Contacts of the helix formed by residues 480 - 490 (chain F) 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 ASN 480 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475F ALA* 2.9 19.1 + - + +
476F LEU 4.4 0.2 + - - -
478F SER* 3.5 8.7 + - - +
479F TYR* 1.4 73.5 + - - +
481F CYS* 1.3 63.6 + - - +
482F LYS* 3.4 4.4 + - - +
483F GLU* 3.1 45.8 + - - +
484F ALA* 3.2 18.5 + - - +
667F GLN* 5.5 7.4 - - - +
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Residues in contact with CYS 481 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476F LEU* 5.0 5.6 - - - +
479F TYR* 3.5 20.5 + - - -
480F ASN* 1.3 74.1 - - - +
482F LYS* 1.3 58.2 + - - +
484F ALA* 3.0 10.8 + - - +
485F ILE* 2.8 34.4 + - - +
508F ALA* 3.5 33.7 - - - +
511F GLU* 3.7 22.0 - - - -
512F LEU* 3.8 24.6 - - + +
667F GLN* 4.5 7.1 + - - -
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Residues in contact with LYS 482 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480F ASN* 3.4 3.5 + - - +
481F CYS* 1.3 74.4 - - - +
483F GLU* 1.3 65.6 + - + +
485F ILE* 3.4 8.3 + - + +
486F ASN* 3.1 24.8 + - - +
512F LEU* 3.9 34.2 - - + +
514F GLU* 4.2 10.4 + - - -
698F ILE 5.7 2.8 + - - -
699F ASP* 5.3 6.7 + - - -
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Residues in contact with GLU 483 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475F ALA* 4.9 9.4 - - + +
480F ASN* 3.1 38.7 + - - +
481F CYS 3.4 0.2 - - - -
482F LYS* 1.3 78.2 - - + +
484F ALA* 1.3 52.6 + - - +
486F ASN* 3.3 4.5 + - - +
487F ILE* 2.7 46.5 + - + +
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Residues in contact with ALA 484 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472F GLY* 3.7 27.5 - - - +
475F ALA* 4.1 4.6 - - + +
476F LEU* 3.9 22.9 - - + +
480F ASN 3.2 10.9 + - - +
481F CYS* 3.0 12.5 + - - +
483F GLU* 1.3 76.4 - - - +
485F ILE* 1.3 64.4 + - - +
487F ILE* 3.3 1.6 + - - +
488F LEU* 2.9 32.9 + - + +
508F ALA* 4.7 4.0 - - + -
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Residues in contact with ILE 485 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481F CYS* 2.8 25.8 + - + +
482F LYS* 3.6 8.7 - - + +
484F ALA* 1.3 73.0 - - - +
486F ASN* 1.3 65.6 + - - +
488F LEU* 3.4 4.7 + - - +
489F SER* 3.2 23.7 + - - -
505F ILE* 3.4 35.4 - - + +
508F ALA* 3.7 24.0 - - + -
509F TYR* 3.5 46.9 - - + +
512F LEU* 4.8 3.1 - - + -
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Residues in contact with ASN 486 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482F LYS 3.1 14.5 + - - +
483F GLU* 3.8 4.9 - - - +
485F ILE* 1.3 81.2 - - + +
487F ILE* 1.3 57.5 + - + +
489F SER* 2.9 21.5 + - - -
490F HIS* 2.5 46.6 + - - -
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Residues in contact with ILE 487 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468F GLU* 3.5 26.8 - - + +
471F LYS* 3.9 19.7 - - + -
472F GLY* 3.6 20.4 - - - +
483F GLU* 2.7 31.4 + - + +
484F ALA 3.9 2.5 - - - +
486F ASN* 1.3 76.0 - - + +
488F LEU* 1.3 61.3 + - - +
489F SER 3.4 0.3 + - - -
490F HIS* 3.4 28.6 + - + +
491F LEU* 4.3 5.9 - - - +
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Residues in contact with LEU 488 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469F MET* 4.6 22.4 - - + +
472F GLY* 4.7 10.1 - - - -
473F TYR* 5.4 0.9 - - - +
476F LEU* 4.9 8.1 - - + -
484F ALA* 2.9 25.3 + - + +
485F ILE* 3.9 4.5 - - - +
486F ASN 3.3 0.2 - - - -
487F ILE* 1.3 74.5 - - - +
489F SER* 1.3 64.1 + - - +
491F LEU* 3.2 38.6 + - + +
496F TYR* 4.3 7.6 - - - -
500F TRP* 4.9 3.8 - - + -
501F VAL* 3.9 21.8 - - + -
504F GLN* 4.0 23.1 - - + -
505F ILE* 3.8 32.5 - - + +
508F ALA* 5.7 0.4 - - + -
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Residues in contact with SER 489 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485F ILE* 3.2 15.8 + - - -
486F ASN* 2.9 25.2 + - - -
487F ILE 3.3 0.4 - - - -
488F LEU* 1.3 76.1 - - - +
490F HIS* 1.3 62.6 + - - +
491F LEU* 3.1 10.1 + - - +
496F TYR* 4.5 21.5 - - - +
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Residues in contact with HIS 490 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468F GLU* 6.3 2.7 - - + -
486F ASN* 2.5 55.8 + - - -
487F ILE* 3.6 21.5 + - + +
488F LEU 3.2 1.0 - - - -
489F SER* 1.3 76.4 - - - +
491F LEU* 1.3 64.3 + - - +
492F PRO* 3.7 4.0 - - - +
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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