Contacts of the helix formed by residues 358 - 367 (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 ASP 358 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345A TYR 4.3 2.3 - - - +
346A ASP* 3.2 23.8 - - - +
347A GLY 2.9 17.5 + - - -
348A SER* 3.2 16.2 + - - +
357A GLY* 1.3 68.3 - - - -
359A THR* 1.3 56.6 + - - +
360A ALA* 3.2 1.9 + - - +
361A ARG* 3.0 34.1 + - + +
362A GLN* 2.9 30.6 + - - +
364A ARG* 5.0 1.6 + - - -
356B GLU* 3.0 16.6 + - - +
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Residues in contact with THR 359 (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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337A PRO* 3.5 8.3 - - + +
338A TRP* 2.9 32.9 + - - -
347A GLY 2.7 24.2 + - - +
355A PHE* 4.0 10.8 - - + -
356A GLU 4.3 3.4 - - - +
357A GLY 2.9 15.5 + - - +
358A ASP* 1.3 70.5 - - - +
360A ALA* 1.3 61.1 + - - +
362A GLN* 3.6 18.2 - - - +
363A PHE 3.1 16.3 + - - -
391A TYR* 3.8 28.5 - - + -
398A TRP* 3.7 15.6 - - - -
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Residues in contact with ALA 360 (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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338A TRP* 3.9 11.7 - - - +
342A GLN 3.4 13.2 - - - +
343A VAL* 3.4 19.7 - - - +
345A TYR 3.3 24.0 - - - +
347A GLY* 3.7 8.4 - - - +
358A ASP* 3.2 4.2 + - - +
359A THR* 1.3 78.3 + - - +
361A ARG* 1.3 65.2 + - - +
363A PHE* 3.2 4.2 + - - +
364A ARG* 3.0 29.2 + - - +
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Residues in contact with ARG 361 (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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105A ASP* 3.0 28.8 + - - -
106A VAL* 3.4 22.6 - - - +
109A GLU* 3.4 32.8 + - - -
358A ASP* 3.0 34.3 + - + +
360A ALA* 1.3 75.8 - - - +
362A GLN* 1.3 58.2 + - + +
364A ARG* 3.8 14.7 - - - +
365A HIS* 2.9 53.8 + - + +
356B GLU* 6.1 2.2 - - - +
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Residues in contact with GLN 362 (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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356A GLU 3.0 27.9 + - - +
357A GLY* 3.5 9.5 - - - -
358A ASP 2.9 15.6 + - - +
359A THR* 3.6 10.5 - - - +
360A ALA 3.2 0.2 - - - -
361A ARG* 1.3 76.8 - - + +
363A PHE* 1.3 58.2 + - - +
365A HIS* 5.0 0.7 - - - -
366A ASP* 2.9 51.3 + - - +
367A VAL* 4.9 0.3 - - - +
389A PHE* 5.2 2.5 - - + -
398A TRP* 3.1 32.0 + - + +
356B GLU* 2.7 29.5 + - - +
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Residues in contact with PHE 363 (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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195A VAL* 4.8 2.2 - - + -
197A GLU* 4.1 9.0 - - - -
300A MSE 3.8 27.4 - - - -
302A LEU* 3.2 28.3 - - + -
334A VAL* 3.9 18.6 - - + -
338A TRP* 4.0 13.2 - + + -
343A VAL* 3.4 24.2 - - + -
359A THR 3.1 14.4 + - - +
360A ALA 3.2 5.4 + - - +
362A GLN* 1.3 77.0 - - - +
364A ARG* 1.3 65.7 + - + +
367A VAL* 3.1 22.6 + - + -
368A LEU* 2.9 54.3 + - + -
389A PHE* 4.2 16.7 - + + -
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Residues in contact with ARG 364 (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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102A ALA* 3.7 13.1 + - - +
103A GLY* 3.5 26.8 - - - -
105A ASP* 2.9 37.5 + - - -
106A VAL* 3.4 22.2 - - + +
343A VAL* 2.8 37.7 + - + +
344A ASN* 3.8 8.4 - - - -
345A TYR 3.2 22.6 + - - -
358A ASP* 5.0 1.4 + - - -
360A ALA* 3.0 22.0 + - - +
361A ARG* 3.3 22.2 + - - +
363A PHE* 1.3 85.4 - - + +
365A HIS* 1.3 56.3 + - - +
368A LEU* 3.5 18.7 - - + +
369A ARG* 3.0 25.6 + - - +
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Residues in contact with HIS 365 (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* 3.9 6.5 - - + -
109A GLU* 4.4 7.4 - - - -
361A ARG* 2.9 55.8 + - + +
362A GLN* 5.0 0.4 - - - -
364A ARG* 1.3 77.7 - - - +
366A ASP* 1.3 84.4 + - - +
367A VAL 3.5 0.2 - - - -
369A ARG* 3.7 9.5 - - + +
370A PRO* 3.4 17.5 - - - +
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Residues in contact with ASP 366 (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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362A GLN* 2.9 39.0 + - - +
365A HIS* 1.3 99.1 + - - +
367A VAL* 1.3 67.1 + - + +
370A PRO* 3.6 14.0 - - - +
389A PHE* 5.8 1.3 - - + -
400A ARG* 4.6 15.5 + - - +
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Residues in contact with VAL 367 (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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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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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