Contacts of the helix formed by residues 505 - 520 (chain A) in PDB entry 5TQW
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 505 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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494A TYR* 3.6 7.2 - - - -
498A MET* 4.9 9.5 - - + +
503A SER 3.6 2.9 + - - +
504A SER* 1.3 81.2 + - - +
506A LYS* 1.3 56.8 + - - +
507A MET 3.0 5.8 - - - -
508A LEU* 3.0 42.6 + - + +
509A LYS* 3.3 22.0 + - + +
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Residues in contact with LYS 506 (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 SER* 3.1 31.3 + - - +
505A GLU* 1.3 77.7 - - + +
507A MET* 1.3 67.0 + - - +
509A LYS* 4.5 8.2 - - - +
510A ALA* 2.7 39.1 + - - +
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Residues in contact with MET 507 (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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494A TYR* 3.4 23.8 - - + +
503A SER* 3.7 9.9 - - - +
504A SER 3.3 11.6 + - - +
505A GLU 3.0 0.8 - - - -
506A LYS* 1.3 92.3 - - + +
508A LEU* 1.3 60.1 + - - +
510A ALA* 3.9 6.7 - - + -
511A TRP* 2.9 74.8 + - + +
514A MET* 6.1 0.2 - - + -
645A LYS 5.6 0.2 - - - +
646A ARG* 5.6 2.0 - - - -
649A GLU* 3.7 38.1 - - + -
653A LEU* 5.9 0.9 - - + -
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Residues in contact with LEU 508 (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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491A LEU* 4.1 21.5 - - + +
494A TYR* 3.6 30.4 - - + -
495A SER* 5.2 7.4 - - - +
498A MET* 5.7 6.5 - - + -
505A GLU* 3.0 26.5 + - + +
507A MET* 1.3 76.8 - - - +
509A LYS* 1.3 60.9 + - + +
511A TRP* 3.0 4.9 + - - +
512A LYS* 2.8 35.0 + - + +
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Residues in contact with LYS 509 (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 GLU* 3.3 24.3 + - + +
506A LYS* 4.5 5.8 - - - +
508A LEU* 1.3 80.3 - - + +
510A ALA* 1.3 60.4 + - - +
512A LYS* 3.6 9.5 - - + +
513A GLU* 2.9 41.8 + - - +
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Residues in contact with ALA 510 (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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506A LYS 2.7 24.7 + - - +
507A MET* 3.5 13.0 - - + +
509A LYS* 1.3 76.7 - - - +
511A TRP* 1.3 65.8 + - + +
513A GLU* 3.1 10.7 + - - +
514A MET* 2.9 35.3 + - + +
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Residues in contact with TRP 511 (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* 4.2 13.7 - - + +
490A ASP* 3.3 36.3 - - + -
491A LEU* 3.7 26.0 - - + -
494A TYR* 3.5 34.3 - + + -
497A GLN* 5.5 0.4 - - - -
507A MET* 2.9 54.4 + - + +
508A LEU 3.8 2.0 - - - +
510A ALA* 1.3 76.5 - - + +
512A LYS* 1.3 61.8 + - - +
514A MET* 3.4 34.8 - - + +
515A GLU* 2.9 31.1 + - - +
646A ARG* 3.6 34.1 - - + +
649A GLU* 5.8 0.9 - - + -
650A ILE* 5.6 6.1 - - + -
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Residues in contact with LYS 512 (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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491A LEU* 5.1 12.6 - - + -
508A LEU* 2.8 25.3 + - + +
509A LYS* 3.6 11.2 - - + +
510A ALA 3.2 0.2 - - - -
511A TRP* 1.3 77.2 - - - +
513A GLU* 1.3 59.2 + - + +
515A GLU* 3.1 26.1 + - - +
516A GLU* 2.8 42.5 + - - +
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Residues in contact with GLU 513 (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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509A LYS* 2.9 27.8 + - + +
510A ALA* 3.7 6.6 - - - +
512A LYS* 1.3 73.8 - - + +
514A MET* 1.3 60.0 + - - +
516A GLU* 3.3 20.3 + - - +
517A LYS* 2.9 39.4 + - - +
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Residues in contact with MET 514 (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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483A PHE* 4.3 11.9 - - + -
487A ILE* 4.5 2.7 - - + -
507A MET* 6.1 0.2 - - + -
510A ALA* 2.9 21.1 + - + +
511A TRP* 3.4 42.0 - - + +
513A GLU* 1.3 76.4 - - - +
515A GLU* 1.3 57.2 + - - +
517A LYS* 3.1 7.2 + - - +
518A ALA* 2.9 24.6 + - - +
642A MET* 3.5 61.8 - - + +
645A LYS* 4.6 13.0 - - + +
646A ARG* 3.8 25.4 - - + +
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Residues in contact with GLU 515 (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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484A HIS* 3.1 35.1 + - + +
487A ILE* 3.3 40.0 - - + +
488A GLN* 5.7 1.9 - - - +
491A LEU* 4.3 5.4 - - - +
511A TRP 2.9 16.9 + - - +
512A LYS* 3.1 29.3 + - + +
514A MET* 1.3 75.7 - - - +
516A GLU* 1.3 58.2 + - + +
518A ALA* 3.0 9.0 + - + +
519A ILE* 2.9 36.6 + - + +
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Residues in contact with GLU 516 (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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512A LYS* 2.8 28.5 + - + +
513A GLU* 3.5 24.6 - - - +
515A GLU* 1.3 74.5 - - + +
517A LYS* 1.3 64.4 + - + +
519A ILE* 3.2 20.1 + - + -
520A HIS* 3.0 42.4 + - + +
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Residues in contact with LYS 517 (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 GLU* 2.9 23.1 + - - +
514A MET* 3.1 8.0 + - - +
516A GLU* 1.3 77.9 - - + +
518A ALA* 1.3 60.8 + - - +
520A HIS* 3.2 10.5 + - + +
521A TYR* 3.1 35.1 - - + +
638A THR* 6.0 1.7 - - + +
642A MET* 3.7 43.0 - - + +
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Residues in contact with ALA 518 (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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480A LEU* 3.4 50.8 - - + +
483A PHE* 4.7 16.4 - - + -
484A HIS* 5.7 4.5 - - + +
487A ILE* 5.2 1.1 - - + -
514A MET 2.9 12.6 + - - +
515A GLU* 3.0 17.9 + - + +
517A LYS* 1.3 76.8 - - - +
519A ILE* 1.3 61.8 + - - +
520A HIS 3.5 0.2 + - - -
521A TYR 4.3 0.3 + - - -
639A VAL* 6.2 1.3 - - + -
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Residues in contact with ILE 519 (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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480A LEU* 5.4 0.3 - - - +
515A GLU* 2.9 18.7 + - + +
516A GLU* 3.3 30.7 - - + +
517A LYS 3.2 0.4 - - - -
518A ALA* 1.3 80.6 - - - +
520A HIS* 1.3 72.4 + - + +
521A TYR* 2.8 12.2 + - - -
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Residues in contact with HIS 520 (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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516A GLU* 3.0 38.9 + - + +
517A LYS* 3.2 14.4 + - + +
519A ILE* 1.3 94.2 - - + +
521A TYR* 1.3 77.1 + - + +
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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