Contacts of the helix formed by residues 415 - 419 (chain B) in PDB entry 1PG4
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 GLN 415 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B TRP* 4.0 8.7 - - + -
414B TRP* 1.3 99.4 - - - +
416B THR* 1.3 67.9 + - - +
417B GLU* 3.4 15.6 + - - +
418B THR* 2.8 25.0 + - + +
419B GLY 3.5 0.3 + - - -
496B TYR* 2.8 37.1 + - - -
498B SER* 2.7 34.2 + - - -
500B ASP* 3.4 4.8 + - - -
515B ARG* 3.3 6.3 - - - +
526B ARG* 4.4 0.2 - - - +
998B PRX 2.7 43.4 + - - +
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Residues in contact with THR 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B LEU* 4.1 18.8 - - + -
264B THR* 3.4 29.1 + - - +
274B VAL* 3.9 16.7 - - + +
276B HIS* 2.8 33.6 + - + +
310B VAL* 3.7 30.6 + - + +
415B GLN* 1.3 71.9 - - - +
417B GLU* 1.3 58.1 + - - +
418B THR 3.3 0.7 + - - -
419B GLY 3.5 1.9 + - - -
998B PRX 2.8 31.6 + - - -
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Residues in contact with GLU 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B THR* 4.5 1.6 - - - +
274B VAL* 4.0 17.8 - - + +
415B GLN* 3.0 12.0 - - - +
416B THR* 1.3 80.5 + - - +
418B THR* 1.3 58.1 + - - +
419B GLY 3.5 0.4 - - - -
470B TRP* 4.1 3.8 - - - -
473B GLN* 3.9 3.6 - - - +
474B ALA* 2.9 35.9 + - + +
484B PHE* 5.9 1.3 - - + -
488B TYR* 2.6 45.6 + - + +
496B TYR* 3.1 24.1 + - + +
526B ARG* 2.8 42.8 + - - -
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Residues in contact with THR 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B TRP* 5.2 2.7 - - + -
414B TRP* 3.3 2.6 - - - +
415B GLN* 2.8 46.9 + - + +
417B GLU* 1.3 80.1 - - - +
419B GLY* 1.3 52.2 + - - +
420B GLY 2.7 30.8 + - - +
422B MET* 3.5 26.0 - - + -
470B TRP* 2.8 39.6 + - + +
472B GLY* 3.2 11.4 - - - +
496B TYR* 4.2 7.2 - - + +
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Residues in contact with GLY 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B HIS* 3.3 21.4 - - - -
281B TYR* 3.6 13.5 - - - -
284B TYR* 4.7 3.1 - - - -
285B ALA* 5.1 2.1 - - - +
310B VAL* 5.0 1.3 - - - -
314B SER* 2.8 28.1 + - - -
414B TRP* 3.4 10.1 - - - -
415B GLN 3.5 4.6 + - - -
416B THR 3.5 1.7 + - - -
418B THR* 1.3 73.5 + - - +
420B GLY* 1.3 55.1 + - - -
472B GLY* 3.3 14.1 - - - -
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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