 - - - -
270D LYS* 3.1 31.3 + - + +
271D LEU 3.3 7.6 - - - +
273D GLU* 1.3 96.7 + - + +
275D ALA* 1.3 64.3 + - - +
276D ALA 3.2 4.1 - - - +
278D ASP* 2.5 39.9 + - - +
280D PHE* 3.4 34.6 - + + +
281D TRP* 2.8 33.1 + - - +
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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