Contacts of the helix formed by residues 519 - 530 (chain G) in PDB entry 4D1Q
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 CYS 519 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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516G PRO* 4.9 6.3 - - + +
518G VAL* 1.3 82.0 - - - +
520G PRO* 1.3 88.7 - - + +
521G SER* 3.8 12.8 - - - -
522G ASP* 2.8 36.4 + - - +
523G GLU* 2.8 16.9 + - - -
553G LYS* 6.0 0.2 - - - -
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Residues in contact with PRO 520 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455G LEU* 4.7 12.1 - - + -
458G MET* 4.5 35.4 - - + +
459G GLU* 4.3 20.6 - - - +
462G GLU* 4.5 13.5 - - - +
519G CYS* 1.3 93.5 - - + +
521G SER* 1.3 59.3 + - - +
522G ASP 2.8 1.2 + - - -
523G GLU* 2.7 21.9 + - + +
524G PHE* 3.0 12.4 + - - +
553G LYS* 4.1 21.3 - - + -
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Residues in contact with SER 521 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451G LYS* 4.1 20.0 + - - +
455G LEU* 4.4 12.8 - - - +
519G CYS* 3.8 13.5 - - - -
520G PRO* 1.3 76.1 - - - +
522G ASP* 1.3 59.7 + - - +
524G PHE* 3.8 9.6 - - - +
525G GLU* 3.1 32.7 + - - +
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Residues in contact with ASP 522 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518G VAL* 4.3 9.9 - - + -
519G CYS* 2.8 50.7 + - - +
521G SER* 1.3 73.5 + - - +
523G GLU* 1.3 51.2 + - - +
524G PHE 3.1 1.3 - - - -
525G GLU* 3.0 6.0 + - - +
526G PHE* 2.7 47.8 + - + -
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Residues in contact with GLU 523 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458G MET* 5.2 1.1 - - - -
518G VAL* 4.6 9.9 - - + +
519G CYS* 2.8 24.7 + - - +
520G PRO* 2.7 11.5 + - + +
522G ASP* 1.3 71.3 - - - +
524G PHE* 1.3 58.7 - - - +
526G PHE* 3.1 12.5 + - + +
527G TYR* 2.8 29.6 + - - +
550G LYS 5.3 0.7 - - - +
551G TYR* 2.9 46.9 - - + +
552G PRO* 3.7 9.4 - - + +
553G LYS* 3.0 38.1 + - - +
554G LEU* 3.1 20.9 + - + -
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Residues in contact with PHE 524 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434G PHE* 3.4 38.8 - + - -
447G VAL* 4.0 11.2 - - + -
450G ILE* 4.4 0.7 - - + -
451G LYS* 3.5 57.9 - - + -
454G CYS* 4.2 21.8 - - + -
455G LEU* 4.4 4.5 - - + -
458G MET* 5.2 0.7 - - + -
520G PRO 3.0 12.0 + - - +
521G SER* 3.8 12.3 - - - +
523G GLU* 1.3 78.2 - - - +
525G GLU* 1.3 66.3 + - - +
527G TYR* 3.0 10.1 + - + +
528G ARG* 2.9 44.5 + - + +
554G LEU* 4.7 15.1 - - + +
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Residues in contact with GLU 525 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451G LYS* 3.0 29.3 + - - +
521G SER 3.1 21.2 + - - +
522G ASP* 3.0 7.6 + - - +
524G PHE* 1.3 83.8 - - - +
526G PHE* 1.3 63.2 + - + +
528G ARG* 3.6 33.8 + - - +
529G LYS* 3.5 24.8 + - - +
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Residues in contact with PHE 526 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531B ILE* 3.7 44.6 - - + -
533B ILE* 5.8 2.9 - - + -
518G VAL* 3.4 31.6 - - + -
522G ASP* 2.7 33.5 + - + -
523G GLU* 3.4 9.2 - - - +
525G GLU* 1.3 72.2 - - + +
527G TYR* 1.3 65.6 - - - +
529G LYS* 3.2 30.7 - - + +
530G GLU* 3.6 10.9 + - - +
550G LYS* 4.9 5.2 + - + -
551G TYR* 3.8 16.6 - + + -
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Residues in contact with TYR 527 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434G PHE* 3.4 50.0 + + - -
435G PHE* 4.0 4.3 - + - -
437G PRO* 3.1 38.0 - - + +
439G ALA* 3.8 16.3 - - + +
523G GLU 2.8 13.2 + - - +
524G PHE* 3.2 9.0 - - + +
526G PHE* 1.3 72.4 - - - +
528G ARG* 1.3 53.2 + - - +
529G LYS 2.7 3.9 + - - -
530G GLU* 2.6 41.3 + - + +
543G TRP* 3.8 21.5 - + - -
544G TRP* 3.3 35.2 - + - -
551G TYR* 3.6 12.8 - + + -
554G LEU* 3.6 17.0 - - + -
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Residues in contact with ARG 528 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434G PHE* 4.1 26.0 - - + -
439G ALA* 5.5 6.5 - - + +
443G GLN* 5.4 15.2 - - - +
447G VAL* 4.1 34.7 + - - +
451G LYS* 5.7 2.0 - - - +
524G PHE* 2.9 24.3 + - + +
525G GLU* 3.7 34.7 + - - +
526G PHE 3.4 0.4 - - - -
527G TYR* 1.3 78.3 - - - +
529G LYS* 1.3 59.6 + - - +
530G GLU 3.3 3.9 + - - +
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Residues in contact with LYS 529 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525G GLU 3.5 14.0 + - - +
526G PHE* 3.2 28.1 + - + +
527G TYR 2.7 3.4 + - - -
528G ARG* 1.3 76.0 - - - +
530G GLU* 1.3 64.3 + - - +
531G ILE* 3.7 12.6 + - - +
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Residues in contact with GLU 530 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529B LYS* 3.2 30.9 + - - +
437G PRO* 5.1 7.3 - - + +
439G ALA* 5.8 3.5 - - - +
440G LEU* 5.8 2.6 - - - +
526G PHE 3.6 7.8 + - - +
527G TYR* 2.6 29.6 + - + +
528G ARG 4.3 4.0 - - - +
529G LYS* 1.3 76.8 - - - +
531G ILE* 1.3 63.5 + - - +
532G VAL* 4.1 6.7 + - + -
543G TRP* 3.4 27.3 - - + -
547G ASN* 3.7 8.7 - - - +
550G LYS* 2.9 21.2 + - - -
551G TYR* 2.6 27.5 + - - +
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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