Contacts of the helix formed by residues 530 - 539 (chain A) in PDB entry 6EJ9
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 SER 530 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458A PHE* 5.1 2.0 - - - -
462A GLN* 5.7 1.6 - - - -
464A LEU* 3.6 24.9 - - - +
489A VAL* 4.2 1.2 - - - +
490A ASP 2.9 22.1 + - - +
491A GLY* 4.1 2.0 - - - -
521A TYR* 2.7 30.9 + - - -
526A LEU 4.8 3.8 - - - -
527A PRO 3.0 2.3 + - - -
528A ALA 3.2 0.8 - - - -
529A GLU* 1.3 82.3 - - - +
531A PHE* 1.3 66.8 + - - +
532A PHE 3.4 2.2 + - - -
533A HIS* 3.4 3.5 + - - -
534A THR* 3.0 27.7 + - - -
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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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398A LEU* 3.8 25.8 - - + -
402A LEU* 4.2 10.5 - - + -
506A VAL* 4.0 21.1 - - + -
514A VAL* 5.1 3.4 - - + -
517A MET* 3.9 21.3 - - + -
518A LYS* 4.0 21.3 - - + -
521A TYR* 3.5 41.0 - + + -
527A PRO 3.0 15.8 + - - +
528A ALA 4.6 0.4 - - - -
530A SER* 1.3 75.7 - - - +
532A PHE* 1.3 87.4 + + + +
534A THR* 3.3 1.6 + - - -
535A VAL* 3.0 56.2 + - + +
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Residues in contact with PHE 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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398A LEU* 3.8 29.2 - - + -
401A TYR* 4.4 13.0 - + + -
402A LEU* 4.5 2.0 - - + -
405A MET* 3.7 36.6 - - + -
448A LEU* 4.0 23.5 - - + +
496A PHE* 3.7 28.0 - + + -
498A LEU* 3.9 18.2 - - + -
502A PHE* 4.2 12.8 - + + -
506A VAL* 4.5 10.5 - - + -
528A ALA* 4.3 12.8 + - + +
530A SER 3.4 0.6 - - - -
531A PHE* 1.3 91.0 - + - +
533A HIS* 1.3 67.7 + - - +
535A VAL* 4.8 2.0 - - - -
536A LEU* 3.1 27.5 + - - +
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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
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448A LEU* 3.7 37.3 - - + +
449A LYS 3.0 28.2 + - - -
450A SER* 4.2 4.0 - - - -
490A ASP* 3.7 23.1 - - + +
491A GLY* 3.6 12.6 - - - -
492A GLY 3.8 2.8 + - - -
493A SER 3.3 23.5 + - - -
496A PHE* 5.6 0.2 - + - -
528A ALA 4.7 3.5 + - - -
529A GLU 3.7 24.9 + - - -
530A SER* 3.8 1.2 - - - +
531A PHE 3.4 0.2 - - - -
532A PHE* 1.3 78.1 + - - +
534A THR* 1.3 63.2 + - - +
536A LEU* 4.0 1.2 - - - +
537A GLU* 3.1 35.4 + - - +
545A MET* 4.1 12.6 - - + -
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Residues in contact with THR 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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487A ILE* 4.4 9.2 - - + -
488A ALA 3.8 16.8 - - - +
489A VAL* 3.8 7.5 - - + -
490A ASP* 3.2 22.1 + - - +
513A LEU* 4.8 1.2 - - + +
517A MET* 4.0 26.2 - - + -
521A TYR* 3.4 14.7 + - - +
530A SER* 3.0 18.0 + - - -
531A PHE* 3.9 2.9 - - - -
533A HIS* 1.3 76.2 - - - +
535A VAL* 1.3 64.9 + - - +
537A GLU* 3.7 1.1 + - - -
538A ASN* 2.8 34.4 + - - +
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Residues in contact with VAL 535 (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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502A PHE* 4.2 12.6 - - + -
505A TYR* 4.0 26.0 - - + -
506A VAL* 4.4 7.0 - - + -
513A LEU* 3.6 12.3 - - + +
514A VAL* 4.4 13.0 - - + -
517A MET* 4.1 19.1 - - + -
521A TYR* 6.1 0.2 - - + -
531A PHE* 3.0 46.6 + - + +
532A PHE* 4.2 2.9 - - - +
534A THR* 1.3 76.5 - - - +
536A LEU* 1.3 64.2 + - - +
538A ASN 3.2 3.3 + - - -
539A SER* 2.9 24.9 + - - -
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Residues in contact with LEU 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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446A ASN* 3.9 19.3 - - + +
448A LEU* 3.5 26.7 - - + -
502A PHE* 3.7 23.1 - - + -
532A PHE 3.1 19.0 + - - +
533A HIS 4.0 2.2 - - - +
535A VAL* 1.3 76.9 - - - +
537A GLU* 1.3 62.8 + - - +
538A ASN 3.2 0.2 + - - -
539A SER* 2.9 20.4 + - - -
541A HIS* 3.2 41.1 - - + +
542A CYS* 3.3 15.3 - - - -
544A THR* 3.8 5.2 - - - +
545A MET* 3.8 30.5 - - + -
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Residues in contact with GLU 537 (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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299A ARG* 3.5 11.4 + - - +
301A CYS* 3.4 9.9 - - - +
305A GLY 5.1 1.4 - - - +
306A LYS* 3.3 31.4 - - + +
488A ALA* 4.6 12.2 - - + +
490A ASP* 2.6 45.5 - - - +
533A HIS* 3.1 18.7 + - - +
534A THR 4.3 2.2 - - - +
536A LEU* 1.3 77.2 - - - +
538A ASN* 1.3 62.0 + - - +
542A CYS* 3.3 21.4 - - - +
545A MET* 3.5 29.6 - - + +
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Residues in contact with ASN 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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299A ARG* 2.7 38.6 + - + +
300A PHE 2.9 28.2 + - - -
301A CYS* 3.2 6.5 + - - -
487A ILE* 3.7 14.6 - - + +
488A ALA* 2.8 41.8 + - - +
513A LEU* 3.5 23.3 - - + +
534A THR* 2.8 25.7 + - - +
535A VAL 3.2 1.4 + - - -
536A LEU 3.2 0.8 - - - -
537A GLU* 1.3 77.4 - - - +
539A SER* 1.3 60.9 + - - +
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Residues in contact with SER 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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300A PHE* 4.5 0.2 - - - -
301A CYS* 3.4 21.0 - - - +
502A PHE* 4.3 1.0 - - - -
505A TYR* 3.6 24.7 - - - -
513A LEU* 3.8 4.9 - - - -
535A VAL 2.9 13.1 + - - -
536A LEU* 2.9 21.8 + - - +
538A ASN* 1.3 81.2 - - - +
540A PRO* 1.3 74.6 - - - +
541A HIS* 3.1 18.9 + - - +
542A CYS 3.4 5.0 + - - -
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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