Contacts of the helix formed by residues 480 - 490 (chain A) 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 ASP 480 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272A LYS* 4.7 10.6 + - + +
477A LEU* 2.9 22.5 + - + +
478A PHE 4.1 5.6 - - - +
479A GLY* 1.3 80.5 - - - +
481A HIS* 1.3 62.6 + - - +
482A GLU* 3.6 3.5 + - - +
483A ARG* 2.9 52.2 + - + +
484A PHE 3.3 13.0 + - - -
51B PRO* 3.6 31.2 - - - +
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Residues in contact with HIS 481 (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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65A VAL* 2.8 29.1 + - + -
66A SER* 5.4 1.6 - - - -
475A ARG 3.7 11.9 - - - -
476A THR* 2.9 30.0 + - - +
479A GLY 4.1 0.4 - - - -
480A ASP* 1.3 71.8 - - - +
482A GLU* 1.3 65.2 + - + +
484A PHE* 3.2 25.6 + + - +
485A GLU* 2.9 55.1 + - - +
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Residues in contact with GLU 482 (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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480A ASP* 3.2 7.3 - - - +
481A HIS* 1.3 78.6 - - + +
483A ARG* 1.3 57.9 + - - +
485A GLU* 3.3 18.3 + - - +
486A GLN* 3.0 27.9 + - - +
48B TRP 3.6 8.2 - - - +
49B ILE* 2.3 41.1 - - + +
50B THR* 3.7 6.1 - - + +
51B PRO* 3.5 14.9 - - - +
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Residues in contact with ARG 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A THR* 5.2 11.3 + - - -
269A GLY* 5.3 8.3 - - - -
272A LYS* 4.1 30.8 - - + +
477A LEU* 3.9 13.2 - - + -
480A ASP* 2.9 49.4 + - + +
481A HIS 3.3 0.2 - - - -
482A GLU* 1.3 73.6 - - - +
484A PHE* 1.3 57.8 + - - +
486A GLN* 4.6 11.0 - - - +
487A THR* 2.8 58.0 + - - +
50B THR* 3.9 18.8 - - + +
51B PRO 4.2 8.9 + - - -
72B ASP* 3.5 37.6 + - - +
74B THR* 6.3 0.2 - - - -
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Residues in contact with PHE 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 3.9 15.0 - - + -
67A ILE* 4.3 2.7 - - + -
417A GLU* 5.7 2.7 - - + -
473A GLN* 5.1 1.3 - - - -
474A ALA* 3.4 32.5 - - + -
475A ARG 3.4 14.8 - - - -
476A THR* 3.6 22.7 - - - -
477A LEU* 3.7 27.0 - - + +
480A ASP 3.3 4.8 + - - +
481A HIS* 3.2 29.1 + + - +
483A ARG* 1.3 78.5 - - - +
485A GLU* 1.3 63.1 + - - +
488A TYR* 3.2 55.1 + + - -
489A PHE* 3.6 31.0 - + - -
496A TYR* 5.8 2.2 - + - -
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Residues in contact with GLU 485 (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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63A GLY* 3.3 33.0 + - - +
64A ASN* 3.3 6.6 + - - -
65A VAL* 2.9 35.7 + - + +
481A HIS* 2.9 43.4 + - + +
482A GLU* 3.6 22.1 - - - +
484A PHE* 1.3 77.3 - - + +
486A GLN* 1.3 57.1 + - - +
489A PHE* 3.0 39.6 + - - +
490A SER* 3.5 3.3 + - - -
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Residues in contact with GLN 486 (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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482A GLU 3.0 17.6 + - - +
483A ARG* 3.8 13.6 - - - +
485A GLU* 1.3 76.3 - - - +
487A THR* 1.3 66.4 + - - +
488A TYR 3.5 0.3 + - - -
490A SER* 2.5 40.2 + - - +
491A THR* 4.6 1.0 + - - -
49B ILE* 4.0 4.3 - - + +
50B THR* 3.2 14.8 + - + +
74B THR* 2.9 44.4 + - - +
252B ALA* 3.3 19.3 - - + +
254B ASN* 5.1 3.0 - - - +
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Residues in contact with THR 487 (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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266A GLY* 6.2 3.6 - - - -
267A SER 6.2 1.1 - - - +
477A LEU* 4.7 2.4 - - + +
483A ARG* 2.8 46.9 + - - +
486A GLN* 1.3 76.0 - - - +
488A TYR* 1.3 92.1 + - + +
491A THR* 4.7 8.5 + - - -
497A PHE* 5.0 7.3 - - - +
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Residues in contact with TYR 488 (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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264A THR* 5.8 0.3 - - - -
272A LYS* 6.1 0.2 - - - +
274A VAL* 4.4 2.4 - - - +
417A GLU* 2.6 43.7 + - + +
477A LEU* 4.3 19.1 - - + +
484A PHE* 3.2 48.7 + + - -
487A THR* 1.3 101.4 - - + +
489A PHE* 1.3 76.0 + - + +
490A SER 3.8 1.1 - - - -
491A THR* 5.4 0.9 - - - -
492A PHE 5.8 0.2 + - - -
495A MET 3.3 3.6 - - - +
496A TYR* 3.6 28.9 - + + -
497A PHE* 2.9 42.6 + - - +
498A SER* 5.8 1.8 - - - -
515A ARG* 6.3 0.9 - - - -
526A ARG* 4.3 5.2 + - - -
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Residues in contact with PHE 489 (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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60A PHE* 3.5 44.2 - + + +
61A ALA 5.4 0.4 - - - +
62A PRO* 4.8 11.3 - - + +
63A GLY 5.9 0.9 - - - +
65A VAL* 3.5 34.1 - - + -
67A ILE* 4.4 0.2 - - + -
473A GLN* 3.6 20.0 - - - -
484A PHE* 3.6 37.9 - + - -
485A GLU* 3.0 13.7 + - - +
488A TYR* 1.3 92.2 - - + +
490A SER* 1.3 60.6 + - - +
491A THR 3.8 0.7 - - - -
492A PHE 4.0 10.2 - - - +
493A LYS* 4.2 8.7 - - - +
494A ASN 4.5 1.9 + - - -
495A MET 3.6 19.7 - - - +
496A TYR* 3.8 20.2 - + + -
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Residues in contact with SER 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PRO* 6.3 1.1 - - - -
485A GLU 3.5 1.0 + - - -
486A GLN* 2.5 42.9 + - - +
488A TYR 3.8 0.2 - - - -
489A PHE* 1.3 77.7 - - - +
491A THR* 1.3 71.1 + - - +
492A PHE* 3.3 2.7 + - - -
493A LYS* 4.4 17.3 + - - +
251B GLU* 4.7 11.5 - - - +
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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