Contacts of the helix formed by residues 495 - 507 (chain A) in PDB entry 1PG2
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 LEU 495 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353A ASP* 3.2 46.2 - - + +
357A TYR* 3.8 18.2 - - + -
385A ILE* 4.4 17.5 - - + -
488A MET* 5.1 1.3 - - + -
491A LEU* 3.0 36.9 + - + +
492A LYS 4.0 1.3 - - - -
494A VAL* 1.3 88.4 - - + +
496A PRO* 1.3 57.5 - - - +
497A LYS 3.4 1.8 - - - -
498A LEU* 4.0 26.7 - - + -
499A THR* 2.7 37.5 + - - +
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Residues in contact with PRO 496 (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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36A ARG* 3.6 45.5 - - - +
88A ASN* 4.3 14.6 - - + -
353A ASP* 3.3 9.0 - - - +
356A ARG* 3.4 20.4 - - - +
492A LYS* 4.0 7.2 - - + +
494A VAL 3.2 12.8 - - - +
495A LEU* 1.3 85.2 - - - +
497A LYS* 1.3 61.3 + - + +
499A THR* 3.5 4.4 + - - -
500A GLU* 3.2 29.4 + - - +
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Residues in contact with LYS 497 (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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88A ASN* 3.5 38.0 + - - +
351A ASP* 6.0 0.4 - - - +
352A ALA* 6.1 1.1 - - + -
353A ASP* 3.5 13.6 + - - +
495A LEU 3.4 1.0 - - - -
496A PRO* 1.3 73.6 - - - +
498A LEU* 1.3 67.6 + - - +
499A THR 3.1 1.3 - - - -
500A GLU* 3.1 35.0 + - - +
501A ARG* 3.1 40.8 + - - +
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Residues in contact with LEU 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ASP* 2.9 20.2 + - - +
385A ILE* 4.0 26.9 - - + -
389A VAL* 5.4 2.0 - - + -
390A VAL* 4.1 13.0 - - + -
484A PHE* 6.0 0.7 - - + -
488A MET* 3.7 24.2 - - + -
495A LEU* 3.5 20.4 + - + -
497A LYS* 1.3 73.1 - - - +
499A THR* 1.3 58.4 + - - +
501A ARG* 3.1 15.0 + - + +
502A ALA* 2.8 27.5 + - + +
530A LEU* 3.4 45.3 - - + +
531A TYR* 4.4 5.8 - - + -
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Residues in contact with THR 499 (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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488A MET* 3.6 17.5 - - - +
491A LEU 4.3 0.3 + - - -
492A LYS* 3.4 53.9 - - + -
495A LEU 2.7 22.0 + - - -
496A PRO* 3.6 7.4 - - - -
498A LEU* 1.3 78.5 - - - +
500A GLU* 1.3 57.5 + - + +
502A ALA* 3.1 2.5 + - - +
503A GLU* 2.8 48.1 + - + +
510A LEU* 4.1 9.9 - - + -
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Residues in contact with GLU 500 (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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496A PRO* 3.2 17.3 + - - +
497A LYS* 3.1 39.7 + - - +
499A THR* 1.3 75.7 - - + +
501A ARG* 1.3 63.9 + - + +
503A GLU* 3.3 16.3 + - - +
504A ALA* 3.0 23.6 + - - +
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Residues in contact with ARG 501 (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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351A ASP* 4.7 4.6 + - - -
353A ASP* 4.5 1.6 + - - -
497A LYS* 3.1 29.3 + - - +
498A LEU* 3.1 22.8 + - + +
500A GLU* 1.3 77.6 - - + +
502A ALA* 1.3 61.6 + - - +
504A ALA* 3.4 8.1 + - - +
505A PHE* 3.1 21.5 + - - +
527A PHE* 5.8 0.2 - - - +
529A ALA 4.9 3.6 + - - -
530A LEU* 2.8 51.2 + - + +
531A TYR* 3.6 23.8 - - - +
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Residues in contact with ALA 502 (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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484A PHE* 4.0 28.7 - - + -
488A MET* 4.0 18.4 - - + -
498A LEU* 2.8 13.4 + - + +
499A THR* 3.5 8.7 - - - +
501A ARG* 1.3 75.4 - - - +
503A GLU* 1.3 60.4 + - - +
505A PHE* 3.2 7.1 + - - +
506A LEU* 2.9 38.3 + - + +
510A LEU* 5.1 2.0 - - + -
530A LEU* 4.3 6.9 - - + +
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Residues in contact with GLU 503 (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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492A LYS* 2.8 22.7 + - - -
499A THR* 2.8 27.5 + - - +
500A GLU* 3.7 17.5 - - - +
502A ALA* 1.3 76.3 - - - +
504A ALA* 1.3 58.6 + - - +
506A LEU* 4.5 3.1 - - - +
507A ASN* 2.9 25.1 + - - -
508A THR 3.2 27.5 + - - +
509A GLU* 3.7 7.0 - - - +
510A LEU* 2.8 39.7 + - + +
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Residues in contact with ALA 504 (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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500A GLU 3.0 13.6 + - - +
501A ARG* 3.6 11.0 - - - +
502A ALA 3.2 0.2 - - - -
503A GLU* 1.3 76.3 - - - +
505A PHE* 1.3 60.3 + - - +
507A ASN* 3.4 6.8 + - - +
525A ASN* 3.0 27.1 + - - +
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Residues in contact with PHE 505 (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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393A ALA* 4.2 12.6 - - + -
397A ALA* 4.1 19.5 - - + -
401A ASN* 4.9 0.4 - - - -
481A ILE* 4.2 22.0 - - + -
484A PHE* 4.0 20.4 - + - -
501A ARG 3.1 10.3 + - - +
502A ALA* 3.5 8.1 - - - +
504A ALA* 1.3 80.1 - - - +
506A LEU* 1.3 85.5 + - + +
507A ASN 3.4 0.3 + - - -
524A VAL* 3.5 17.1 - - + +
525A ASN* 2.9 59.8 + - - -
526A PRO 5.3 0.7 - - - -
527A PHE* 3.5 36.8 - + + -
530A LEU* 4.7 5.2 - - + -
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Residues in contact with LEU 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A ILE* 3.5 36.1 - - + +
484A PHE* 4.3 11.2 - - + -
485A ARG* 4.0 32.1 - - + -
488A MET* 5.6 0.2 - - + -
502A ALA* 2.9 24.8 + - + +
503A GLU* 4.2 3.4 - - - +
505A PHE* 1.3 91.3 - - + +
507A ASN* 1.3 57.3 + - - +
508A THR* 3.1 7.8 + - - +
510A LEU* 4.1 14.1 - - + -
519A LEU* 4.1 16.6 - - + -
522A HIS* 2.6 35.4 + - - -
524A VAL* 4.4 6.5 - - + -
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Residues in contact with ASN 507 (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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503A GLU 2.9 9.4 + - - -
504A ALA* 3.4 3.4 + - - +
505A PHE 3.2 4.0 - - - -
506A LEU* 1.3 80.1 - - - +
508A THR* 1.3 62.4 + - - +
522A HIS* 3.6 11.4 - - + +
523A LYS* 2.9 28.1 - - - +
525A ASN* 2.6 44.3 + - - +
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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