Contacts of the helix formed by residues 503 - 511 (chain A) in PDB entry 2AG1
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 SER 503 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502A GLY* 1.3 67.6 - - - -
504A TYR* 1.3 63.4 + - - +
505A HIS* 3.1 31.9 + - - -
506A GLY* 3.1 16.3 + - - -
507A VAL* 3.2 12.2 + - - +
541A ASN* 4.6 1.3 - - - +
510B ALA* 2.9 26.3 + - - +
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Residues in contact with TYR 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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448A ASP* 3.4 34.8 + - + +
451A VAL* 4.1 5.8 - - + -
452A GLY* 5.3 1.1 - - - -
455A ILE* 3.8 24.1 - - + +
458A PHE* 5.0 0.7 - - - -
472A ILE* 3.6 25.6 - - + -
474A ASN* 3.5 31.0 - - - -
476A GLN* 6.0 1.1 - - - -
499A LEU* 4.7 4.4 + - - +
501A ASN 3.9 10.4 + - - -
502A GLY 3.4 13.8 + - - -
503A SER* 1.3 71.7 - - - +
505A HIS* 1.3 61.8 + - - +
507A VAL* 3.2 8.7 + - - +
508A ALA* 3.2 20.1 + - - +
539A CYS* 4.0 4.6 - - - -
541A ASN* 3.5 10.1 - - - +
48B ARG* 3.0 32.9 + - - -
511B PHE* 4.1 21.3 - + - -
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Residues in contact with HIS 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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503A SER* 3.1 23.6 + - - -
504A TYR* 1.3 77.6 - - - +
506A GLY* 1.3 61.0 + - - +
508A ALA* 3.1 6.4 + - - +
509A ALA* 2.8 34.6 + - - +
515A GLY* 4.0 9.8 - - - -
516A TYR 3.3 36.1 - - - +
517A HIS* 3.6 30.0 - + + +
539A CYS* 3.9 11.4 - - - -
541A ASN* 3.1 22.3 + - + +
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Residues in contact with GLY 506 (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 SER* 3.1 15.4 + - - -
505A HIS* 1.3 88.2 - - - +
507A VAL* 1.3 55.4 + - - +
509A ALA* 3.7 7.8 - - - +
510A ALA* 2.8 32.1 + - - +
510B ALA* 3.6 13.3 - - - +
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Residues in contact with VAL 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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455A ILE* 3.5 32.5 - - + -
458A PHE* 5.0 0.2 - - + -
503A SER 3.2 13.3 + - - +
504A TYR* 3.2 10.3 + - - +
506A GLY* 1.3 75.6 - - - +
508A ALA* 1.3 62.1 + - - +
510A ALA* 3.5 2.9 + - - +
511A PHE* 3.1 33.9 + - + -
507B VAL* 3.8 26.2 - - + +
510B ALA* 3.5 12.8 - - + +
511B PHE* 3.6 34.5 - - + -
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Residues in contact with ALA 508 (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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458A PHE* 4.0 29.6 - - + -
504A TYR 3.2 8.4 + - - +
505A HIS 3.1 9.7 + - - +
507A VAL* 1.3 72.4 - - - +
509A ALA* 1.3 64.4 + - - +
511A PHE* 3.0 9.0 + - - -
512A GLY 3.1 0.3 + - - -
513A ALA* 3.0 32.2 + - + +
514A ASP 4.8 1.1 - - - +
515A GLY* 4.9 0.2 - - - -
539A CYS* 3.4 30.7 - - + -
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Residues in contact with ALA 509 (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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505A HIS 2.8 16.6 + - - +
506A GLY* 3.7 8.7 - - - +
508A ALA* 1.3 76.6 - - - +
510A ALA* 1.3 58.1 + - - +
512A GLY* 2.8 21.1 + - - -
513A ALA 3.3 13.8 + - - +
515A GLY* 4.9 7.4 - - - +
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Residues in contact with ALA 510 (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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506A GLY 2.8 22.2 + - - +
507A VAL 3.7 0.2 - - - +
508A ALA 3.4 0.2 - - - -
509A ALA* 1.3 70.9 - - - +
511A PHE* 1.3 59.6 + - - +
512A GLY 3.7 0.3 + - - -
502B GLY* 3.7 0.5 - - - -
503B SER* 2.9 41.3 + - - +
506B GLY* 3.6 9.4 - - - -
507B VAL* 3.5 36.6 - - + +
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Residues in contact with PHE 511 (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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48A ARG* 5.2 1.6 - - - -
455A ILE 4.0 0.7 - - - -
456A GLY* 3.9 25.1 - - - -
458A PHE* 3.8 26.2 - - + -
459A ASP* 3.7 28.2 - - + +
462A VAL* 3.4 8.9 - - - +
507A VAL* 3.1 31.0 + - + -
508A ALA 3.0 9.7 + - - +
509A ALA 3.0 1.4 - - - -
510A ALA* 1.3 77.9 - - - +
512A GLY* 1.3 55.1 - - - +
513A ALA 3.5 1.1 - - - +
452B GLY* 5.9 1.8 - - - -
455B ILE* 4.3 17.7 - - + -
501B ASN* 2.8 27.5 + - - -
502B GLY* 4.1 15.3 - - - -
504B TYR* 4.0 23.6 - + - -
507B VAL* 3.6 25.6 - - + -
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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