Contacts of the strand formed by residues 538 - 543 (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 VAL 538 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467B VAL 2.9 13.1 + - - +
468B ILE* 4.1 9.2 - - + -
469B ASN* 2.8 32.0 + - - -
511B MET* 4.0 2.0 - - - -
512B GLN 3.3 16.8 - - - +
514B PHE* 3.9 28.5 - - + -
529B ALA* 3.6 35.9 - - + +
532B ILE* 3.9 18.8 - - + -
533B ALA* 4.1 10.5 - - + +
537B PRO* 1.3 77.3 - - - +
539B LEU* 1.3 67.6 + - - +
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Residues in contact with LEU 539 (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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457B LEU* 3.8 30.7 - - + -
469B ASN* 3.2 22.9 - - + +
471B VAL* 3.9 18.6 - - + -
502B PHE* 3.5 40.6 - - + +
503B SER* 4.0 6.1 - - - +
506B ALA* 4.1 8.1 - - + -
511B MET* 4.0 9.6 - - - -
512B GLN 3.0 7.3 + - - -
513B ALA* 3.0 5.4 - - + +
514B PHE* 2.9 26.3 + - - -
538B VAL* 1.3 77.1 - - - +
540B ILE* 1.3 64.3 + - - +
541B ASP* 3.7 17.9 - - + +
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Residues in contact with ILE 540 (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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468B ILE* 4.9 3.4 - - + -
469B ASN 2.7 11.4 + - - +
470B VAL* 3.4 12.0 - - + +
471B VAL 2.9 26.0 + - - -
514B PHE* 3.5 9.2 - - + +
516B VAL* 4.0 26.0 - - + -
525B VAL* 3.8 21.1 - - + -
526B PHE* 3.6 46.0 - - + -
529B ALA* 3.6 31.0 - - + -
538B VAL 5.9 0.2 - - - -
539B LEU* 1.3 79.8 - - - +
541B ASP* 1.3 62.5 + - - +
542B ALA* 3.6 4.8 + - + +
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Residues in contact with ASP 541 (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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471B VAL* 3.9 6.9 - - - +
473B THR* 2.5 30.5 + - - -
500B ILE 3.7 1.0 - - - +
502B PHE* 3.0 26.7 + - + -
503B SER 4.1 3.4 - - - +
514B PHE 2.7 15.9 + - - +
515B ARG* 2.5 40.7 + - - +
516B VAL 3.0 27.2 + - - +
539B LEU* 3.7 14.0 - - + +
540B ILE* 1.3 71.4 - - - +
542B ALA* 1.3 57.9 + - - +
543B VAL* 3.6 0.9 + - - -
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Residues in contact with ALA 542 (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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371B LEU* 4.0 6.3 - - + -
376B VAL* 3.7 39.9 - - + -
470B VAL* 4.8 1.6 - - + -
471B VAL 2.8 16.5 + - - +
472B PHE* 3.7 2.1 - - + -
473B THR 2.8 25.4 + - - -
516B VAL* 3.7 12.1 - - + -
522B LEU* 5.7 0.2 - - + -
540B ILE* 3.6 6.1 + - + -
541B ASP* 1.3 71.6 - - - +
543B VAL* 1.3 59.4 + - - +
544B ILE* 3.2 9.7 + - + +
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Residues in contact with VAL 543 (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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371B LEU* 3.6 21.0 - - - +
473B THR* 3.4 16.4 - - + +
475B CYS* 6.5 0.7 - - - -
499B ASP* 5.7 0.7 - - - +
515B ARG* 3.5 47.6 - - + +
516B VAL 2.8 19.0 + - - +
517B ASN* 3.7 21.1 - - + +
541B ASP 4.6 0.2 - - - +
542B ALA* 1.3 68.3 - - - +
544B ILE* 1.3 64.5 + - - +
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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