Contacts of the strand formed by residues 540 - 545 (chain A) in PDB entry 4DAY
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 TYR 540 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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494A LEU* 4.4 0.7 - - - -
498A MET* 4.3 5.2 - - - +
515A VAL* 4.2 13.2 - - + -
533A LYS* 4.4 17.3 - - + -
534A VAL 3.5 6.3 - - - +
535A SER* 4.1 11.7 - - - -
539A ALA* 1.3 82.6 - - - +
541A LEU* 1.3 67.3 + - - +
17B LEU* 3.5 26.0 - - + +
18B PRO* 3.1 28.2 + - - +
19B ARG 3.8 10.5 - - - -
20B SER 3.2 13.5 + - - -
21B PRO* 3.6 20.4 - - + -
22B PRO* 3.4 24.7 - - + +
105B MET* 3.6 14.0 - - + +
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Residues in contact with LEU 541 (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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494A LEU* 3.8 23.6 - - + -
498A MET* 4.3 12.8 - - + -
533A LYS* 3.2 6.4 - - - +
534A VAL* 2.7 46.4 + - + +
540A TYR* 1.3 79.9 - - - +
542A ASP* 1.3 68.7 + - - +
543A VAL* 3.6 13.6 + - + -
594A ILE* 4.1 21.1 - - + -
596A PHE* 3.8 29.4 - - + -
601A SER 5.1 4.0 - - - +
602A LYS* 5.7 0.2 - - - -
603A ALA* 3.6 25.1 - - + +
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Residues in contact with ASP 542 (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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518A THR* 3.7 24.3 + - - +
531A THR* 6.3 0.2 - - - -
532A ALA 3.5 2.2 - - - +
533A LYS* 3.2 35.1 + - - +
541A LEU* 1.3 75.4 - - - +
543A VAL* 1.3 61.6 + - - +
602A LYS* 3.7 34.8 + - + +
603A ALA 3.3 22.0 + - - +
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Residues in contact with VAL 543 (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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530A ILE 3.5 0.9 - - - +
531A THR* 3.2 7.6 - - - -
532A ALA 2.7 43.0 + - - +
534A VAL* 3.8 28.3 - - + -
541A LEU* 3.8 22.4 - - + -
542A ASP* 1.3 79.4 - - - +
544A ASP* 1.3 65.0 + - - +
545A PHE* 3.8 21.8 - - + -
594A ILE* 4.5 3.8 - - + -
602A LYS* 4.8 0.2 - - - -
603A ALA* 3.4 14.8 - - + +
604A MET 4.4 0.2 - - - +
605A VAL* 3.7 24.2 - - + -
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Residues in contact with ASP 544 (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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529A SER* 6.1 2.7 - - - -
530A ILE 3.5 7.2 - - - +
531A THR* 3.8 12.5 - - + +
543A VAL* 1.3 78.4 - - - +
545A PHE* 1.3 67.8 + - - +
602A LYS* 3.3 31.7 - - - +
603A ALA 3.1 15.0 + - - +
604A MET* 3.5 29.0 - - + +
605A VAL 2.9 24.1 + - - -
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Residues in contact with PHE 545 (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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514A ILE* 3.9 24.2 - - + -
528A TRP 4.0 9.7 - - - +
529A SER* 4.0 5.9 - - - -
530A ILE* 3.3 32.0 + - + +
532A ALA* 3.8 16.6 - - + -
534A VAL* 5.1 1.3 - - + -
543A VAL* 3.8 25.8 - - + -
544A ASP* 1.3 79.9 - - - +
546A VAL* 1.3 64.6 + - - +
547A ASP 3.2 3.1 + - - -
549A ILE* 4.1 30.7 - - + -
550A LEU* 3.9 27.7 - - + +
585A LEU* 4.8 9.6 - - + -
588A LEU* 5.2 6.1 - - + -
592A MET* 5.7 2.0 - - - -
604A MET* 5.2 1.6 - - - -
605A VAL* 4.2 19.3 - - + -
608A LEU* 5.2 5.8 - - + -
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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