Contacts of the helix formed by residues 367 - 377 (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 VAL 367 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A MSE 3.9 24.9 - - + -
334A VAL* 5.1 1.8 - - + -
363A PHE* 3.1 22.3 + - + +
365A HIS 3.5 0.2 - - - -
366A ASP* 1.3 89.0 - - + +
368A LEU* 1.3 66.8 + - - +
369A ARG 3.4 1.3 - - - -
370A PRO* 3.5 3.5 - - - +
371A PHE* 3.2 24.3 + - - +
385A THR* 4.4 4.4 + - + +
386A PRO* 4.4 22.7 - - + +
389A PHE* 3.7 42.8 - - + -
400A ARG* 4.6 6.1 - - - +
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Residues in contact with LEU 368 (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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103A GLY 5.5 0.9 - - - +
106A VAL* 4.3 11.7 - - + -
107A PHE* 4.0 17.5 - - + -
171A ILE* 3.8 23.6 - - + -
195A VAL* 3.8 30.1 - - + -
197A GLU* 4.9 0.7 - - - +
300A MSE 4.9 3.4 - - - -
363A PHE* 2.9 41.1 + - + +
364A ARG* 3.5 19.1 - - + +
367A VAL* 1.3 74.9 - - - +
369A ARG* 1.3 64.5 + - - +
371A PHE* 3.3 5.7 + - + +
372A PHE* 3.0 36.2 + - + +
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Residues in contact with ARG 369 (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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106A VAL* 3.5 32.2 + - + +
107A PHE* 5.6 2.0 - - - -
109A GLU* 4.1 15.6 + - - +
110A GLY* 3.4 35.7 + - - +
112A TYR* 4.4 5.8 - - - -
364A ARG 3.0 19.0 + - - +
365A HIS* 3.7 12.4 - - + +
368A LEU* 1.3 78.1 - - - +
370A PRO* 1.3 66.2 - - + +
372A PHE* 3.4 3.9 + - - +
373A ASP* 2.8 67.1 + - - +
377A VAL* 6.1 0.4 - - - +
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Residues in contact with PRO 370 (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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365A HIS 3.4 13.7 - - - +
366A ASP* 3.6 17.9 - - - +
367A VAL* 3.5 12.8 - - - +
369A ARG* 1.3 97.2 - - + +
371A PHE* 1.3 56.3 + - - +
373A ASP* 3.7 8.0 - - + +
374A GLN* 3.0 30.8 + - - +
381A PRO 4.9 1.0 - - - +
383A ALA* 3.5 23.1 - - + +
384A ASP 5.6 0.2 - - - +
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Residues in contact with PHE 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A VAL* 3.3 33.0 - - + -
194A ALA 4.4 1.6 - - - -
195A VAL* 4.2 5.8 - - + -
298A PRO* 4.1 16.6 - - + -
300A MSE 3.7 36.1 - - + -
332A TYR* 3.8 35.9 - + - -
367A VAL 3.2 18.5 + - - +
368A LEU* 3.4 5.6 - - + +
370A PRO* 1.3 79.6 - - - +
372A PHE* 1.3 68.3 + + - +
374A GLN* 3.5 6.6 + - - +
375A TYR* 3.4 43.7 - + - -
383A ALA* 4.0 2.4 - - - +
385A THR* 3.7 25.1 - - + +
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Residues in contact with PHE 372 (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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76A VAL* 3.7 26.9 - - + -
107A PHE* 3.5 29.2 - + + -
112A TYR* 3.4 11.4 - + + +
169A GLY* 4.2 3.4 - - - -
170A MSE 3.8 23.3 - - - -
171A ILE* 4.2 9.6 - - + -
193A VAL* 3.7 27.4 - - + -
195A VAL* 3.5 24.9 - - + -
368A LEU* 3.0 24.9 + - + +
369A ARG* 3.8 3.1 - - - +
371A PHE* 1.3 75.3 - + - +
373A ASP* 1.3 65.8 + - - +
375A TYR* 3.2 2.8 + - - -
376A LEU* 2.9 48.1 + - + +
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Residues in contact with ASP 373 (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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112A TYR* 2.5 31.2 + - - -
369A ARG* 2.8 59.7 + - - +
370A PRO* 3.7 7.8 - - + +
372A PHE* 1.3 75.2 - - - +
374A GLN* 1.3 63.8 + - - +
377A VAL* 2.9 33.6 + - - +
380A ALA* 3.1 22.0 - - + +
381A PRO* 5.8 2.2 - - + +
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Residues in contact with GLN 374 (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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370A PRO 3.0 17.4 + - - +
371A PHE* 3.6 7.4 - - - +
372A PHE 3.2 0.2 - - - -
373A ASP* 1.3 78.2 - - - +
375A TYR* 1.3 95.8 + - + +
377A VAL 4.7 3.3 - - - +
380A ALA* 4.2 8.6 - - - +
381A PRO 3.7 18.8 - - - +
382A LYS* 3.7 13.6 - - - +
383A ALA* 2.8 37.5 + - - +
385A THR* 4.8 2.3 + - - -
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Residues in contact with TYR 375 (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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167A LYS* 3.9 10.3 + - - +
192A LYS* 3.3 41.2 - - + +
193A VAL* 4.1 15.7 - - + -
298A PRO* 3.5 36.3 - - + +
329A THR* 3.7 22.7 + - - -
330A LEU* 5.7 0.2 - - - +
332A TYR* 5.1 2.4 + - - -
371A PHE* 3.4 35.3 - + - -
372A PHE 3.2 3.2 + - - +
373A ASP 3.2 0.2 - - - -
374A GLN* 1.3 109.1 + - + +
376A LEU* 1.3 59.6 + - - +
377A VAL 5.4 0.2 - - - -
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Residues in contact with LEU 376 (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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74A PRO* 3.5 16.6 - - + +
75A ILE 4.4 3.1 - - - +
112A TYR* 3.7 15.0 - - + -
165A ASN* 2.8 26.5 + - - -
167A LYS* 3.5 13.0 - - - +
168A VAL* 3.4 39.9 - - - +
169A GLY* 3.9 8.5 - - - +
192A LYS* 3.9 9.6 - - + -
193A VAL* 3.6 13.7 - - + -
372A PHE* 2.9 46.1 + - + +
373A ASP 3.3 0.2 + - - -
375A TYR* 1.3 86.2 - - - +
377A VAL* 1.3 62.1 + - - +
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Residues in contact with VAL 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PRO* 4.0 18.2 - - + -
110A GLY 5.2 5.4 - - - +
112A TYR* 3.9 11.0 - - + +
165A ASN* 4.5 1.3 - - - +
167A LYS* 4.7 2.9 + - - -
369A ARG* 6.1 0.4 - - - +
373A ASP* 2.9 37.7 + - + +
374A GLN 4.7 3.6 - - - +
375A TYR 5.4 0.2 - - - -
376A LEU* 1.3 78.2 - - - +
378A ASP* 1.3 74.6 + - - +
379A GLY 3.2 1.0 + - - -
380A ALA* 3.1 26.9 + - + +
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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