Contacts of the helix formed by residues 501 - 508 (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 LEU 501 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470Z VAL* 4.5 15.3 - - + +
478Z ARG* 4.5 6.1 - - - +
482Z ILE* 3.2 45.1 - - + +
485Z LEU* 3.7 33.7 - - + -
497Z VAL 4.1 0.4 + - - -
498Z LEU 3.8 4.1 + - - +
500Z LEU* 1.3 95.7 - - + +
502Z LEU* 1.3 60.7 + - - +
503Z PRO 3.4 1.1 - - - -
504Z VAL* 3.3 31.2 + - + +
505Z MET 3.1 19.6 + - - -
518Z THR* 4.4 1.9 - - - +
522Z CYS* 3.9 18.6 - - - -
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Residues in contact with LEU 502 (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* 3.4 34.0 + - + +
499Z THR* 4.0 8.3 - - + -
501Z LEU* 1.3 75.4 - - - +
503Z PRO* 1.3 66.8 - - + +
504Z VAL 3.2 0.2 - - - -
505Z MET* 3.3 10.2 + - + +
506Z GLY* 2.9 24.1 + - - -
519Z ALA* 6.2 0.2 - - - -
522Z CYS* 3.7 26.9 - - + -
534Z VAL* 3.8 29.4 - - + -
536Z SER* 4.0 20.5 - - - -
537Z THR* 3.2 29.8 - - + +
540Z GLN* 4.9 4.7 - - + +
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Residues in contact with PRO 503 (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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499Z THR* 3.3 23.3 - - - +
500Z LEU 3.7 9.4 - - - +
501Z LEU 3.6 1.3 - - - -
502Z LEU* 1.3 94.5 - - + +
504Z VAL* 1.3 58.3 + - + +
506Z GLY* 3.5 2.7 - - - +
507Z ASP* 3.0 37.1 + - - +
536Z SER* 5.7 2.0 - - - +
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Residues in contact with VAL 504 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478Z ARG* 3.0 45.1 - - - +
482Z ILE* 4.5 0.7 - - + -
500Z LEU 4.3 4.7 - - - +
501Z LEU* 3.3 32.6 + - + +
502Z LEU 3.2 0.6 - - - -
503Z PRO* 1.3 76.2 - - + +
505Z MET* 1.3 63.4 + - - +
507Z ASP* 3.8 5.8 + - - +
508Z SER 3.8 9.9 + - - -
513Z GLU* 3.9 9.3 - - + +
514Z VAL* 3.1 44.4 - - + +
518Z THR* 5.1 0.4 - - - -
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Residues in contact with MET 505 (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 3.1 10.3 + - - +
502Z LEU* 3.3 13.0 + - + +
504Z VAL* 1.3 75.2 - - - +
506Z GLY* 1.3 56.6 + - - +
508Z SER* 3.1 20.9 + - - +
514Z VAL 4.1 2.9 - - - -
515Z ALA* 4.3 4.0 - - - -
516Z GLY 4.2 8.5 - - - +
518Z THR* 3.7 24.1 - - + +
519Z ALA* 3.4 28.5 - - + +
522Z CYS* 4.4 4.7 - - - -
540Z GLN* 3.5 34.9 - - - +
554Z TYR* 3.5 26.2 - - + +
558Z LEU* 3.6 25.4 - - + -
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Residues in contact with GLY 506 (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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502Z LEU 2.9 15.2 + - - -
503Z PRO* 3.1 6.4 + - - -
505Z MET* 1.3 76.7 - - - +
507Z ASP* 1.3 64.7 + - - +
508Z SER* 3.2 8.0 + - - -
540Z GLN* 3.8 19.3 - - - -
543Z MET* 3.7 20.5 - - - +
544Z GLU* 5.4 0.5 - - - +
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Residues in contact with ASP 507 (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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503Z PRO* 3.0 23.6 + - - +
504Z VAL* 3.8 2.9 + - - +
506Z GLY* 1.3 76.8 - - - +
508Z SER* 1.3 68.0 + - - +
509Z LYS* 3.4 1.4 + - - +
513Z GLU* 3.5 37.2 - - + +
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Residues in contact with SER 508 (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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504Z VAL 3.8 7.1 + - - -
505Z MET* 3.1 18.4 + - - +
506Z GLY 3.2 8.0 + - - -
507Z ASP* 1.3 81.7 - - - +
509Z LYS* 1.3 59.1 + - - +
514Z VAL 4.6 0.9 - - - -
515Z ALA* 4.1 16.0 - - - +
540Z GLN* 4.5 2.9 + - - -
543Z MET* 5.8 0.2 - - - +
544Z GLU* 4.0 24.2 + - - +
554Z TYR* 3.3 20.9 + - - -
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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