Contacts of the strand formed by residues 496 - 504 (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 TYR 496 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60B PHE* 4.0 9.9 - - + -
413B TRP* 5.6 0.4 - + - -
415B GLN* 2.8 29.2 + - - -
417B GLU* 3.1 30.8 - - + +
418B THR* 4.2 7.7 - - + +
465B VAL* 3.1 7.0 - - - -
466B ILE* 2.9 59.9 + - + +
470B TRP* 3.8 12.3 - + + -
473B GLN* 3.7 20.4 - - - +
484B PHE* 5.9 2.7 - + - -
488B TYR* 3.6 37.9 - + + -
489B PHE* 3.8 15.7 - + + -
495B MET* 1.3 72.3 - - - +
497B PHE* 1.3 62.2 + - - +
498B SER* 3.9 12.4 + - - -
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Residues in contact with PHE 497 (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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463B ASN* 3.7 24.5 - - + -
464B LEU 3.5 10.5 - - - -
465B VAL* 3.9 5.2 - - + -
487B THR 4.8 7.0 - - - +
488B TYR* 2.8 43.2 + - - +
491B THR* 4.0 23.3 - - + -
492B PHE* 3.7 35.7 - + + +
495B MET 3.6 1.7 + - - +
496B TYR* 1.3 73.3 - - - +
498B SER* 1.3 64.2 + - - +
499B GLY* 3.4 20.9 + - - -
500B ASP 3.9 5.4 - - - -
516B VAL* 3.6 25.6 - - + -
517B ASP* 5.8 4.3 - - + -
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Residues in contact with SER 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B TRP* 3.8 19.3 - - - -
415B GLN* 2.7 45.6 + - - -
464B LEU* 2.7 30.0 + - - +
465B VAL* 5.4 0.4 - - - -
466B ILE* 5.8 0.7 - - - -
488B TYR* 5.8 2.8 - - - -
496B TYR* 3.8 10.6 + - - -
497B PHE* 1.3 72.3 - - - +
499B GLY* 1.3 57.9 + - - +
500B ASP* 3.1 20.8 + - - +
515B ARG* 3.3 9.0 + - - -
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Residues in contact with GLY 499 (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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497B PHE* 3.3 26.8 - - - -
498B SER* 1.3 78.3 + - - +
500B ASP* 1.3 52.8 - - - +
515B ARG* 3.3 16.0 + - - -
516B VAL* 2.8 33.1 + - - +
517B ASP* 3.5 19.6 - - - +
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Residues in contact with ASP 500 (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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413B TRP* 3.0 14.9 + - - +
415B GLN* 3.4 5.7 + - - -
463B ASN* 3.9 3.3 - - - -
464B LEU* 2.9 33.9 + - + +
497B PHE* 3.9 3.6 - - - -
498B SER* 3.1 10.9 + - - +
499B GLY* 1.3 80.9 - - - +
501B GLY* 1.3 65.0 + - - +
512B ILE* 4.3 4.0 - - + -
514B GLY* 3.3 13.3 - - - +
515B ARG* 3.2 9.6 - - - -
516B VAL* 4.1 3.8 - - - +
998B PRX 2.5 53.7 + - - -
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Residues in contact with GLY 501 (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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462B GLY 3.4 10.5 - - - -
463B ASN* 4.5 0.2 - - - -
464B LEU* 4.7 0.4 - - - -
500B ASP* 1.3 75.7 - - - +
502B ALA* 1.3 63.7 + - - +
512B ILE* 3.9 5.4 - - - +
513B THR* 3.1 29.4 + - - -
514B GLY 2.8 13.2 + - - +
516B VAL* 3.6 19.1 - - - +
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Residues in contact with ALA 502 (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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448B LEU* 3.7 18.4 - - + +
461B GLU* 3.2 3.7 - - - +
462B GLY 3.0 32.0 + - - +
464B LEU* 4.4 8.1 - - + -
501B GLY* 1.3 77.5 - - - +
503B ARG* 1.3 63.3 + - - +
510B TYR* 4.8 5.2 - - + -
511B TRP 3.3 15.5 - - - +
512B ILE* 4.0 19.1 - - + -
513B THR* 3.8 6.6 + - - -
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Residues in contact with ARG 503 (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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448B LEU* 4.1 2.2 - - - -
460B THR 3.2 13.2 - - - +
461B GLU* 3.7 17.0 - - + +
502B ALA* 1.3 75.5 - - - +
504B ARG* 1.3 61.3 + - - +
505B ASP* 6.5 0.4 - - - -
510B TYR* 3.4 4.6 - - - +
511B TRP* 2.7 78.3 + - + +
513B THR* 3.2 27.5 - - + +
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Residues in contact with ARG 504 (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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446B PRO 5.1 0.4 + - - -
447B ALA* 4.6 2.8 - - - +
448B LEU* 3.8 30.6 - - + +
456B GLN 3.0 25.7 + - - -
457B GLU* 3.6 5.4 + - - +
458B GLY* 2.9 36.5 + - - +
459B ALA* 3.1 4.9 - - - +
460B THR* 2.9 32.1 + - - +
503B ARG* 1.3 76.8 - - - +
505B ASP* 1.3 62.2 + - - +
508B GLY* 3.6 24.9 - - - +
509B TYR 3.1 11.4 - - - +
510B TYR* 3.1 38.8 + - + -
511B TRP* 4.9 0.4 - - - -
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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