Contacts of the helix formed by residues 511 - 523 (chain C) in PDB entry 5G04
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 THR 511 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475C LYS* 5.6 9.5 - - - +
478C GLU* 5.8 0.2 - - - -
490C TYR* 5.7 1.2 + - - -
509C GLU* 4.7 10.7 + - - +
510C SER* 1.3 79.5 + - - +
512C ALA* 1.3 71.3 + - - +
513C PHE 3.3 0.9 - - - -
514C ARG* 3.1 48.2 + - - +
515C TYR* 3.2 10.7 + - - +
536C CYS* 6.1 0.4 - - - -
543C ARG* 6.3 1.6 - - - +
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Residues in contact with ALA 512 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478C GLU* 5.2 0.4 - - - -
490C TYR* 3.6 43.7 - - + -
493C TYR* 6.4 1.6 - - + -
494C ILE* 5.1 7.2 - - + -
509C GLU* 4.8 7.4 - - + +
510C SER 2.4 18.3 + - - +
511C THR* 1.3 73.9 + - - +
513C PHE* 1.3 60.0 + - + +
515C TYR* 3.2 11.3 + - - +
516C LEU* 2.9 32.4 + - - +
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Residues in contact with PHE 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494C ILE* 3.7 44.2 - - + -
498C TYR* 5.4 6.7 - + - -
509C GLU 3.8 17.7 - - - -
510C SER* 3.2 8.6 + - - +
512C ALA* 1.3 73.0 - - + +
514C ARG* 1.3 66.3 + - - +
516C LEU* 3.2 9.7 + - + -
517C ALA* 3.0 21.0 + - - +
532C CYS* 3.1 38.1 - - - +
535C LYS* 5.2 9.6 - - + -
536C CYS* 4.7 10.8 - - + +
539C PHE* 3.5 42.0 - + - -
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Residues in contact with ARG 514 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511C THR* 3.1 45.1 + - - +
513C PHE* 1.3 76.5 - - - +
515C TYR* 1.3 65.7 + - - +
517C ALA* 3.3 8.8 + - - +
518C GLN* 3.1 40.4 + - - +
536C CYS* 3.7 26.7 - - - -
543C ARG* 3.4 41.1 - - - +
545C GLU* 4.0 13.1 + - - -
546C GLY* 5.1 0.7 - - - -
549C LEU* 3.8 14.1 - - + +
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Residues in contact with TYR 515 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478C GLU* 3.0 38.8 - - + +
482C GLU 4.5 6.3 - - - -
483C SER* 2.4 41.9 + - - -
486C ALA* 2.9 12.7 - - + +
487C ALA* 2.9 35.8 + - + -
490C TYR* 3.7 17.7 - + - -
511C THR 3.2 7.5 + - - +
512C ALA 3.2 7.7 + - - +
514C ARG* 1.3 86.0 - - - +
516C LEU* 1.3 62.4 + - + +
518C GLN* 3.2 30.7 - - - +
519C TYR* 3.0 24.3 + - + +
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Residues in contact with LEU 516 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487C ALA* 3.6 38.6 - - + +
490C TYR* 3.8 13.2 - - + -
491C ILE* 4.0 15.5 - - + -
494C ILE* 3.7 29.4 - - + -
512C ALA 2.9 19.2 + - - +
513C PHE* 3.2 19.7 + - + +
515C TYR* 1.3 79.7 - - + +
517C ALA* 1.3 59.1 + - - +
519C TYR* 3.3 7.5 + - + +
520C TYR* 2.9 45.2 + - + -
532C CYS* 3.7 9.0 - - - -
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Residues in contact with ALA 517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513C PHE 3.0 13.2 + - - +
514C ARG* 3.3 10.5 + - - +
516C LEU* 1.3 75.9 - - - +
518C GLN* 1.3 56.8 + - - +
520C TYR 3.4 0.9 + - - -
521C PHE* 2.9 26.7 + - - +
529C ALA* 3.5 31.9 - - + +
532C CYS* 3.7 8.0 - - + -
533C ALA* 3.9 13.7 - - + +
549C LEU* 3.7 20.4 - - + +
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Residues in contact with GLN 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478C GLU* 5.2 0.2 - - - +
514C ARG* 3.1 26.1 + - - +
515C TYR* 3.2 43.3 - - - +
517C ALA* 1.3 72.3 - - - +
519C TYR* 1.3 60.2 + - - +
521C PHE* 3.4 10.7 - - + +
522C LYS* 3.1 27.5 + - - +
549C LEU* 4.1 15.6 - - + +
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Residues in contact with TYR 519 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483C SER* 3.6 30.5 - - - +
484C GLU* 4.5 26.4 + - + +
487C ALA* 3.8 27.4 - - + -
491C ILE* 6.6 0.2 - - + -
515C TYR* 3.0 17.5 + - + +
516C LEU* 3.3 15.5 + - + +
518C GLN* 1.3 76.6 - - - +
520C TYR* 1.3 100.6 + + - +
522C LYS* 3.3 5.0 + - - +
523C CYS* 2.9 53.4 + - + +
525C LEU* 5.7 0.5 - - - +
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Residues in contact with TYR 520 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491C ILE* 5.0 12.7 - - + +
516C LEU* 2.9 37.8 + - + +
517C ALA* 3.4 0.6 + - - -
519C TYR* 1.3 102.4 - + - +
521C PHE* 1.3 56.9 + - - +
523C CYS* 3.4 3.7 + - + -
524C LYS* 3.0 22.3 + - - -
525C LEU* 3.1 37.3 + - + +
528C GLU* 3.2 48.7 + - + -
529C ALA* 3.6 23.8 - - + -
532C CYS* 5.0 5.2 - - + -
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Residues in contact with PHE 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517C ALA 2.9 14.8 + - - +
518C GLN* 3.4 14.6 - - + +
520C TYR* 1.3 76.1 - - - +
522C LYS* 1.3 64.4 + - + +
524C LYS* 3.2 6.4 + - - +
526C TRP* 3.2 44.1 - + - -
529C ALA* 4.0 3.5 - - - +
549C LEU* 3.8 13.9 - - + -
552C GLN* 4.0 35.0 - - + -
553C ILE* 3.2 30.5 - - + -
556C LEU* 5.0 5.2 - - + -
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Residues in contact with LYS 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483C SER* 4.2 25.5 - - - +
518C GLN 3.1 13.1 + - - +
519C TYR* 3.8 5.8 - - - +
521C PHE* 1.3 79.1 - - + +
523C CYS* 1.3 60.5 + - - +
524C LYS* 3.1 9.1 + - - +
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Residues in contact with CYS 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519C TYR* 2.9 44.0 + - + +
520C TYR* 3.7 11.4 - - - +
521C PHE 3.3 0.4 - - - -
522C LYS* 1.3 75.1 - - - +
524C LYS* 1.3 74.1 + - - +
525C LEU* 3.2 26.7 + - + +
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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