Contacts of the helix formed by residues 357 - 366 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304B THR* 4.2 1.0 + - - +
356B THR* 1.3 84.4 + - - +
358B PRO* 1.3 71.8 - - + +
359B THR 3.2 2.5 - - - +
360B ALA* 3.1 14.4 + - - +
361B ILE* 3.1 16.7 + - - +
386B VAL 3.5 15.7 - - - +
388B GLU* 4.4 2.5 - - - +
524B GLY* 5.7 0.4 - - - -
991B COA 3.5 43.7 - - + +
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Residues in contact with PRO 358 (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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357B ALA* 1.3 84.6 - - + +
359B THR* 1.3 55.9 + - - +
361B ILE* 3.0 13.3 + - + +
362B ARG* 2.7 56.2 + - + +
385B SER* 3.3 22.0 - - - +
386B VAL 3.3 16.8 - - - +
388B GLU* 3.4 31.6 - - + +
389B PRO 3.5 7.4 - - - +
390B ILE* 4.0 12.6 - - + -
394B ALA* 6.2 0.2 - - + -
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Residues in contact with THR 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ALA 3.2 1.2 + - - -
358B PRO* 1.3 78.4 - - - +
360B ALA* 1.3 57.7 + - - +
362B ARG* 3.3 12.4 + - - +
363B ALA* 2.8 27.7 + - - +
388B GLU* 2.7 31.4 + - - -
523B SER* 3.3 38.9 - - - +
554B ILE* 3.9 17.3 - - + +
555B LYS* 3.9 2.1 + - + -
991B COA 3.5 28.3 - - + +
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Residues in contact with ALA 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B PRO* 4.1 15.9 - - + -
342B MET* 5.8 1.6 - - - -
356B THR* 4.1 14.1 - - + +
357B ALA 3.1 8.7 + - - +
359B THR* 1.3 77.8 - - - +
361B ILE* 1.3 59.0 + - + +
363B ALA* 3.2 2.9 + - - +
364B LEU* 2.8 40.1 + - + +
991B COA 3.1 39.2 - - - +
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Residues in contact with ILE 361 (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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342B MET* 6.0 2.7 - - + -
356B THR* 4.0 12.6 - - + -
357B ALA 3.4 21.8 - - - +
358B PRO* 3.0 12.5 + - + +
360B ALA* 1.3 77.6 - - + +
362B ARG* 1.3 52.9 + - - +
364B LEU* 3.4 6.3 + - - -
365B MET* 2.7 35.6 + - + +
385B SER* 4.5 5.2 - - - +
390B ILE* 4.3 9.6 - - + -
394B ALA* 4.0 20.2 - - + +
397B TRP* 3.8 16.9 - - + -
398B TYR* 3.8 59.0 - - + -
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Residues in contact with ARG 362 (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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358B PRO* 2.7 41.0 + - - +
359B THR* 3.3 10.8 + - - +
361B ILE* 1.3 70.2 - - - +
363B ALA* 1.3 68.0 + - - +
365B MET* 3.5 17.6 - - + +
366B ALA* 3.0 19.2 + - - +
388B GLU* 2.7 28.7 + - - -
389B PRO 3.7 11.9 + - - -
390B ILE* 4.8 2.2 - - - +
391B ASN* 4.1 21.3 - - - +
394B ALA* 4.2 18.1 - - + +
552B HIS 5.4 0.2 - - - -
553B ALA 3.2 24.0 + - - +
554B ILE* 2.9 42.1 + - + +
556B GLY* 3.7 16.4 - - - +
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Residues in contact with ALA 363 (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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334B PRO* 6.4 0.2 - - + -
335B ASN* 4.5 14.8 - - - +
359B THR 2.8 18.6 + - - +
360B ALA* 3.2 10.7 + - - +
362B ARG* 1.3 79.3 - - - +
364B LEU* 1.3 62.6 + - + +
366B ALA* 3.7 11.8 + - - +
367B GLU* 4.0 11.4 - - - +
554B ILE* 4.2 19.4 - - + +
991B COA 4.3 13.0 - - + -
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Residues in contact with LEU 364 (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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334B PRO* 3.8 13.0 - - + +
335B ASN* 3.7 27.1 - - + -
339B PRO* 3.1 31.9 - - + +
342B MET* 3.9 41.5 - - + -
343B CYS* 6.2 0.7 - - - -
360B ALA 2.8 22.4 + - - +
361B ILE* 3.9 4.7 - - - +
363B ALA* 1.3 73.6 - - + +
365B MET* 1.3 62.5 + - - +
366B ALA 3.1 2.0 - - - -
367B GLU* 2.8 28.3 + - + +
368B GLY 3.5 3.5 + - - +
371B ALA* 3.9 18.2 - - + +
397B TRP* 4.0 9.6 - - + -
402B ILE* 5.6 0.4 - - + -
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Residues in contact with MET 365 (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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361B ILE 2.7 22.8 + - - +
362B ARG* 3.2 19.5 + - + +
364B LEU* 1.3 73.4 - - - +
366B ALA* 1.3 59.7 + - - +
367B GLU 3.0 0.2 - - - -
368B GLY* 3.0 18.9 + - - -
391B ASN* 5.1 1.3 - - - +
393B GLU* 3.6 30.3 - - - +
394B ALA* 3.8 28.7 - - + -
397B TRP* 3.6 53.5 + - + -
553B ALA 5.8 0.7 - - - +
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Residues in contact with ALA 366 (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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362B ARG 3.0 15.9 + - - +
363B ALA 3.7 8.5 - - - +
364B LEU 3.1 0.4 - - - -
365B MET* 1.3 76.4 - - - +
367B GLU* 1.3 67.5 + - - +
368B GLY 3.3 1.3 + - - -
554B ILE* 4.2 15.0 - - + -
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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