Contacts of the helix formed by residues 514 - 524 (chain Z) in PDB entry 5GJQ
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 514 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475Z ASN 3.4 25.6 - - - +
478Z ARG* 3.7 11.4 - - + -
479Z LEU* 3.8 12.6 - - + +
482Z ILE* 5.3 2.5 - - + +
509Z LYS 2.4 17.1 + - - -
510Z SER* 3.2 20.0 - - - +
512Z MET 3.0 2.4 - - - +
513Z GLU* 1.3 70.5 - - - +
515Z ALA* 1.3 61.9 + - - -
516Z GLY* 2.9 5.5 + - - -
517Z VAL* 3.4 15.0 + - + +
518Z THR* 3.4 8.1 + - - -
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Residues in contact with ALA 515 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501Z LEU 4.4 0.4 - - - +
504Z VAL* 3.1 43.7 - - + +
505Z MET* 3.4 16.4 - - + +
508Z SER* 4.6 6.1 - - - +
509Z LYS 3.5 2.0 + - - -
513Z GLU* 2.9 7.0 + - + +
514Z VAL* 1.3 74.2 - - - +
516Z GLY* 1.3 67.8 + - - +
518Z THR* 3.0 20.3 + - - -
519Z ALA* 3.1 13.0 + - - +
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Residues in contact with GLY 516 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508Z SER* 5.9 0.4 - - - +
509Z LYS 4.8 1.6 + - - +
510Z SER* 4.6 16.8 - - - +
514Z VAL 2.9 3.4 + - - -
515Z ALA* 1.3 81.9 - - - +
517Z VAL* 1.3 59.2 + - - -
518Z THR 3.0 0.2 + - - -
519Z ALA* 3.2 10.4 + - - +
520Z LEU 3.9 1.0 + - - -
554Z TYR* 5.8 4.5 - - - -
557Z TRP* 3.0 33.2 - - - +
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Residues in contact with VAL 517 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479Z LEU* 6.0 3.1 - - - +
482Z ILE* 5.1 4.9 - - + +
510Z SER* 5.8 1.0 - - - -
514Z VAL 3.4 7.1 + - - +
516Z GLY* 1.3 72.9 - - - +
518Z THR* 1.3 62.2 + - - +
519Z ALA 3.4 0.2 - - - -
520Z LEU* 3.0 14.9 + - + +
521Z ALA* 2.9 18.8 + - - +
557Z TRP* 4.9 1.6 - - - -
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Residues in contact with THR 518 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478Z ARG* 6.6 0.2 - - - -
482Z ILE* 4.2 15.4 - - - +
501Z LEU* 4.1 23.1 - - - -
505Z MET* 6.2 0.4 - - - -
514Z VAL 3.4 6.2 + - - -
515Z ALA* 3.0 25.3 + - - -
516Z GLY 3.0 1.0 - - - -
517Z VAL* 1.3 74.0 - - - +
519Z ALA* 1.3 52.9 + - - +
521Z ALA* 2.7 13.5 + - - +
522Z CYS* 2.3 39.1 + - - +
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Residues in contact with ALA 519 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505Z MET* 6.0 4.7 - - + -
515Z ALA 3.1 7.0 + - - +
516Z GLY 3.5 7.9 - - - +
518Z THR* 1.3 76.5 - - - +
520Z LEU* 1.3 51.2 + - - +
522Z CYS* 3.2 11.6 - - - +
523Z GLY* 2.4 33.1 + - - -
557Z TRP* 3.2 25.6 - - + +
558Z LEU* 4.0 10.5 - - + -
561Z GLY* 3.6 10.1 - - - -
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Residues in contact with LEU 520 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516Z GLY 3.9 0.8 + - - +
517Z VAL* 3.0 20.4 + - + +
518Z THR 3.0 0.8 - - - -
519Z ALA* 1.3 76.9 - - - +
521Z ALA* 1.3 57.9 + - - +
523Z GLY* 3.0 6.5 + - - +
524Z MET* 2.9 24.3 + - - +
557Z TRP* 3.9 10.8 + - - +
560Z LEU* 5.6 3.8 - - + -
561Z GLY* 4.7 4.5 - - - +
794Z ALA 5.6 0.5 - - - +
798Z THR* 5.4 18.4 - - - -
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Residues in contact with ALA 521 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482Z ILE* 3.0 35.7 - - + +
483Z PHE* 5.0 1.3 - - - -
486Z GLY* 3.5 18.4 - - - +
517Z VAL 2.9 9.9 + - - +
518Z THR* 2.7 15.2 + - - +
520Z LEU* 1.3 69.1 - - - +
522Z CYS* 1.3 57.3 + - - +
524Z MET* 2.7 28.8 + - - +
525Z ILE* 3.3 5.9 + - - +
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Residues in contact with CYS 522 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498Z LEU* 5.7 12.8 - - + +
501Z LEU* 5.8 4.7 - - + -
518Z THR 2.3 27.6 + - - +
519Z ALA* 3.2 18.4 - - - +
521Z ALA* 1.3 63.1 - - - +
523Z GLY* 1.3 59.2 + - - +
524Z MET 3.0 4.3 - - - -
525Z ILE* 3.0 23.6 + - - +
526Z ALA* 4.1 3.5 + - - +
565Z ASN* 5.0 3.6 - - - +
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Residues in contact with GLY 523 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519Z ALA 2.4 20.8 + - - -
520Z LEU 3.0 8.2 + - - -
522Z CYS* 1.3 68.7 - - - +
524Z MET* 1.3 57.0 + - - +
525Z ILE 3.3 1.0 + - - -
527Z VAL* 4.2 7.3 - - - +
560Z LEU 5.0 0.2 - - - -
561Z GLY* 3.3 27.1 + - - -
564Z LEU* 3.2 27.3 - - - +
565Z ASN* 4.0 9.8 + - - -
794Z ALA* 4.4 0.4 - - - +
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Residues in contact with MET 524 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486Z GLY* 3.9 14.8 - - - +
487Z LEU* 5.4 0.4 - - - -
490Z ALA* 3.1 31.4 + - + +
520Z LEU 2.9 9.2 + - - +
521Z ALA* 2.7 19.0 + - - +
523Z GLY* 1.3 78.7 - - - +
525Z ILE* 1.3 56.7 + - - +
527Z VAL* 4.7 5.9 - - - +
794Z ALA* 4.2 25.5 - - + +
798Z THR* 6.2 1.1 - - - -
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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