Contacts of the strand formed by residues 469 - 474 (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 ILE 469 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441A ARG* 3.3 30.3 - - - +
442A THR 3.4 5.3 + - - -
443A ILE* 3.6 14.7 - - + -
444A LEU* 2.8 33.1 + - - +
467A PRO 3.6 0.2 + - - -
468A LEU* 1.3 75.9 - - - +
470A VAL* 1.3 59.3 + - - +
471A ILE* 3.9 13.7 - - + -
528A LEU* 4.4 4.0 - - + -
531A ALA* 3.9 12.3 - - + -
532A LEU* 3.4 42.0 - - + +
538A ALA* 3.7 9.6 - - + +
540A ILE* 3.9 28.9 - - + -
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Residues in contact with VAL 470 (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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425A PHE* 4.0 11.4 - - + -
444A LEU* 3.6 22.0 - - + -
446A THR* 4.2 13.2 - - + -
451A VAL* 4.2 6.3 - - + -
458A PHE* 3.8 32.5 - - + -
461A LEU* 4.5 1.6 - - + -
468A LEU* 3.7 30.7 - - + -
469A ILE* 1.3 73.0 - - - +
471A ILE* 1.3 57.5 + - - +
472A ILE* 3.9 10.2 + - + -
538A ALA 3.0 13.6 + - - +
539A CYS* 3.3 2.8 - - - -
540A ILE 2.8 31.7 + - - +
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Residues in contact with ILE 471 (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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379A ILE* 3.6 20.6 - - + -
443A ILE* 3.5 24.9 - - + -
444A LEU 2.7 15.0 + - - +
445A VAL* 3.5 4.5 - - + +
446A THR* 2.8 34.7 + - - +
469A ILE* 3.9 13.0 - - + -
470A VAL* 1.3 75.0 - - - +
472A ILE* 1.3 60.2 + - - +
473A MSE 3.9 15.9 + - + -
524A PHE* 3.6 25.8 - - + -
528A LEU* 3.9 19.7 - - + -
540A ILE* 3.5 10.5 - - + +
542A VAL* 3.7 14.8 - - + -
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Residues in contact with ILE 472 (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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446A THR* 3.4 5.8 - - + -
447A GLY 3.9 0.9 - - - -
448A ASP* 3.5 40.6 - - + +
451A VAL* 3.8 31.9 - - + -
458A PHE* 5.2 1.8 - - + -
470A VAL* 4.2 5.4 - - + -
471A ILE* 1.3 74.1 - - - +
473A MSE 1.3 61.3 + - - +
474A ASN* 3.2 9.3 + - + +
504A TYR* 3.6 30.1 - - + -
539A CYS* 3.8 21.1 - - - -
540A ILE 2.9 12.4 + - - +
541A ASN* 4.3 7.4 - - - +
542A VAL* 2.8 33.9 + - - +
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Residues in contact with MSE 473 (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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372A PRO* 5.3 3.8 - - + +
375A ALA* 3.8 34.3 - - + +
376A SER* 4.6 7.0 - - - +
379A ILE* 3.3 34.3 - - + -
396A THR* 3.4 39.4 + - + +
400A LEU* 5.6 0.4 - - + -
445A VAL* 3.7 11.4 - - + -
446A THR 2.8 8.8 + - - +
447A GLY* 3.7 3.5 - - - -
448A ASP* 3.3 21.8 + - - +
471A ILE* 3.9 8.3 + - + -
472A ILE* 1.3 68.1 - - - +
474A ASN* 1.3 59.7 + - - +
475A ASN* 3.6 6.3 + - - +
524A PHE* 4.4 2.5 - - + -
542A VAL* 3.9 10.8 - - - -
544A VAL* 4.0 22.4 - - + -
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Residues in contact with ASN 474 (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* 3.5 17.3 - - + +
472A ILE* 3.2 3.1 + - + +
473A MSE 1.3 69.4 - - - +
475A ASN* 1.3 58.8 + - - +
476A GLN* 3.0 34.8 + - - +
502A GLY 4.7 2.6 + - - -
504A TYR* 3.5 23.9 - - - -
517A HIS* 5.4 4.1 - - + -
541A ASN* 3.1 29.9 + - - +
542A VAL 2.7 19.9 + - - +
543A ALA* 3.8 4.5 - - - -
544A VAL* 3.0 24.9 + - - +
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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