Contacts of the helix formed by residues 357 - 366 (chain A) in PDB entry 1PG3
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 ALA 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304A THR* 4.3 0.8 + - - +
356A THR* 1.3 84.0 + - - +
358A PRO* 1.3 72.0 - - + +
359A THR 4.3 3.8 - - - +
360A ALA* 3.0 18.9 + - + +
361A ILE* 3.0 16.9 + - - +
386A VAL 3.4 14.1 - - - +
387A GLY* 5.5 0.2 - - - -
388A GLU* 4.4 2.5 - - - +
524A GLY* 5.8 0.4 - - - -
990A COA 4.0 38.6 - - + +
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Residues in contact with PRO 358 (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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357A ALA* 1.3 83.8 - - + +
359A THR* 1.3 55.6 + - - +
361A ILE* 3.3 11.6 + - + +
362A ARG* 2.8 51.9 + - + +
385A SER* 3.4 21.5 - - - +
386A VAL 3.2 17.3 - - - +
388A GLU* 3.4 40.4 - - + +
389A PRO 3.8 2.0 - - - +
390A ILE* 3.9 16.2 - - + -
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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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357A ALA 3.1 1.0 + - - -
358A PRO* 1.3 78.2 - - - +
360A ALA* 1.3 58.6 + - - +
362A ARG* 3.2 7.4 + - - +
363A ALA* 2.9 27.5 + - - +
388A GLU* 2.9 25.2 + - - -
523A SER* 3.2 39.6 - - - +
554A ILE* 3.8 23.1 + - + +
555A LYS* 4.5 2.5 - - + -
990A COA 4.0 31.9 - - + +
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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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334A PRO* 4.2 12.6 - - + -
342A MET* 5.8 0.9 - - - -
356A THR* 3.9 17.7 - - + +
357A ALA* 3.0 12.0 + - - +
359A THR* 1.3 78.3 - - - +
361A ILE* 1.3 58.5 + - - +
363A ALA* 3.3 2.4 + - - +
364A LEU* 3.0 37.4 + - + +
990A COA 3.1 38.7 + - - +
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Residues in contact with ILE 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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342A MET* 6.1 1.1 - - + -
356A THR* 3.8 16.2 - - + -
357A ALA 3.0 19.6 + - - +
358A PRO* 3.5 7.2 - - + +
360A ALA* 1.3 76.6 - - - +
362A ARG* 1.3 57.4 + - + +
364A LEU* 3.4 8.7 + - + +
365A MET* 2.8 28.3 + - + +
385A SER* 4.5 4.7 - - - +
390A ILE* 4.1 16.6 - - + -
394A ALA* 4.0 18.8 - - + +
397A TRP* 4.1 14.0 - - + -
398A TYR* 3.6 58.3 - - + -
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Residues in contact with ARG 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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358A PRO* 2.8 31.7 + - + +
359A THR* 3.4 8.9 + - - +
361A ILE* 1.3 71.8 - - - +
363A ALA* 1.3 60.1 + - - +
365A MET* 3.7 15.3 - - + +
366A ALA* 2.9 30.1 + - - +
388A GLU* 2.5 33.9 + - - -
389A PRO 3.5 21.4 + - - -
390A ILE* 4.7 5.3 - - - +
391A ASN* 5.3 4.0 + - - +
394A ALA* 4.5 19.5 - - + +
552A HIS 5.4 0.2 - - - -
553A ALA 3.2 22.4 + - - +
554A ILE* 2.5 38.2 + - + +
556A GLY* 3.6 16.0 - - - +
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Residues in contact with ALA 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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335A ASN* 4.2 14.7 - - - +
359A THR 2.9 9.9 + - - +
360A ALA 3.6 1.6 - - - +
362A ARG* 1.3 76.2 - - - +
364A LEU* 1.3 63.4 + - + +
366A ALA* 3.5 13.7 - - - +
367A GLU* 3.8 12.5 - - - +
554A ILE* 4.0 20.8 - - + +
990A COA 3.3 32.3 - - + +
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Residues in contact with LEU 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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334A PRO* 4.1 12.1 - - + +
335A ASN* 3.9 15.9 - - + -
339A PRO* 3.0 40.2 - - + +
342A MET* 3.7 42.4 - - + -
343A CYS* 6.1 0.4 - - - -
360A ALA 3.0 23.6 + - - +
361A ILE* 3.8 6.7 - - - +
363A ALA* 1.3 73.9 - - + +
365A MET* 1.3 57.8 + - - +
366A ALA 3.0 1.6 - - - -
367A GLU* 2.7 32.3 + - - +
368A GLY 3.6 2.8 + - - +
371A ALA* 3.9 17.1 - - + +
397A TRP* 4.0 7.4 - - + -
402A ILE* 5.3 3.6 - - + -
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Residues in contact with MET 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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361A ILE 2.8 22.7 + - - +
362A ARG* 3.7 17.3 - - + +
364A LEU* 1.3 72.5 - - - +
366A ALA* 1.3 62.0 + - - +
367A GLU 3.0 0.2 - - - -
368A GLY* 3.0 14.6 + - - -
391A ASN* 5.2 1.1 - - - +
393A GLU* 4.2 19.3 - - + +
394A ALA* 3.8 32.8 - - + +
397A TRP* 3.4 60.3 + - + +
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Residues in contact with ALA 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 ARG 2.9 16.8 + - - +
363A ALA* 3.5 10.3 - - - +
364A LEU 3.0 0.4 - - - -
365A MET* 1.3 79.1 - - - +
367A GLU* 1.3 66.2 + - - +
368A GLY 3.3 1.0 + - - -
554A ILE* 4.0 17.3 - - + -
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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