Contacts of the helix formed by residues 517 - 527 (chain Z) in PDB entry 5L4K
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 517 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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479Z LEU* 4.2 25.6 - - + -
483Z PHE* 4.4 18.6 - - + -
515Z ALA 3.2 3.3 + - - +
516Z GLY* 1.3 70.8 - - - -
518Z THR* 1.3 60.1 + - - +
519Z ALA 3.3 0.4 - - - -
520Z LEU* 3.1 25.4 + - + -
521Z ALA* 3.0 22.9 + - - +
557Z TRP* 3.3 37.5 - - + +
796Z LEU* 4.0 28.5 - - + -
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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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479Z LEU* 4.7 3.3 - - - +
482Z ILE* 3.3 30.7 - - + +
501Z LEU 4.4 1.6 - - - +
505Z MET* 3.7 30.7 - - + +
514Z VAL* 3.4 34.0 - - + +
515Z ALA 3.7 3.0 + - - -
516Z GLY 3.0 1.0 + - - -
517Z VAL* 1.3 79.6 - - - +
519Z ALA* 1.3 60.7 + - - +
521Z ALA* 3.3 7.2 + - + +
522Z CYS* 2.9 35.4 + - - -
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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* 3.4 22.3 - - + -
516Z GLY 3.4 0.6 + - - -
517Z VAL 3.3 0.6 - - - -
518Z THR* 1.3 78.8 - - - +
520Z LEU* 1.3 57.2 + - - +
522Z CYS* 3.5 7.4 + - - +
523Z GLY 2.9 21.1 + - - -
537Z THR* 5.2 4.7 - - + +
540Z GLN* 4.1 7.4 - - - +
558Z LEU* 3.8 46.2 - - + +
561Z GLY* 3.2 12.9 - - - -
565Z ASN* 4.5 0.9 + - - -
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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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483Z PHE* 5.5 2.7 - - + -
516Z GLY 4.3 0.2 + - - -
517Z VAL* 3.1 25.2 + - + +
519Z ALA* 1.3 76.8 - - - +
521Z ALA* 1.3 60.4 + - - +
522Z CYS 3.2 0.2 - - - -
523Z GLY 3.3 0.5 + - - -
524Z MET* 2.8 41.7 + - + +
557Z TRP* 3.8 33.0 + - + +
560Z LEU* 3.4 39.5 - - + -
561Z GLY* 3.9 8.3 - - - +
564Z LEU* 4.0 13.2 - - + -
782Z HIS* 5.3 3.6 - - + -
783Z SER* 4.7 19.1 - - - +
797Z LEU* 6.3 1.6 - - + -
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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* 4.1 7.4 - - + +
483Z PHE* 3.9 40.1 - - + +
486Z GLY* 3.3 17.1 - - - +
517Z VAL* 3.0 13.3 + - - +
518Z THR* 3.3 11.2 + - + +
520Z LEU* 1.3 76.7 - - - +
522Z CYS* 1.3 58.8 + - - +
524Z MET* 3.7 11.4 - - - -
525Z ILE 2.9 20.4 + - - -
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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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482Z ILE 6.1 0.9 - - - -
498Z LEU* 3.8 3.7 - - - +
501Z LEU* 3.9 27.6 - - - -
502Z LEU* 3.7 33.9 - - + -
505Z MET* 4.4 3.4 - - - -
518Z THR* 2.9 32.8 + - - +
519Z ALA* 3.7 7.9 - - - +
520Z LEU 3.2 0.2 - - - -
521Z ALA* 1.3 76.0 - - - +
523Z GLY* 1.3 59.5 + - - +
525Z ILE* 2.9 26.9 - - + +
526Z ALA* 3.0 13.3 + - - +
537Z THR* 5.9 0.4 - - + -
565Z ASN* 3.6 6.6 - - - +
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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 2.9 13.0 + - - -
520Z LEU 3.3 3.1 + - - -
522Z CYS* 1.3 75.2 - - - +
524Z MET* 1.3 64.6 + - - +
526Z ALA* 3.7 0.3 - - - +
527Z VAL* 3.0 19.6 + - - +
561Z GLY* 3.4 25.6 - - - -
564Z LEU* 3.1 21.8 - - - +
565Z ASN* 3.4 6.2 - - - +
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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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483Z PHE* 3.9 31.4 - - + -
486Z GLY 3.7 3.6 - - - +
487Z LEU* 4.2 27.4 - - + +
490Z ALA* 2.8 24.1 - - + +
520Z LEU* 2.8 29.5 + - + +
521Z ALA* 3.5 14.1 - - - +
522Z CYS 3.3 0.2 - - - -
523Z GLY* 1.3 74.8 - - - +
525Z ILE* 1.3 65.8 + - - +
526Z ALA 3.2 0.2 + - - -
527Z VAL* 3.1 17.4 - - - +
564Z LEU* 4.3 6.1 - - + -
779Z CYS* 4.0 25.1 - - + -
783Z SER* 5.1 6.5 - - - -
799Z VAL* 4.2 17.9 - - + -
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Residues in contact with ILE 525 (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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485Z LEU* 3.3 43.5 - - + +
486Z GLY* 2.9 17.3 + - - +
489Z TYR* 2.9 45.6 - - + +
490Z ALA* 3.7 4.1 - - - -
494Z ARG 5.5 0.4 - - - +
497Z VAL 3.6 16.6 - - - +
498Z LEU* 3.3 30.0 - - + +
521Z ALA 2.9 7.2 + - - +
522Z CYS* 2.9 32.3 - - + +
524Z MET* 1.3 75.5 - - - +
526Z ALA* 1.3 62.9 + - - +
529Z SER* 3.3 4.3 + - - -
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Residues in contact with ALA 526 (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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495Z GLU* 5.7 1.3 - - - +
498Z LEU* 4.0 16.2 - - + -
522Z CYS 3.0 11.5 + - - +
523Z GLY 3.7 1.8 - - - +
524Z MET 3.1 0.4 - - - -
525Z ILE* 1.3 76.6 - - - +
527Z VAL* 1.3 63.8 + - - +
529Z SER* 3.2 24.7 + - - -
531Z ASN* 3.4 13.0 + - - +
534Z VAL* 5.3 0.9 - - + -
565Z ASN* 3.0 44.6 - - + +
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Residues in contact with VAL 527 (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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312Z GLU* 3.3 29.2 - - + +
490Z ALA* 2.6 27.0 - - - +
523Z GLY 3.0 14.4 + - - +
524Z MET* 3.1 23.1 - - - +
526Z ALA* 1.3 77.9 - - - +
528Z GLY* 1.3 56.2 + - - +
531Z ASN* 3.5 7.6 - - - +
564Z LEU* 3.5 23.5 + - + +
567Z LEU* 3.9 24.0 - - + +
775Z THR* 4.9 10.5 - - + +
778Z LEU* 6.1 0.9 - - + -
779Z CYS* 4.4 11.9 - - - -
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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