Contacts of the helix formed by residues 558 - 566 (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 LEU 558 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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519Z ALA* 4.0 12.5 - - + +
538Z ILE* 4.9 12.6 - - + +
541Z THR* 6.2 1.8 - - - -
542Z ILE* 4.3 22.9 - - + +
554Z TYR 3.6 18.1 + - - +
555Z ALA 3.6 2.6 + - - +
556Z ARG 3.1 0.6 - - - -
557Z TRP* 1.3 76.8 - - - +
559Z PRO* 1.4 70.8 - - - +
561Z GLY* 3.1 6.9 + - - -
562Z LEU* 3.4 7.4 + - - +
579Z ALA* 3.9 8.5 - - + +
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Residues in contact with PRO 559 (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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555Z ALA 3.0 17.6 - - - +
556Z ARG* 3.0 12.3 - - + +
558Z LEU* 1.4 80.6 - - - +
560Z LEU* 1.3 60.9 + - - +
561Z GLY 2.8 3.3 + - - -
562Z LEU* 2.9 13.9 + - - +
563Z GLY 3.4 6.2 + - - -
579Z ALA* 3.1 29.8 - - - +
580Z LEU* 3.6 22.4 - - + +
587Z PHE* 6.6 0.2 - - + -
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Residues in contact with LEU 560 (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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520Z LEU* 5.6 4.4 - - + -
523Z GLY* 5.0 0.3 - - - -
556Z ARG 3.1 10.7 + - - +
557Z TRP* 5.1 0.9 - - - +
559Z PRO* 1.3 77.5 - - + +
561Z GLY* 1.3 64.0 + - - +
562Z LEU 3.3 0.2 - - - -
563Z GLY* 3.2 13.3 + - - +
564Z LEU* 3.4 14.2 + - - +
580Z LEU* 5.0 1.1 - - - +
797Z LEU* 6.4 1.6 - - + -
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Residues in contact with GLY 561 (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* 3.6 24.9 - - - -
520Z LEU* 4.7 2.0 - - - +
522Z CYS 4.9 0.2 - - - -
523Z GLY* 3.3 22.6 - - - -
557Z TRP 3.5 11.2 + - - -
558Z LEU 3.1 8.3 + - - -
559Z PRO 2.8 4.0 + - - -
560Z LEU* 1.3 77.3 - - - +
562Z LEU* 1.3 58.4 + - - -
564Z LEU 3.9 2.8 + - - -
565Z ASN* 4.1 6.2 + - - +
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Residues in contact with LEU 562 (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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534Z VAL* 5.7 7.0 - - - +
535Z THR* 6.5 0.4 - - - -
538Z ILE* 5.7 5.8 - - + -
558Z LEU 3.4 5.4 + - - +
559Z PRO 2.9 7.0 + - - +
561Z GLY* 1.3 74.9 - - - +
563Z GLY* 1.3 65.2 + - - +
564Z LEU 3.1 1.0 + - - -
565Z ASN* 3.4 12.0 + - - +
566Z HIS* 3.8 8.8 + - - +
575Z ALA 4.7 2.0 - - - +
576Z ILE* 3.5 44.9 - - + +
579Z ALA* 4.8 6.1 - - + -
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Residues in contact with GLY 563 (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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559Z PRO 3.4 5.5 + - - -
560Z LEU* 3.2 12.8 + - - -
562Z LEU* 1.3 79.1 - - - +
564Z LEU* 1.3 59.5 + - - +
566Z HIS* 4.7 2.8 + - - +
567Z LEU* 5.2 5.2 + - - +
576Z ILE* 4.8 7.6 + - - -
580Z LEU* 6.0 3.4 - - - -
598Z CYS* 6.0 1.4 - - - +
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Residues in contact with LEU 564 (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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523Z GLY* 3.2 25.4 - - - +
527Z VAL* 3.9 3.8 - - - +
528Z GLY 3.4 10.2 + - - -
560Z LEU 3.4 11.8 + - - +
561Z GLY 3.9 0.2 + - - -
562Z LEU 3.2 0.8 - - - -
563Z GLY* 1.3 81.2 - - - +
565Z ASN* 1.3 66.1 + - - +
566Z HIS 3.2 1.3 + - - -
567Z LEU* 3.7 9.5 + - - +
790Z GLN* 6.0 0.5 - - - +
794Z ALA* 4.7 16.6 - - + -
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Residues in contact with ASN 565 (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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522Z CYS 5.0 2.2 - - - +
523Z GLY* 4.0 8.0 + - - +
526Z ALA* 3.1 22.0 - - + +
527Z VAL* 3.1 12.0 - - - +
528Z GLY 2.4 5.4 + - - -
529Z SER 2.4 40.8 + - - +
531Z ASN* 5.7 4.5 - - + -
534Z VAL* 5.8 6.7 - - + -
561Z GLY 4.1 9.3 + - - +
562Z LEU* 3.4 8.7 + - - +
564Z LEU* 1.3 79.3 - - - +
566Z HIS* 1.3 51.0 + - - +
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Residues in contact with HIS 566 (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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528Z GLY 3.7 4.3 - - - -
529Z SER 3.2 12.2 + - - +
530Z CYS* 5.0 2.7 - - - +
562Z LEU 3.8 11.5 + - - +
563Z GLY 5.4 2.0 - - - +
564Z LEU 3.2 1.2 + - - -
565Z ASN* 1.3 79.5 - - - +
567Z LEU* 1.3 68.8 + - - +
568Z GLY 3.2 2.6 + - - -
569Z LYS* 3.6 18.0 + - - +
573Z ILE* 3.9 28.2 - - + +
576Z ILE* 4.6 9.9 - - + -
598Z CYS* 5.8 1.6 - - + -
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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