Contacts of the strand formed by residues 534 - 541 (chain A) in PDB entry 3A8P
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 LYS 534 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512A PHE* 4.0 4.3 - - - -
513A PHE* 2.7 43.0 + - + +
530A ARG* 3.9 24.9 - - - +
532A LYS* 3.8 37.2 - - + +
533A TRP* 1.3 79.4 - - - +
535A GLN* 1.3 60.2 + - - +
536A TYR* 3.7 32.1 + - + +
519C LEU 6.0 0.2 + - - -
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Residues in contact with GLN 535 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510A TRP* 3.6 44.3 - - + +
511A LEU 3.4 11.7 - - - +
512A PHE* 3.6 44.0 - - + -
534A LYS* 1.3 74.0 - - - +
536A TYR* 1.3 75.2 + - - +
549A GLU* 5.2 6.1 - - - +
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Residues in contact with TYR 536 (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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510A TRP* 3.5 10.3 - - - -
511A LEU 2.9 31.5 + - - +
513A PHE* 3.8 29.2 - + + -
534A LYS* 3.7 43.0 + - + +
535A GLN* 1.3 81.0 - - - +
537A TRP* 1.3 62.5 + - - +
538A VAL* 3.4 8.3 + - + +
547A PHE* 3.5 40.4 - + + -
548A TYR 3.5 14.6 - - - +
549A GLU* 3.9 28.8 + - + +
563A ARG* 4.6 9.9 - - + +
564A CYS* 5.0 8.1 - - - -
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Residues in contact with TRP 537 (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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508A ALA* 3.8 21.2 - - + +
509A GLY* 3.5 24.0 - - - -
510A TRP* 3.6 47.4 - + + -
536A TYR* 1.3 70.6 - - - +
538A VAL* 1.3 58.8 + - - +
539A THR* 3.8 23.1 - - + +
547A PHE 3.8 0.2 - - - -
548A TYR* 2.8 45.8 + + + +
550A THR 3.7 23.1 - - - +
551A TYR* 3.6 42.0 - + - -
552A GLY* 4.1 20.1 + - - -
553A LYS 5.0 2.9 - - - -
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Residues in contact with VAL 538 (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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508A ALA* 3.1 4.5 - - - +
509A GLY 2.9 38.7 + - - +
511A LEU* 4.0 24.0 - - + +
536A TYR* 3.8 12.3 - - + +
537A TRP* 1.3 76.5 + - - +
539A THR* 1.3 70.5 + - - +
545A LEU* 3.9 25.8 - - + -
546A LEU 3.4 8.3 - - - +
547A PHE* 3.8 33.4 - - + -
598A PHE* 5.5 0.2 - - + -
609A TRP* 3.7 16.4 - - + -
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Residues in contact with THR 539 (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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505A VAL* 4.4 18.4 - - + +
507A LYS 3.4 6.5 - - - -
508A ALA* 3.9 9.0 - - + -
537A TRP* 3.8 20.9 - - + +
538A VAL* 1.3 82.5 - - - +
540A LEU* 1.3 60.7 + - - +
541A LYS* 5.0 1.0 + - - +
544A THR 3.5 0.9 - - - +
545A LEU* 3.3 5.2 - - - -
546A LEU* 2.9 56.4 + - - +
548A TYR* 3.7 18.1 + - + -
609A TRP* 4.9 0.4 - - - -
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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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505A VAL* 3.4 3.7 - - - -
506A ARG* 2.7 62.1 + - + +
507A LYS* 2.8 18.3 + - + +
539A THR* 1.3 72.5 - - - +
541A LYS* 1.3 56.8 + - - +
542A GLY 3.5 21.8 - - - +
543A CYS* 4.2 4.9 - - - -
544A THR 3.5 17.3 - - - +
545A LEU* 3.9 20.6 - - + -
568A ALA* 5.8 1.6 - - + -
609A TRP* 4.4 5.8 - - + -
612A ALA* 3.6 28.3 - - + +
613A ILE* 3.8 15.7 - - + +
616A ALA* 4.3 4.0 - - + -
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Residues in contact with LYS 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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504A VAL* 2.7 54.1 - - - +
505A VAL* 4.2 12.4 - - + +
539A THR* 4.0 1.1 - - - +
540A LEU* 1.3 72.5 - - - +
542A GLY* 1.3 64.5 + - - +
543A CYS 3.2 0.2 + - - -
544A THR* 3.0 30.9 + - - +
546A LEU* 4.6 22.7 - - + -
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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