Contacts of the strand formed by residues 540 - 544 (chain B) in PDB entry 5ZE3
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 GLY 540 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446B GLY 2.9 15.7 - - - -
447B ARG* 4.1 1.1 - - - -
448B VAL* 4.2 2.5 - - - -
468B TRP* 3.1 18.4 + - - -
488B ALA* 3.8 0.3 - - - -
489B PHE* 3.2 28.0 + - - +
495B TRP* 3.9 12.6 - - - -
538B GLY 3.8 1.2 + - - -
539B ALA* 1.3 73.8 - - - +
541B VAL* 1.3 65.2 + - - +
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Residues in contact with VAL 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B LEU* 3.9 24.7 - - + -
445B GLU* 3.1 5.4 - - - +
446B GLY 2.9 30.8 + - - -
448B VAL* 3.7 16.8 - - + -
468B TRP* 3.9 7.9 - - + -
473B ALA* 3.7 28.5 - - + -
476B VAL* 4.2 7.4 - - + -
477B CYS* 3.8 20.9 - - - -
487B ASN 3.5 10.8 - - - +
489B PHE* 3.7 8.5 - - - -
495B TRP* 3.8 2.4 - - - -
540B GLY* 1.3 81.1 - - - +
542B ALA* 1.3 60.9 + - - +
543B CYS* 3.9 6.7 - - - -
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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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444B TYR 3.6 6.5 - - - +
445B GLU* 3.9 18.4 - - + +
477B CYS* 3.5 1.9 - - - -
485B ALA* 3.4 6.4 - - - -
486B SER* 2.8 38.9 + - - +
487B ASN* 3.1 28.3 + - + +
489B PHE* 3.9 6.9 - - + -
541B VAL* 1.3 74.1 - - - +
543B CYS* 1.3 59.0 + - - +
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Residues in contact with CYS 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B LEU* 4.8 1.8 - - - -
444B TYR* 3.0 36.7 + - + +
477B CYS* 2.0 50.7 - - + -
482B LEU* 3.5 30.3 - - + +
484B PHE 3.1 8.7 - - - +
486B SER* 3.9 4.4 + - - -
541B VAL* 3.9 8.3 - - - -
542B ALA* 1.3 75.7 - - - +
544B SER* 1.3 66.0 + - - +
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Residues in contact with SER 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B TYR* 4.9 3.8 - - - -
482B LEU 3.9 6.7 - - - -
483B GLY* 3.7 0.3 - - - -
484B PHE* 2.9 33.1 + - - +
486B SER* 4.2 14.5 + - - +
543B CYS* 1.3 78.1 - - - +
545B GLU* 1.3 63.2 + - - +
546B THR* 3.1 29.8 + - - -
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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