Contacts of the helix formed by residues 358 - 367 (chain C) 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 ASP 358 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345C TYR 4.3 1.9 - - - +
346C ASP* 3.2 24.4 - - - +
347C GLY 2.9 18.1 + - - -
348C SER* 3.2 16.4 + - - +
357C GLY* 1.3 67.5 - - - -
359C THR* 1.3 57.5 + - - +
360C ALA* 3.5 1.7 - - - +
361C ARG* 3.0 33.8 + - + +
362C GLN* 2.9 30.2 + - - +
364C ARG* 4.9 1.7 + - - -
355D PHE 5.4 0.2 + - - -
356D GLU* 3.1 16.9 + - - +
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Residues in contact with THR 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337C PRO* 3.6 8.3 - - + +
338C TRP* 3.0 33.4 + - - -
347C GLY 2.7 21.3 + - - +
355C PHE* 3.9 10.8 - - + -
356C GLU 4.3 3.8 - - - +
357C GLY 2.9 18.5 + - - +
358C ASP* 1.3 70.6 - - - +
360C ALA* 1.3 55.8 + - - +
362C GLN* 3.6 18.2 - - - +
363C PHE 3.1 20.4 + - - -
391C TYR* 3.7 28.7 - - + -
398C TRP* 3.7 15.0 - - - -
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Residues in contact with ALA 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338C TRP* 3.9 11.9 - - - +
342C GLN 3.4 18.6 - - - +
343C VAL* 3.5 12.5 - - - +
345C TYR 3.2 24.7 - - - +
347C GLY* 3.6 7.8 - - - +
358C ASP* 3.1 4.4 + - - +
359C THR* 1.3 78.8 + - - +
361C ARG* 1.3 65.1 + - - +
363C PHE* 3.3 4.0 + - - +
364C ARG* 3.0 29.9 + - - +
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Residues in contact with ARG 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C ASP* 3.0 28.6 + - - -
106C VAL* 3.4 20.8 - - - +
109C GLU* 3.3 27.8 + - - -
358C ASP* 3.0 34.5 + - + +
360C ALA* 1.3 73.3 - - - +
362C GLN* 1.3 61.3 + - + +
364C ARG* 3.3 14.8 + - - +
365C HIS* 2.9 62.7 + - + +
356D GLU* 5.9 2.5 - - - +
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Residues in contact with GLN 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356C GLU 2.9 26.7 + - - +
357C GLY* 3.5 9.1 - - - -
358C ASP 2.9 15.0 + - - +
359C THR* 3.6 11.5 - - - +
360C ALA 3.2 0.2 - - - -
361C ARG* 1.3 77.6 - - + +
363C PHE* 1.3 56.9 + - - +
365C HIS* 5.1 0.9 - - - -
366C ASP* 2.9 50.6 + - - +
367C VAL* 5.1 0.2 - - - +
389C PHE* 5.2 3.1 - - + -
398C TRP* 3.1 32.8 + - + +
356D GLU* 2.7 29.5 + - - +
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Residues in contact with PHE 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C VAL* 4.8 2.2 - - + -
197C GLU* 4.2 9.4 - - - -
300C MSE 3.7 28.0 - - - -
302C LEU* 3.2 27.4 - - + -
334C VAL* 3.8 18.4 - - + -
338C TRP* 3.9 13.7 - + + -
343C VAL* 3.4 24.7 - - + -
359C THR 3.1 14.8 + - - +
360C ALA 3.3 5.1 + - - +
362C GLN* 1.3 76.8 - - - +
364C ARG* 1.3 68.9 + - + +
367C VAL* 3.1 23.0 + - + -
368C LEU* 3.0 49.5 + - + -
389C PHE* 4.1 18.1 - + + -
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Residues in contact with ARG 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C ALA* 3.7 11.8 + - - +
103C GLY* 3.3 27.3 + - - -
105C ASP* 2.9 35.6 + - - -
106C VAL* 3.5 17.9 - - + +
343C VAL* 2.9 36.0 + - + +
344C ASN* 3.8 9.6 - - - +
345C TYR 3.2 22.4 + - - -
358C ASP* 4.9 1.6 + - - -
360C ALA* 3.0 21.0 + - - +
361C ARG* 3.3 23.5 + - - +
363C PHE* 1.3 86.4 - - + +
365C HIS* 1.3 56.3 + - - +
368C LEU* 3.4 17.4 - - + +
369C ARG* 3.0 30.0 + - - +
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Residues in contact with HIS 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C VAL* 3.9 7.4 - - + -
109C GLU* 4.3 8.3 - - - -
361C ARG* 2.9 55.0 + - + +
362C GLN* 5.1 0.2 - - - -
364C ARG* 1.3 77.9 - - - +
366C ASP* 1.3 81.9 + - - +
367C VAL 3.5 0.2 - - - -
369C ARG* 3.7 13.6 + - + +
370C PRO* 3.4 16.8 - - - +
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Residues in contact with ASP 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C GLN* 2.9 34.9 + - - +
365C HIS* 1.3 95.9 + - - +
367C VAL* 1.3 67.2 + - + +
370C PRO* 3.5 15.0 - - - +
389C PHE* 5.7 1.9 - - + -
400C ARG* 4.5 16.4 + - - +
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Residues in contact with VAL 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300C MSE 3.8 25.1 - - + -
334C VAL* 5.0 2.7 - - + -
363C PHE* 3.1 24.5 + - + +
366C ASP* 1.3 87.1 - - + +
368C LEU* 1.3 69.4 + - - +
369C ARG 3.5 1.1 - - - -
370C PRO* 3.5 3.6 - - - +
371C PHE* 3.2 24.4 + - - +
385C THR* 4.3 12.4 + - + +
386C PRO* 4.5 15.7 - - + -
389C PHE* 3.7 41.5 - - + -
400C ARG* 4.6 5.4 - - - +
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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