Contacts of the helix formed by residues 528 - 539 (chain A) in PDB entry 5LUQ
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 VAL 528 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495A VAL* 4.2 26.0 - - + +
526A ASP* 3.2 3.5 - - + +
527A TYR* 1.3 83.2 - - + +
529A ASP* 1.3 73.4 + - - +
531A PHE* 2.9 30.0 + - + +
532A ARG 4.3 0.7 + - - -
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Residues in contact with ASP 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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447A PRO* 4.5 12.9 - - + +
454A GLN* 5.6 4.9 - - - +
525A LYS* 3.9 3.8 - - - -
526A ASP* 2.8 45.0 + - - +
527A TYR 3.3 1.2 - - - -
528A VAL* 1.3 79.4 - - - +
530A LEU* 1.3 63.2 + - + +
531A PHE 2.7 12.1 + - - -
532A ARG* 3.0 22.7 + - - +
533A HIS* 4.2 5.1 + - - -
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Residues in contact with LEU 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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446A PHE* 3.2 39.3 - - + -
447A PRO* 3.4 35.9 - - + -
487A LEU* 3.4 38.4 - - + +
490A ILE* 4.4 19.1 - - + -
491A CYS* 6.1 0.4 - - - -
525A LYS* 5.2 5.2 - - + +
526A ASP 3.6 20.6 - - - +
527A TYR* 3.9 6.5 - - - +
528A VAL 3.1 0.4 + - - -
529A ASP* 1.3 74.4 - - + +
531A PHE* 1.3 63.5 + - - +
533A HIS* 3.1 18.1 + - - +
534A LEU* 3.2 10.7 + - - +
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Residues in contact with PHE 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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484A HIS* 5.5 3.1 - + - -
487A LEU* 3.4 26.0 - - + -
488A ILE* 5.8 1.6 - - + -
527A TYR* 2.7 58.6 - + - -
528A VAL* 2.9 22.7 - - + +
529A ASP 2.7 3.4 + - - -
530A LEU* 1.3 77.2 - - - +
532A ARG* 1.3 57.6 + - - +
534A LEU* 3.0 15.9 + - + +
535A LEU* 2.6 54.4 + - + +
619A ASP* 2.8 46.9 - - + +
622A ALA* 5.6 2.9 - - + -
623A PHE* 5.5 0.9 - - + -
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Residues in contact with ARG 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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454A GLN* 5.1 19.1 + - - -
458A CYS* 5.4 2.0 - - - -
528A VAL 4.3 0.8 + - - -
529A ASP 3.0 12.3 + - - +
531A PHE* 1.3 76.0 - - - +
533A HIS* 1.3 61.1 + - + +
535A LEU* 4.3 6.8 - - - +
536A SER* 2.8 42.2 + - - -
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Residues in contact with HIS 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A PHE* 2.2 69.0 + + + +
447A PRO* 4.9 1.1 - - + -
449A TYR* 4.3 3.8 - + - -
454A GLN* 3.3 45.7 + - + +
458A CYS* 4.1 25.0 + - + +
461A ILE* 5.0 6.3 - - + +
529A ASP 4.5 4.3 - - - -
530A LEU* 3.1 15.1 + - - +
532A ARG* 1.3 82.7 - - + +
534A LEU* 1.3 54.4 + - + +
536A SER* 3.6 0.7 - - - -
537A SER* 2.7 36.2 + - - -
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Residues in contact with LEU 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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443A ILE* 5.3 11.2 - - + -
446A PHE* 5.1 3.6 - - + -
483A VAL* 6.2 3.6 - - + -
484A HIS* 4.3 20.4 - - + +
487A LEU* 3.5 31.6 - - + -
530A LEU 3.2 7.3 + - - +
531A PHE* 3.0 18.7 + - + +
533A HIS* 1.3 72.6 - - + +
535A LEU* 1.3 70.0 + - - +
537A SER* 2.9 24.9 + - - +
538A ASP* 3.1 8.0 + - - +
619A ASP* 5.6 0.2 - - - +
623A PHE* 4.6 21.2 - - + -
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Residues in contact with LEU 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A PHE* 2.6 41.7 + - + +
532A ARG* 4.1 4.9 - - - +
534A LEU* 1.3 74.6 - - - +
536A SER* 1.3 63.9 + - - +
538A ASP* 2.9 11.3 + - - +
539A GLN* 3.0 13.6 + - - +
622A ALA* 3.2 31.4 - - + +
623A PHE* 3.4 31.2 - - + +
626A LEU* 3.5 38.1 - - + +
627A VAL* 3.7 9.1 - - + +
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Residues in contact with SER 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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458A CYS* 3.3 24.3 - - - -
532A ARG* 2.8 30.7 + - - -
535A LEU* 1.3 73.6 - - - +
537A SER* 1.3 55.8 + - - +
539A GLN* 4.0 5.1 + - - +
540A MSE 3.0 35.0 + - - +
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Residues in contact with SER 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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458A CYS* 4.8 6.5 - - - -
461A ILE* 5.4 12.3 - - - -
462A VAL* 4.8 17.5 - - - +
533A HIS 2.7 23.4 + - - -
534A LEU* 2.9 16.1 + - - +
536A SER* 1.3 75.8 - - - +
538A ASP* 1.3 74.9 + - - +
539A GLN 3.4 0.3 + - - -
540A MSE 3.5 9.7 + - - +
545A LEU* 3.2 16.1 - - - +
548A GLU* 4.9 1.0 - - - +
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Residues in contact with ASP 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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534A LEU 3.1 5.4 + - - +
535A LEU 2.9 7.6 + - - +
537A SER* 1.3 88.7 + - - +
539A GLN* 1.3 61.1 + - - +
540A MSE 3.6 0.2 - - - -
545A LEU* 2.9 29.9 - - - +
548A GLU* 4.4 8.3 - - - +
549A ALA* 3.0 45.1 + - + +
552A SER* 4.0 14.1 + - - -
623A PHE* 4.4 10.1 - - + -
627A VAL* 3.7 25.5 - - + +
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Residues in contact with GLN 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 LEU 3.0 12.0 + - - +
536A SER* 3.5 7.7 + - - +
538A ASP* 1.3 81.5 - - + +
540A MSE 1.3 58.5 + - - +
542A ASP* 3.9 18.9 + - - +
545A LEU* 3.9 6.7 - - - +
626A LEU* 4.6 24.5 - - + +
627A VAL* 5.3 7.2 - - + -
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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