Contacts of the helix formed by residues 265 - 274 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A PHE* 3.9 38.1 - - + +
224A THR* 4.4 1.8 - - + +
227A LEU* 3.8 37.0 - - + +
228A SER* 4.8 0.9 - - - +
262A LEU* 3.0 33.9 + - + +
264A GLN* 1.3 80.6 - - - +
266A PRO* 1.3 71.6 - - + +
267A TRP 4.3 4.9 - - - +
268A TRP* 3.1 15.2 + - + +
269A HIS* 3.5 14.7 - - - -
30C ASP 4.5 4.0 - - - +
32C THR* 5.9 1.8 - - + +
36C PHE* 4.0 27.4 - - + -
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Residues in contact with PRO 266 (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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264A GLN 3.5 9.6 - - - +
265A LEU* 1.3 82.4 - - - +
267A TRP* 1.3 62.1 + - - +
269A HIS* 3.1 14.2 + - + +
270A LYS* 3.0 26.8 + - - +
24C THR* 4.1 9.2 - - + +
28C THR* 4.1 19.7 - - + -
29C PRO 3.3 22.7 - - - +
30C ASP* 3.7 22.4 - - - +
32C THR* 3.6 19.5 - - + -
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Residues in contact with TRP 267 (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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131A MSE 3.6 46.8 - - + +
132A THR* 4.3 6.1 - - - -
209A TRP* 3.4 36.9 - + - -
223A PHE* 3.3 42.4 - + - -
227A LEU* 3.5 20.2 - - + -
265A LEU* 3.1 1.8 - - + -
266A PRO* 1.3 76.2 - - - +
268A TRP* 1.3 63.5 + - - +
270A LYS* 3.1 26.9 + - + +
271A LEU* 3.1 42.0 + - + +
280A PHE* 4.3 12.6 - + - -
281A TRP* 4.2 14.8 - + - -
284A GLN* 4.9 3.6 - - - -
30C ASP* 3.1 19.3 + - - +
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Residues in contact with TRP 268 (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 PHE* 3.7 16.2 - + - -
220A PHE* 3.5 30.7 - + - -
223A PHE* 4.2 8.3 - + + -
253A ALA 4.1 5.6 - - - -
254A GLY* 4.1 11.5 + - - -
257A ALA* 3.4 25.9 - - + +
258A LYS 5.1 0.4 - - - +
262A LEU* 3.4 41.7 - - + +
263A GLU* 4.2 17.3 + - + +
265A LEU* 3.1 9.4 + - + +
267A TRP* 1.3 80.9 - - - +
269A HIS* 1.3 66.4 + + - +
271A LEU* 3.3 19.2 + - + +
272A THR* 3.2 41.1 + - + +
608A PHE* 3.6 27.6 - + - -
609A PHE* 5.3 4.2 - + - -
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Residues in contact with HIS 269 (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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263A GLU* 2.7 53.2 + - + -
265A LEU 3.5 20.2 - - - -
266A PRO* 3.1 11.7 + - + +
268A TRP* 1.3 78.2 - + + +
270A LYS* 1.3 60.1 + - - +
272A THR* 3.5 8.0 + - - -
273A GLU* 3.0 43.5 + - - +
24C THR* 3.6 19.5 + - - +
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Residues in contact with LYS 270 (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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130A VAL* 4.3 2.2 - - - +
266A PRO 3.0 14.8 + - - +
267A TRP* 3.1 29.0 + - + +
269A HIS* 1.3 77.9 - - - +
271A LEU* 1.3 62.4 + - + +
273A GLU* 4.6 2.7 - - - -
274A HIS* 3.1 36.9 + - + +
280A PHE* 4.1 28.6 - - + -
24C THR* 4.2 20.0 - - + +
25C SER 3.5 21.1 - - - +
26C PRO* 3.1 16.8 + - + -
28C THR* 3.1 18.0 + - - -
30C ASP* 2.8 35.8 + - - +
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Residues in contact with LEU 271 (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 TRP* 4.1 11.2 - - + -
210A PHE* 3.8 17.0 - - + -
215A PHE* 4.2 6.3 - - + -
223A PHE* 3.5 37.7 - - + -
267A TRP* 3.1 31.2 + - + +
268A TRP* 3.6 26.9 - - + +
269A HIS 3.3 0.4 - - - -
270A LYS* 1.3 77.4 - - + +
272A THR* 1.3 61.2 + - - +
274A HIS 3.3 21.0 + - - +
275A ALA 3.5 1.7 + - - -
281A TRP* 3.8 31.4 - - + -
608A PHE* 3.5 15.0 - - + -
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Residues in contact with THR 272 (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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268A TRP* 3.2 48.7 + - + +
269A HIS* 3.5 15.2 + - - -
271A LEU* 1.3 76.2 - - - +
273A GLU* 1.3 64.3 + - - +
274A HIS 3.3 0.6 + - - -
275A ALA 4.2 3.6 + - - -
606A ASN* 2.8 26.9 + - - -
608A PHE* 3.7 22.2 - - + -
609A PHE* 3.5 31.0 - - + -
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Residues in contact with GLU 273 (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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269A HIS* 3.0 33.5 + - - +
270A LYS* 4.7 0.9 - - - -
272A THR* 1.3 79.0 - - - +
274A HIS* 1.3 82.5 + - + +
275A ALA 3.7 1.2 + - - -
278A ASP* 4.2 2.1 - - - +
24C THR* 2.9 52.3 + - - +
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Residues in contact with HIS 274 (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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204A TRP* 4.2 0.7 + - - -
210A PHE* 4.4 1.6 - - - -
270A LYS* 3.1 30.1 + - + +
271A LEU 3.3 7.1 - - - +
273A GLU* 1.3 97.9 + - + +
275A ALA* 1.3 64.0 + - - +
276A ALA 3.2 3.3 - - - +
278A ASP* 2.5 35.2 + - - +
280A PHE* 3.4 35.1 - + + +
281A TRP* 2.8 33.2 + - - +
24C THR 4.9 6.9 + - - -
26C PRO* 6.2 0.8 - - - +
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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