Contacts of the helix formed by residues 527 - 539 (chain A) in PDB entry 3LJK
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 ASP 527 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525A ASN 3.6 1.8 + - - -
526A LEU* 1.3 79.3 - - - +
528A ASP* 1.3 59.0 + - - +
529A SER* 3.0 17.5 + - - +
530A THR* 2.7 42.2 + - - -
531A ARG* 3.0 22.0 + - - +
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Residues in contact with ASP 528 (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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526A LEU 3.8 1.0 + - - -
527A ASP* 1.3 71.8 - - - +
529A SER* 1.3 60.5 + - - +
531A ARG* 3.0 23.3 + - - +
532A GLN* 2.9 61.4 + - - +
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Residues in contact with SER 529 (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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527A ASP* 3.0 10.8 + - - -
528A ASP* 1.3 76.3 - - - +
530A THR* 1.3 66.1 + - - +
532A GLN* 3.3 3.5 + - - +
533A LEU* 3.0 38.5 + - - +
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Residues in contact with THR 530 (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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511A ILE* 3.8 32.1 - - + +
526A LEU* 3.9 18.6 - - + -
527A ASP* 2.7 32.2 + - - -
529A SER* 1.3 76.2 + - - +
531A ARG* 1.3 64.4 + - - +
533A LEU* 3.3 11.1 + - + +
534A ILE* 3.0 31.5 + - + +
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Residues in contact with ARG 531 (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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523A TYR* 3.0 65.2 + - + +
524A GLN* 3.1 15.2 + - - +
526A LEU* 2.9 41.0 + - + +
527A ASP 3.0 10.0 + - - +
528A ASP* 3.0 36.8 + - - +
529A SER 3.2 0.2 - - - -
530A THR* 1.3 77.4 - - - +
532A GLN* 1.3 66.9 + - - +
534A ILE* 3.3 5.7 + - - +
535A ALA* 3.0 25.6 + - + +
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Residues in contact with GLN 532 (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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528A ASP* 2.9 50.2 + - - +
529A SER* 4.1 3.6 - - - +
531A ARG* 1.3 86.8 - - - +
533A LEU* 1.3 59.7 + - - +
535A ALA* 3.3 14.9 + - - +
536A LYS* 2.9 41.9 + - + +
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Residues in contact with LEU 533 (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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529A SER* 3.0 34.2 + - - +
530A THR* 3.7 9.0 - - + +
532A GLN* 1.3 73.2 - - - +
534A ILE* 1.3 66.6 + - + +
536A LYS* 3.2 9.9 + - + +
537A VAL* 3.1 29.4 + - + +
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Residues in contact with ILE 534 (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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511A ILE* 4.1 18.8 - - + -
514A ALA* 4.4 8.5 - - + -
515A MSE 3.8 35.6 - - + +
523A TYR* 4.8 11.4 - - + -
526A LEU* 3.6 30.3 - - + -
530A THR* 3.0 15.3 + - + +
531A ARG* 3.6 6.7 - - - +
533A LEU* 1.3 77.3 - - + +
535A ALA* 1.3 62.1 + - - +
537A VAL* 3.2 7.5 + - - +
538A LYS* 3.1 48.1 + - - +
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Residues in contact with ALA 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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523A TYR* 5.4 5.4 - - - +
531A ARG* 3.0 14.8 + - + +
532A GLN* 3.6 22.4 - - - +
533A LEU 3.3 0.2 - - - -
534A ILE* 1.3 78.6 - - - +
536A LYS* 1.3 62.6 + - + +
538A LYS* 3.3 4.6 + - - -
539A ASN* 2.9 42.6 + - - +
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Residues in contact with LYS 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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532A GLN* 2.9 29.0 + - - +
533A LEU* 3.2 12.3 + - + +
535A ALA* 1.3 77.3 - - + +
537A VAL* 1.3 66.1 + - + +
539A ASN* 4.2 2.9 - - - -
540A LYS* 3.4 20.4 + - - +
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Residues in contact with VAL 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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515A MSE 4.4 21.1 - - + -
533A LEU* 3.1 17.3 + - + +
534A ILE* 3.6 9.9 - - - +
535A ALA 3.2 0.2 - - - -
536A LYS* 1.3 78.1 - - + +
538A LYS* 1.3 59.3 + - + +
540A LYS* 3.1 32.6 - - + +
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Residues in contact with LYS 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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514A ALA 4.4 1.8 + - - -
515A MSE 2.7 42.5 + - + +
518A ASP* 6.3 1.2 - - - +
523A TYR* 5.9 1.4 - - - -
534A ILE* 3.1 36.7 + - + +
535A ALA* 3.3 6.3 + - - +
537A VAL* 1.3 80.8 - - + +
539A ASN* 1.3 67.1 + - - +
540A LYS* 3.3 6.1 + - - +
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Residues in contact with ASN 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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535A ALA* 2.9 38.0 + - - +
536A LYS* 4.2 2.7 - - - +
537A VAL 3.3 0.2 - - - -
538A LYS* 1.3 82.6 - - - +
540A LYS* 1.3 69.5 + - - +
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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