Contacts of the strand formed by residues 468 - 473 (chain B) in PDB entry 2EZT
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 468 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383B ILE* 4.2 11.2 - - + -
440B GLN* 3.8 36.3 - - + +
441B VAL 2.9 12.4 + - - +
442B PHE* 3.3 35.9 - - + +
443B ASN 2.9 23.0 + - - +
466B PRO 4.5 1.1 - - - +
467B VAL* 1.3 73.0 - - - +
469B ASN* 1.3 60.8 + - - +
470B VAL* 3.7 12.5 + - + -
529B ALA* 4.5 11.9 - - + +
530B LYS* 4.7 5.8 - - - +
533B ALA* 3.5 29.6 - - + -
538B VAL* 3.8 14.1 - - + -
540B ILE* 4.9 4.0 - - + -
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Residues in contact with ASN 469 (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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443B ASN* 2.9 34.3 + - - +
457B LEU* 3.6 9.8 - - - +
460B GLN* 2.9 39.4 + - - -
467B VAL* 3.5 7.1 + - - +
468B ILE* 1.3 70.8 - - - +
470B VAL* 1.3 58.6 + - - +
471B VAL* 4.1 1.8 - - + -
511B MET* 3.6 14.3 - - - -
538B VAL 2.8 27.8 + - - +
539B LEU* 3.2 18.5 - - + +
540B ILE* 2.7 32.9 + - - +
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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
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376B VAL* 3.7 29.2 - - + -
380B VAL* 4.3 4.5 - - + -
442B PHE* 4.5 1.3 - - + -
443B ASN* 2.7 11.1 + - - +
444B LEU* 3.7 24.1 - - + -
445B ALA* 3.0 26.2 + - - +
468B ILE* 4.2 20.6 - - + +
469B ASN* 1.3 77.3 - - - +
471B VAL* 1.3 65.7 + - - +
472B PHE* 3.7 12.0 - - + -
526B PHE* 4.2 22.2 - - + -
540B ILE* 3.4 13.9 - - + +
542B ALA* 4.8 0.7 - - + -
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Residues in contact with VAL 471 (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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443B ASN* 5.7 2.7 - - - +
445B ALA* 3.2 7.2 - - + +
447B ASP* 3.7 27.1 - - - -
450B ALA* 3.9 19.3 - - + -
469B ASN* 5.1 2.2 - - + -
470B VAL* 1.3 75.7 - - - +
472B PHE* 1.3 62.3 + - - +
473B THR* 3.6 6.7 + - - +
502B PHE* 3.8 25.6 - - + -
539B LEU* 3.9 29.8 - - + -
540B ILE 2.9 9.5 + - - +
541B ASP* 3.9 8.2 - - - +
542B ALA* 2.8 32.7 + - - +
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Residues in contact with PHE 472 (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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373B ALA* 4.0 30.7 - - + -
376B VAL* 3.5 38.1 - - + -
377B LEU* 4.0 16.6 - - + -
380B VAL* 5.4 0.4 - - + -
397B ILE* 3.6 34.1 - - + -
400B ASN* 5.9 0.9 - - + -
444B LEU* 4.3 7.2 - - + -
445B ALA 2.8 23.2 + - - +
446B GLY* 3.7 6.9 - - - -
447B ASP* 3.1 20.9 + - - +
470B VAL* 3.7 24.5 - - + -
471B VAL* 1.3 73.1 - - - +
473B THR* 1.3 59.2 + - - +
474B ASN* 3.4 9.2 + - - +
542B ALA* 3.7 4.5 - - + -
544B ILE* 4.2 15.9 - - + -
1513B MG 4.2 0.3 - - - -
1614B TDM 4.9 4.4 + - - +
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Residues in contact with THR 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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447B ASP* 3.6 22.6 - - + +
471B VAL* 3.6 5.0 + - - +
472B PHE* 1.3 69.3 - - - +
474B ASN* 1.3 57.3 + - - +
475B CYS* 4.2 11.2 - - - -
499B ASP* 3.8 22.7 - - - +
500B ILE 4.3 5.9 + - - +
502B PHE* 4.3 4.2 - - - -
515B ARG* 4.0 7.9 - - - +
541B ASP* 2.5 29.1 + - - -
542B ALA 2.8 11.7 + - - -
543B VAL* 3.4 13.3 - - + +
544B ILE* 2.8 29.7 + - - +
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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