Contacts of the helix formed by residues 540 - 550 (chain A) in PDB entry 1Q9X
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 GLU 540 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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513A PRO* 3.8 24.7 - - + -
536A LYS 3.7 11.5 + - - +
537A SER* 3.6 3.3 + - - +
538A LEU 3.3 0.2 - - - -
539A ASN* 1.3 76.0 - - - +
541A MET* 1.3 52.4 + - - +
542A LEU 3.1 7.5 + - - -
543A PHE* 3.4 42.7 + - - +
544A ARG* 2.7 41.6 + - - +
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Residues in contact with MET 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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495A ASN 5.1 0.2 - - - +
496A GLY* 5.8 0.9 - - - -
499A ILE* 3.7 43.8 - - + +
513A PRO* 3.9 10.8 - - + -
514A LEU* 3.3 50.5 - - + +
518A TYR* 3.2 31.5 + - + +
522A PHE* 5.2 10.3 - - + -
530A ILE* 3.9 14.1 - - + -
533A LEU* 4.7 7.4 - - + -
537A SER 2.9 20.0 + - - +
538A LEU* 3.8 9.2 - - - +
539A ASN 3.4 0.6 - - - -
540A GLU* 1.3 75.7 - - - +
542A LEU* 1.3 56.3 + - - +
543A PHE 3.7 0.2 - - - -
544A ARG* 3.8 6.5 - - - +
545A ALA* 4.2 17.8 + - - +
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Residues in contact with LEU 542 (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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496A GLY* 5.6 6.5 - - - +
499A ILE* 4.9 9.4 - - + -
500A LYS* 5.0 24.0 - - + +
503A LEU* 5.5 7.0 - - + -
538A LEU 3.5 10.7 + - - +
539A ASN* 3.4 20.8 + - - +
540A GLU 3.1 0.8 - - - -
541A MET* 1.3 79.5 - - - +
543A PHE* 1.3 59.7 + - - +
544A ARG 3.2 1.8 - - - -
545A ALA* 4.9 1.3 - - - +
546A GLN* 3.1 35.1 + - + +
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Residues in contact with PHE 543 (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 ASN 3.4 8.4 + - - +
540A GLU* 3.4 39.9 - - - +
542A LEU* 1.3 78.7 - - - +
544A ARG* 1.3 61.0 + - - +
546A GLN* 4.3 3.0 - - - +
547A ARG* 3.2 49.3 + - + +
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Residues in contact with ARG 544 (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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513A PRO* 3.5 31.9 + - - +
514A LEU 5.1 4.0 + - - -
518A TYR* 3.1 56.1 + - + +
540A GLU* 2.7 52.6 + - - +
541A MET* 3.8 2.4 - - - +
542A LEU* 3.2 1.0 - - - +
543A PHE* 1.3 79.6 - - - +
545A ALA* 1.3 58.4 + - - +
546A GLN 3.1 4.9 - - - -
547A ARG* 2.9 20.5 + - + +
548A THR* 3.0 18.9 + - - +
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Residues in contact with ALA 545 (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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492A ALA* 3.1 35.8 - - - +
495A ASN* 3.9 13.0 - - + -
496A GLY* 4.2 9.6 - - - +
518A TYR* 3.7 25.9 - - + -
541A MET 4.2 13.1 + - - +
542A LEU* 5.5 1.3 - - - -
544A ARG* 1.3 76.6 - - - +
546A GLN* 1.3 56.7 + - - +
548A THR* 3.5 8.5 - - - -
549A GLU* 3.3 15.8 + - - +
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Residues in contact with GLN 546 (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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542A LEU* 3.1 28.6 + - + +
543A PHE* 4.3 3.4 - - - +
544A ARG 3.1 0.6 - - - -
545A ALA* 1.3 78.6 - - - +
547A ARG* 1.3 60.5 + - - +
548A THR 3.3 3.1 - - - -
549A GLU* 3.8 8.4 - - + +
550A VAL* 3.3 39.4 + - + +
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Residues in contact with ARG 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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105A HIS* 3.1 34.6 + - - -
106A THR* 3.8 23.8 - - - +
342A ASN* 5.8 0.4 - - - +
543A PHE* 3.2 40.5 + - + +
544A ARG* 2.9 12.2 + - + +
546A GLN* 1.3 83.7 - - - +
548A THR* 1.3 60.8 + - - +
550A VAL* 4.7 8.0 - - + +
551A ALA* 3.5 21.3 + - - +
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Residues in contact with THR 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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488A TYR 4.1 9.5 - - - +
492A ALA* 3.3 19.4 - - - +
517A ASP* 6.0 0.4 - - - +
518A TYR* 3.9 27.9 - - + +
519A ARG* 5.3 9.6 - - + +
544A ARG 3.0 14.9 + - - +
545A ALA* 3.4 6.6 + - - -
547A ARG* 1.3 77.9 - - - +
549A GLU* 1.3 59.7 + - - +
550A VAL 3.1 2.2 - - - -
551A ALA* 4.2 5.4 - - + +
552A GLY* 2.5 34.5 + - - -
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Residues in contact with GLU 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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489A MET* 3.3 44.0 - - - +
492A ALA* 3.5 14.0 - - + +
493A GLN* 2.9 44.6 - - - +
545A ALA 3.3 12.7 + - - +
546A GLN* 3.8 10.7 - - + +
548A THR* 1.3 82.2 + - - +
550A VAL* 1.3 57.3 + - + +
553A MET* 3.1 38.7 + - - +
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Residues in contact with VAL 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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339A GLN* 4.1 28.9 - - + +
342A ASN* 5.8 2.9 - - - +
546A GLN* 3.3 33.0 + - + +
547A ARG* 4.8 7.6 - - + +
548A THR 3.1 0.6 - - - +
549A GLU* 1.3 77.7 - - + +
551A ALA* 1.3 55.2 + - + +
553A MET* 3.1 6.6 + - - +
554A THR* 2.4 51.4 + - - +
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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