Contacts of the strand formed by residues 539 - 545 (chain A) in PDB entry 6TAV
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 ARG 539 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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498A LEU 3.8 1.6 - - - +
499A ILE* 3.4 2.6 - - - -
500A MET* 2.9 52.8 + - + +
537A VAL* 3.9 14.6 - - + -
538A ALA* 1.3 70.4 - - - +
540A LEU* 1.3 58.4 + - - +
541A LEU* 4.3 0.7 + - - +
555A SER* 5.4 5.8 + - - +
556A ALA 3.4 7.2 - - - +
557A LYS* 3.4 40.3 - - + +
626A ASP* 3.3 34.4 + - - +
627A LEU 4.0 13.2 + - - -
628A THR* 3.8 21.5 + - - +
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Residues in contact with LEU 540 (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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461A LEU* 3.9 30.9 - - + +
476A VAL* 4.3 18.6 - - + -
497A TYR* 4.2 17.9 - - + -
498A LEU 3.5 12.8 - - - +
499A ILE* 3.7 17.5 - - + -
526A ILE* 5.5 7.2 - - + -
528A ILE* 4.7 12.3 - - + -
538A ALA 3.5 0.8 + - - +
539A ARG* 1.3 72.8 - - - +
541A LEU* 1.3 79.7 + - - +
554A ASP 4.3 0.2 - - - +
555A SER* 3.3 2.4 - - - -
556A ALA* 2.8 42.4 + - - +
558A TYR* 4.0 19.1 - - + -
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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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34A LEU* 5.0 8.3 - - + -
461A LEU* 4.5 0.2 - - - -
497A TYR* 3.2 8.8 - - - +
498A LEU* 3.0 61.3 + - + +
500A MET* 6.5 1.3 - - - -
539A ARG 4.3 1.3 - - - +
540A LEU* 1.3 79.2 - - - +
542A ILE* 1.3 71.2 + - - +
543A TYR* 3.4 38.1 - - + -
554A ASP 3.3 10.8 - - - +
555A SER* 4.0 11.0 - - - -
666A MET* 4.6 8.7 - - + -
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Residues in contact with ILE 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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459A VAL* 3.7 19.7 - - + -
460A HIS 5.0 0.4 - - - -
461A LEU* 3.4 27.8 - - + -
478A ALA* 4.3 22.0 - - + -
495A PHE* 4.0 27.6 - - + -
496A TYR 3.2 15.9 - - - +
497A TYR* 4.5 8.3 - - + -
524A PHE* 4.8 9.2 - - + -
526A ILE* 5.6 7.4 - - + -
541A LEU* 1.3 77.5 - - - +
543A TYR* 1.3 68.1 + - - +
553A GLY* 3.1 1.4 - - - -
554A ASP* 2.9 41.0 + - + +
666A MET* 4.3 0.3 - - - +
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Residues in contact with TYR 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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30A GLN* 5.3 0.7 - - - -
32A MET* 3.8 33.2 - - + -
34A LEU* 4.7 11.8 - - + +
50A LEU* 3.7 24.0 - - + +
84A LEU* 4.7 7.4 - - + +
459A VAL* 5.6 0.7 - - - -
495A PHE* 3.9 5.3 - - - -
496A TYR* 2.9 59.7 + - + +
498A LEU* 5.2 6.5 - - + +
541A LEU* 3.4 21.8 - - + -
542A ILE* 1.3 78.3 - - - +
544A ALA* 1.3 61.5 + - - +
545A VAL* 4.1 16.6 - - + -
551A VAL* 3.8 21.3 - - + -
552A ILE 3.3 8.3 - - - +
553A GLY* 3.9 0.4 - - - -
666A MET* 3.3 24.0 - - + -
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Residues in contact with ALA 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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459A VAL* 4.9 0.6 - - - +
493A LEU* 4.7 4.0 - - + -
494A SER 4.1 7.0 - - - +
495A PHE* 4.0 28.9 - - + -
543A TYR* 1.3 74.3 - - - +
545A VAL* 1.3 65.7 + - - +
546A LEU* 4.0 8.7 - - + -
551A VAL* 3.6 27.0 - - - +
552A ILE* 2.7 33.6 + - + +
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Residues in contact with VAL 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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30A GLN* 3.4 30.1 - - - +
50A LEU* 3.8 27.8 - - + -
52A SER* 3.1 38.1 - - - +
53A TYR* 2.7 22.4 + - + +
493A LEU* 3.2 16.1 - - + +
494A SER* 4.0 9.7 + - - +
496A TYR* 4.3 9.4 - - + -
543A TYR* 4.1 11.0 - - + -
544A ALA* 1.3 81.2 - - - +
546A LEU* 1.3 54.8 + - - +
550A ASP 4.2 0.2 - - - -
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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