Contacts of the helix formed by residues 520 - 527 (chain F) in PDB entry 5I4V
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 520 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344F ASP* 3.6 10.9 + - - +
348F PHE* 5.4 6.7 - - + -
519F ASP* 1.3 69.8 - - - +
521F PHE* 1.3 79.8 + - + +
523F MET* 3.1 8.9 + - - +
524F GLU* 3.1 19.6 + - - +
537F ILE* 3.6 19.8 - - + +
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Residues in contact with PHE 521 (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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344F ASP* 2.8 17.7 + - - +
347F LEU* 3.5 40.8 - - + -
348F PHE* 3.9 27.6 - + + -
351F VAL* 4.5 3.4 - - + -
520F THR* 1.3 73.1 - - + +
522F LEU* 1.3 67.1 + - - +
524F GLU* 3.0 19.3 + - - +
525F MET* 3.0 39.9 + - + +
537F ILE* 3.7 33.4 - - + -
538F LEU* 4.0 23.6 - - + -
541F LEU* 3.8 20.4 - - + -
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Residues in contact with LEU 522 (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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340F CYS* 3.7 47.1 - - + +
343F ALA* 4.1 10.1 - - + -
344F ASP* 3.1 14.6 + - + +
347F LEU* 3.7 17.3 - - + +
376F TRP* 3.7 34.5 - - + -
507F LEU* 4.7 9.6 - - + -
510F PHE* 6.2 0.2 - - + -
519F ASP* 3.9 12.1 - - + +
521F PHE* 1.3 76.4 - - - +
523F MET* 1.3 61.9 + - - +
525F MET* 3.1 4.7 + - - +
526F LEU* 3.1 40.7 + - + +
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Residues in contact with MET 523 (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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511F LYS* 4.0 40.2 - - + +
519F ASP 3.1 32.2 + - - +
520F THR* 3.1 13.4 + - - +
522F LEU* 1.3 77.6 - - - +
524F GLU* 1.3 62.6 + - - +
526F LEU* 3.2 19.9 + - + +
527F GLU* 3.3 26.1 + - + +
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Residues in contact with GLU 524 (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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520F THR 3.1 8.0 + - - +
521F PHE* 3.0 14.6 + - + +
523F MET* 1.3 78.7 - - - +
525F MET* 1.3 66.8 + - - +
527F GLU* 3.3 24.7 + - - +
534F SER* 3.4 11.6 - - - +
535F HIS* 3.2 38.1 - - + +
536F LYS* 3.1 8.8 + - - +
537F ILE* 2.9 37.5 + - + +
538F LEU* 3.2 28.2 + - - +
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Residues in contact with MET 525 (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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347F LEU* 4.0 24.2 - - + -
372F LEU* 4.8 2.7 - - - +
373F ARG* 4.1 31.3 + - + +
376F TRP* 3.6 47.6 + - + +
521F PHE* 3.0 38.9 + - + +
522F LEU* 3.1 8.7 + - - +
524F GLU* 1.3 94.7 - - + +
526F LEU* 1.3 60.3 + - - +
527F GLU 3.3 6.9 + - - +
535F HIS* 4.7 0.9 - - + -
538F LEU* 3.9 21.5 - - + -
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Residues in contact with LEU 526 (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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376F TRP* 4.6 7.2 - - + -
504F LEU* 4.4 12.1 - - + -
507F LEU* 4.2 31.9 - - + +
508F PHE* 3.7 46.2 - - + -
511F LYS* 3.7 27.9 + - + +
522F LEU* 3.1 39.0 + - + +
523F MET* 3.2 15.4 + - + +
525F MET* 1.3 75.6 - - - +
527F GLU* 1.3 59.9 + - - +
528F ALA 4.1 0.3 + - - -
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Residues in contact with GLU 527 (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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373F ARG* 2.7 27.6 + - - -
511F LYS* 2.8 33.1 + - - +
523F MET* 3.3 24.2 - - + +
524F GLU* 3.6 15.0 - - - +
525F MET 3.2 3.8 - - - +
526F LEU* 1.3 79.7 - - - +
528F ALA* 1.3 58.0 + - - +
534F SER* 4.4 16.2 - - - +
535F HIS* 3.7 3.7 + - - +
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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