Contacts of the strand formed by residues 546 - 554 (chain A) in PDB entry 6VXX
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 LEU 546 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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519A HIS* 4.1 17.9 - - + +
541A PHE* 3.8 9.8 - - + +
542A ASN* 3.3 1.9 + - - -
543A PHE* 2.8 40.2 + - + +
544A ASN 3.3 1.4 + - - +
545A GLY* 1.3 76.0 - - - +
547A THR* 1.3 72.6 + - - +
565A PHE* 3.4 36.8 - - + -
567A ARG* 6.3 0.4 - - - +
573A THR* 3.5 32.5 - - + +
576A VAL* 4.5 4.5 - - + -
976B VAL* 5.4 5.2 - - + -
978B ASN* 5.8 0.9 - - + -
979B ASP* 3.8 23.8 - - - +
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Residues in contact with THR 547 (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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389A ASP* 4.9 2.2 - - - +
540A ASN* 5.1 4.5 - - - +
541A PHE* 3.2 14.2 - - - +
542A ASN* 3.4 31.6 - - + +
545A GLY 3.6 8.2 + - - +
546A LEU* 1.3 88.4 - - - +
548A GLY* 1.3 58.7 + - - +
978B ASN* 3.0 39.9 + - - +
979B ASP* 5.4 0.4 + - - -
982B SER* 4.7 8.8 - - - -
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Residues in contact with GLY 548 (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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540A ASN* 3.6 5.1 + - - +
541A PHE* 2.9 44.4 + - - +
547A THR* 1.3 77.8 - - - +
549A THR* 1.3 64.9 + - - -
978B ASN* 3.7 13.5 - - - -
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Residues in contact with THR 549 (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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320A VAL 5.4 1.1 - - - +
322A PRO* 4.0 26.2 - - + +
538A CYS* 4.0 0.9 - - - -
539A VAL 3.5 11.7 - - - +
540A ASN* 4.2 14.7 + - - +
541A PHE* 3.7 6.1 - - - -
548A GLY* 1.3 76.5 + - - -
550A GLY* 1.3 62.4 + - - +
587A ILE* 4.8 1.9 - - - +
589A PRO* 4.2 12.1 - - - +
590A CYS* 3.9 18.8 + - + -
745B ASP* 4.6 24.4 + - - +
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Residues in contact with GLY 550 (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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539A VAL* 3.1 34.8 + - - +
541A PHE* 3.5 13.0 - - - -
549A THR* 1.3 78.9 - - - +
551A VAL* 1.3 64.2 + - - -
587A ILE* 4.3 3.4 - - - -
588A THR 3.6 9.2 - - - -
589A PRO* 4.1 1.3 - - - -
590A CYS* 3.6 15.3 - - - -
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Residues in contact with VAL 551 (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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536A ASN* 3.7 13.5 - - - -
537A LYS 3.6 22.7 - - - +
538A CYS* 3.9 21.5 - - + +
550A GLY* 1.3 74.5 - - - -
552A LEU* 1.3 62.7 + - - +
553A THR* 3.8 15.0 + - + +
586A ASP 3.2 6.1 - - - +
587A ILE* 3.5 1.4 - - - -
588A THR* 2.8 45.3 + - + +
589A PRO 5.1 0.2 - - - +
590A CYS* 4.1 12.8 - - - -
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Residues in contact with LEU 552 (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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326A ILE* 4.6 5.2 - - + -
533A LEU* 4.0 23.1 - - + -
534A VAL 4.3 9.4 - - - +
535A LYS* 3.4 7.1 - - - +
536A ASN 2.9 23.9 + - - -
537A LYS 4.1 4.0 + - - -
539A VAL* 3.9 23.6 - - + -
541A PHE* 3.9 20.9 - - + -
543A PHE* 3.9 31.2 - - + -
551A VAL* 1.3 73.7 - - - +
553A THR* 1.3 60.5 + - - +
585A LEU* 4.6 14.8 - - + -
586A ASP 3.4 3.1 - - - +
587A ILE* 3.8 26.7 - - + -
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Residues in contact with THR 553 (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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535A LYS* 5.0 3.1 - - - -
536A ASN* 3.5 22.0 - - - +
551A VAL* 3.8 22.0 - - + +
552A LEU* 1.3 79.1 - - - +
554A GLU* 1.3 68.5 + - - +
585A LEU* 3.2 12.8 - - - -
586A ASP* 2.9 44.9 + - - +
588A THR* 5.2 7.7 + - - +
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Residues in contact with GLU 554 (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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535A LYS* 4.0 32.3 + - + +
536A ASN* 4.9 1.8 + - - -
553A THR* 1.3 87.6 + - - +
555A SER* 1.3 60.2 + - - +
583A GLU* 5.6 1.3 - - - +
584A ILE 4.3 3.6 - - - -
585A LEU* 4.8 2.5 - - + -
586A ASP* 4.1 2.4 - - - +
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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