Contacts of the strand formed by residues 469 - 474 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441B ARG* 3.3 30.7 - - - +
442B THR 3.4 5.5 + - - -
443B ILE* 3.6 16.2 - - + -
444B LEU* 2.7 33.8 + - - +
468B LEU* 1.3 76.7 - - - +
470B VAL* 1.3 60.4 + - - +
471B ILE* 3.9 13.2 - - + -
528B LEU* 4.4 4.7 - - + -
531B ALA* 4.0 10.5 - - + -
532B LEU* 3.4 41.5 - - + +
538B ALA* 3.7 9.6 - - + +
540B ILE* 3.9 30.1 - - + -
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Residues in contact with VAL 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B PHE* 4.0 11.4 - - + -
444B LEU* 3.8 22.7 - - + -
446B THR* 4.3 1.8 - - + -
451B VAL* 4.2 17.7 - - + -
458B PHE* 3.7 34.8 - - + -
461B LEU* 4.5 2.0 - - + -
468B LEU* 3.8 26.7 - - + +
469B ILE* 1.3 73.8 - - - +
471B ILE* 1.3 56.8 + - - +
472B ILE* 3.9 10.0 + - + -
538B ALA 2.9 15.3 + - - +
539B CYS* 3.3 2.9 - - - -
540B ILE 2.7 31.9 + - - +
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Residues in contact with ILE 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B ILE* 3.6 19.5 - - + -
443B ILE* 3.5 23.3 - - + -
444B LEU 2.8 16.1 + - - +
445B VAL* 3.5 4.2 - - + +
446B THR* 2.8 30.5 + - - +
469B ILE* 3.9 14.1 - - + -
470B VAL* 1.3 74.4 - - - +
472B ILE* 1.3 62.5 + - - +
473B MSE 3.8 15.8 + - + -
524B PHE* 3.6 26.7 - - + -
528B LEU* 3.9 20.9 - - + -
540B ILE* 3.5 9.4 - - + +
542B VAL* 3.8 14.4 - - + -
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Residues in contact with ILE 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B THR* 3.3 7.4 - - + -
447B GLY 3.9 1.6 - - - -
448B ASP* 3.5 39.0 - - + +
451B VAL* 3.8 31.0 - - + -
458B PHE* 5.2 0.9 - - + -
470B VAL* 4.2 4.7 - - + -
471B ILE* 1.3 73.7 - - - +
473B MSE 1.3 61.4 + - - +
474B ASN* 3.1 9.9 + - + +
504B TYR* 3.6 25.6 - - + -
539B CYS* 3.5 28.5 - - - -
540B ILE 2.9 12.3 + - - +
541B ASN* 4.4 7.6 - - - +
542B VAL* 2.9 32.1 + - - +
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Residues in contact with MSE 473 (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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372B PRO* 5.3 3.1 - - + +
375B ALA* 3.9 35.9 - - + +
376B SER* 4.5 7.0 - - - +
379B ILE* 3.3 34.3 - - + -
396B THR* 3.4 39.5 + - + +
400B LEU* 5.7 0.2 - - + -
445B VAL* 3.8 10.8 - - + -
446B THR 2.8 9.6 + - - +
447B GLY* 3.7 2.9 - - - -
448B ASP* 3.4 21.0 + - - +
471B ILE* 3.8 6.5 + - + -
472B ILE* 1.3 68.8 - - - +
474B ASN* 1.3 60.2 + - - +
475B ASN* 3.5 6.5 + - - +
524B PHE* 4.3 2.5 - - + -
542B VAL* 3.9 12.3 - - - -
544B VAL* 4.0 21.3 - - + -
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Residues in contact with ASN 474 (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 ASP* 3.4 16.5 - - + +
472B ILE* 3.1 3.0 + - + +
473B MSE 1.3 68.9 - - - +
475B ASN* 1.3 59.3 + - - +
476B GLN* 3.0 35.1 + - - +
502B GLY 4.7 3.0 + - - -
504B TYR* 3.5 25.3 - - - -
517B HIS* 5.6 3.3 - - + -
541B ASN* 3.2 27.7 + - - +
542B VAL 2.7 20.2 + - - +
543B ALA* 3.7 4.9 - - - -
544B VAL* 3.0 24.6 + - - +
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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