Contacts of the helix formed by residues 367 - 377 (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 VAL 367 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300B MSE 3.7 25.8 - - + -
334B VAL* 5.0 2.0 - - + -
363B PHE* 3.1 22.1 + - + +
365B HIS 3.5 0.2 - - - -
366B ASP* 1.3 87.8 - - + +
368B LEU* 1.3 68.2 + - - +
369B ARG 3.4 1.3 - - - -
370B PRO* 3.5 3.1 - - - +
371B PHE* 3.2 23.9 + - - +
385B THR* 4.4 12.0 + - + +
386B PRO* 4.5 14.6 - - + +
389B PHE* 3.7 42.2 - - + -
400B ARG* 4.4 6.3 - - - +
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Residues in contact with LEU 368 (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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103B GLY 5.5 0.9 - - - +
106B VAL* 4.4 8.3 - - + -
107B PHE* 4.0 17.0 - - + -
171B ILE* 3.7 23.8 - - + -
195B VAL* 3.8 29.2 - - + -
197B GLU* 4.8 0.9 - - - +
300B MSE 4.9 2.7 - - - -
363B PHE* 2.9 42.7 + - + +
364B ARG* 3.5 22.2 - - + +
367B VAL* 1.3 73.8 - - - +
369B ARG* 1.3 66.1 + - - +
371B PHE* 3.3 6.1 + - + +
372B PHE* 3.0 34.3 + - + +
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Residues in contact with ARG 369 (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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106B VAL* 3.1 52.2 + - + +
107B PHE* 5.0 3.8 - - - -
109B GLU* 3.6 13.3 + - - +
110B GLY* 3.2 27.3 - - - +
112B TYR* 4.1 10.5 - - - -
364B ARG 3.0 12.1 + - - +
365B HIS* 3.7 13.8 - - + +
368B LEU* 1.3 76.8 - - - +
370B PRO* 1.3 66.1 - - + +
372B PHE* 3.7 2.4 - - - -
373B ASP* 2.8 73.2 + - - +
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Residues in contact with PRO 370 (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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365B HIS 3.4 13.9 - - - +
366B ASP* 3.6 17.7 - - - +
367B VAL* 3.5 12.1 - - - +
369B ARG* 1.3 95.6 - - + +
371B PHE* 1.3 55.6 + - - +
373B ASP* 3.7 7.4 - - + +
374B GLN* 3.0 29.3 + - - +
381B PRO 4.7 1.4 - - - +
383B ALA* 3.5 24.2 - - + +
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Residues in contact with PHE 371 (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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193B VAL* 3.2 31.6 - - + -
194B ALA 4.3 2.0 - - - -
195B VAL* 4.2 4.9 - - + -
298B PRO* 3.9 19.5 - - + -
299B THR 4.4 0.7 - - - -
300B MSE 3.8 36.8 - - + -
332B TYR* 3.8 32.1 - + - -
367B VAL 3.2 17.7 + - - +
368B LEU* 3.4 4.9 - - - +
369B ARG 3.2 0.6 - - - -
370B PRO* 1.3 77.7 - - - +
372B PHE* 1.3 71.9 + + - +
374B GLN* 3.5 6.5 + - - +
375B TYR* 3.4 44.8 - + - -
383B ALA* 4.1 1.9 - - - +
385B THR* 3.7 24.9 - - + +
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Residues in contact with PHE 372 (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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76B VAL* 3.8 25.4 - - + -
107B PHE* 3.5 29.2 - + + -
112B TYR* 3.4 12.6 - + + +
169B GLY* 4.2 2.9 - - - -
170B MSE 3.7 28.7 - - - -
171B ILE* 4.2 7.6 - - + -
193B VAL* 3.7 25.6 - - + -
195B VAL* 3.4 27.1 - - + -
368B LEU* 3.0 24.4 + - + +
369B ARG* 3.8 3.1 - - - +
371B PHE* 1.3 75.1 - + - +
373B ASP* 1.3 61.1 + - - +
375B TYR* 3.2 2.8 + - - -
376B LEU* 2.9 53.7 + - + +
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Residues in contact with ASP 373 (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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112B TYR* 2.6 30.8 + - - -
369B ARG* 2.8 61.0 + - - +
370B PRO* 3.7 8.3 - - + +
372B PHE* 1.3 70.8 - - - +
374B GLN* 1.3 64.5 + - - +
377B VAL* 3.0 33.3 + - - +
380B ALA* 3.2 23.6 - - + +
381B PRO* 5.5 1.3 - - + +
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Residues in contact with GLN 374 (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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370B PRO 3.0 16.8 + - - +
371B PHE* 3.6 7.3 - - - +
372B PHE 3.2 0.2 - - - -
373B ASP* 1.3 78.4 - - - +
375B TYR* 1.3 97.9 + - + +
377B VAL 4.8 3.5 - - - +
380B ALA* 4.5 7.0 - - - +
381B PRO 3.6 18.1 + - - +
382B LYS* 3.6 41.5 - - + +
383B ALA* 2.9 27.4 + - - +
385B THR* 4.6 3.5 + - - -
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Residues in contact with TYR 375 (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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167B LYS* 3.6 9.0 - - - +
192B LYS* 3.4 46.3 - - + +
193B VAL* 4.1 15.9 - - + -
298B PRO* 3.4 33.4 - - + +
329B THR* 3.8 16.5 + - - -
330B LEU* 5.3 1.2 - - - +
332B TYR* 5.3 1.4 + - - -
371B PHE* 3.4 32.3 - + - -
372B PHE 3.2 3.6 + - - +
374B GLN* 1.3 111.0 + - + +
376B LEU* 1.3 59.0 + - - +
377B VAL 5.5 0.2 - - - -
382B LYS* 6.2 0.2 - - - -
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Residues in contact with LEU 376 (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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74B PRO* 3.4 17.4 - - + +
75B ILE 4.4 4.0 - - - +
112B TYR* 3.7 12.6 - - + -
165B ASN* 2.8 27.5 + - - -
167B LYS* 3.9 15.1 - - + +
168B VAL* 3.5 37.9 - - - +
169B GLY* 3.9 9.4 - - - +
192B LYS* 3.9 7.6 - - + -
193B VAL* 3.6 13.2 - - + -
372B PHE* 2.9 46.7 + - + +
373B ASP 3.3 0.4 + - - -
375B TYR* 1.3 87.7 - - - +
377B VAL* 1.3 62.1 + - - +
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Residues in contact with VAL 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B PRO* 4.0 13.7 - - + -
110B GLY 5.1 6.3 - - - +
112B TYR* 3.6 30.7 - - + +
165B ASN* 4.7 0.2 - - - +
167B LYS* 5.1 1.5 + - - -
373B ASP* 3.0 25.4 + - + +
374B GLN 4.8 3.3 - - - +
375B TYR 5.5 0.2 - - - -
376B LEU* 1.3 77.8 - - - +
378B ASP* 1.3 75.5 + - - +
379B GLY 3.4 0.3 + - - -
380B ALA* 3.2 27.8 + - + +
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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