Contacts of the helix formed by residues 265 - 274 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223B PHE* 4.0 32.1 - - + +
224B THR* 4.5 2.7 - - + +
227B LEU* 3.7 36.6 - - + +
228B SER* 5.0 0.4 - - - -
262B LEU* 3.1 37.2 + - + +
264B GLN* 1.3 82.2 - - - +
266B PRO* 1.3 70.9 - - + +
267B TRP 4.3 4.5 - - - +
268B TRP* 3.1 15.1 + - + +
269B HIS* 3.4 14.1 - - - -
30D ASP 4.4 4.0 - - - +
32D THR* 5.8 2.0 - - + +
36D PHE* 4.0 27.6 - - + -
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Residues in contact with PRO 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B GLN 3.5 9.6 - - - +
265B LEU* 1.3 82.8 - - - +
267B TRP* 1.3 61.3 + - - +
269B HIS* 3.1 14.5 + - + +
270B LYS* 3.0 25.6 + - - +
24D THR* 4.1 9.3 - - + +
28D THR* 3.8 24.9 - - + -
29D PRO 3.4 17.7 - - - +
30D ASP* 3.8 23.3 - - - +
32D THR* 3.6 19.3 - - + -
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Residues in contact with TRP 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B VAL* 6.4 0.2 - - + -
131B MSE 3.6 46.1 - - + +
132B THR* 4.4 5.6 - - - -
209B TRP* 3.5 40.1 - + - -
223B PHE* 3.3 42.0 - + - -
227B LEU* 3.5 20.2 - - + -
265B LEU* 3.1 1.5 - - + -
266B PRO* 1.3 76.4 - - - +
268B TRP* 1.3 63.1 + - - +
270B LYS* 3.2 24.8 + - + +
271B LEU* 3.1 42.2 + - + +
280B PHE* 4.4 12.6 - + - -
281B TRP* 4.1 14.6 - + - -
284B GLN* 5.0 3.6 - - - -
30D ASP* 3.1 19.7 + - - +
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Residues in contact with TRP 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B PHE* 3.7 16.2 - + - -
220B PHE* 3.5 32.3 - + - -
223B PHE* 4.3 7.4 - + + -
253B ALA 4.3 0.9 - - - -
254B GLY* 4.0 16.8 + - - -
257B ALA* 3.3 26.1 - - + +
258B LYS 5.1 0.4 - - - +
262B LEU* 3.3 42.6 - - + +
263B GLU* 4.2 16.7 - - + +
265B LEU* 3.1 9.6 + - + +
267B TRP* 1.3 80.8 - - - +
269B HIS* 1.3 66.0 + + - +
271B LEU* 3.4 16.7 + - + -
272B THR* 3.2 40.0 + - + +
608B PHE* 3.6 27.4 - + - -
609B PHE* 5.2 5.0 - + - -
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Residues in contact with HIS 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B LEU 4.8 0.2 - - - -
263B GLU* 2.7 50.8 + - + -
265B LEU 3.4 21.5 - - - -
266B PRO* 3.1 11.0 + - + +
268B TRP* 1.3 78.2 - + + +
270B LYS* 1.3 64.8 + - - +
272B THR* 3.4 7.7 + - - -
273B GLU* 3.0 39.4 + - - +
24D THR* 3.5 18.6 + - - +
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Residues in contact with LYS 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B VAL* 4.3 2.0 - - - +
266B PRO* 3.0 16.8 + - - +
267B TRP* 3.2 23.2 + - + +
269B HIS* 1.3 77.4 - - - +
271B LEU* 1.3 63.2 + - + +
273B GLU* 4.6 2.9 - - - -
274B HIS* 3.1 36.3 + - + +
280B PHE* 4.1 29.4 - - + -
24D THR* 4.0 20.2 - - + +
25D SER 3.5 19.7 - - - +
26D PRO 3.1 17.1 + - - +
28D THR 2.9 20.8 + - - -
30D ASP* 2.8 37.7 + - - +
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Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B TRP* 4.2 7.2 - - + -
210B PHE* 4.0 14.7 - - + -
215B PHE* 4.1 10.8 - - + -
223B PHE* 3.5 36.6 - - + -
267B TRP* 3.1 35.4 + - + +
268B TRP* 3.6 22.0 - - + +
270B LYS* 1.3 75.7 - - - +
272B THR* 1.3 62.5 + - - +
274B HIS 3.2 22.5 + - - +
275B ALA 3.5 1.0 + - - -
281B TRP* 3.6 33.2 - - + -
608B PHE* 3.7 15.3 - - + -
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Residues in contact with THR 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B TRP* 3.2 48.7 + - + +
269B HIS* 3.4 15.2 + - - -
271B LEU* 1.3 75.3 - - - +
273B GLU* 1.3 63.9 + - - +
274B HIS 3.2 0.4 + - - -
275B ALA* 4.1 4.4 + - - +
606B ASN* 2.9 25.1 + - - -
608B PHE* 3.8 23.1 - - + -
609B PHE* 3.6 32.0 - - + -
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Residues in contact with GLU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B HIS* 3.0 32.8 + - - +
270B LYS* 4.0 4.3 - - - +
272B THR* 1.3 80.5 - - - +
274B HIS* 1.3 78.4 + - + +
275B ALA 3.8 1.1 + - - -
278B ASP* 4.1 2.1 - - - +
24D THR* 2.8 52.8 + - - +
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Residues in contact with HIS 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B TRP* 4.3 0.5 + - - -
210B PHE* 4.3 1.9 - - - -
270B LYS* 3.1 31.1 + - + +
271B LEU 3.2 8.1 - - - +
272B THR 3.2 0.2 - - - -
273B GLU* 1.3 96.6 + - + +
275B ALA* 1.3 64.1 + - - +
276B ALA 3.2 2.9 - - - -
278B ASP* 2.6 33.7 + - - +
280B PHE* 3.5 36.9 - + + -
281B TRP* 2.8 33.1 + - - +
24D THR 4.9 8.1 + - - -
26D PRO* 6.1 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