Contacts of the helix formed by residues 424 - 431 (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 LEU 424 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381F ILE* 3.7 23.1 - - + -
382F ALA* 5.7 1.6 - - - -
385F SER* 3.5 28.3 - - - +
420F VAL* 2.9 18.0 + - + +
423F GLU* 1.3 88.9 - - + +
425F VAL* 1.3 61.6 + - - +
426F SER 3.3 0.7 - - - -
427F LYS* 3.2 2.4 + - - +
428F MET* 2.8 45.8 + - + +
492F ARG* 4.6 17.5 - - + +
495F ALA* 5.1 0.7 - - + -
496F LEU* 4.0 31.6 - - + +
499F ILE* 4.1 19.7 - - + -
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Residues in contact with VAL 425 (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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385F SER* 3.5 34.1 - - - +
388F SER* 3.6 36.8 - - - +
389F ILE* 4.1 2.3 - - - +
391F VAL 5.4 0.7 - - - +
394F GLY 5.3 0.7 - - - +
395F ILE* 4.7 2.2 - - + -
420F VAL* 3.1 16.0 + - + +
421F LEU* 3.9 27.1 - - + +
424F LEU* 1.3 79.1 - - - +
426F SER* 1.3 65.1 + - - +
428F MET* 3.3 4.0 + - - +
429F ARG* 2.9 40.0 + - - +
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Residues in contact with SER 426 (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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421F LEU 2.8 24.3 + - - -
422F THR* 3.5 13.0 + - - -
425F VAL* 1.3 73.9 - - - +
427F LYS* 1.3 66.9 + - - +
429F ARG* 3.2 19.6 + - - +
430F ASP* 3.0 40.8 + - - +
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Residues in contact with LYS 427 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393E GLU* 3.1 38.0 + - - +
422F THR* 3.0 29.5 + - - +
423F GLU* 3.2 40.4 + - - +
424F LEU 3.2 2.7 + - - +
426F SER* 1.3 79.8 + - - +
428F MET* 1.3 58.9 + - - +
430F ASP* 3.9 7.3 + - + +
431F MET* 3.0 38.2 + - - +
492F ARG* 3.6 25.6 - - - +
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Residues in contact with MET 428 (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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382F ALA* 3.7 26.9 - - + +
385F SER* 3.8 14.1 - - - -
386F HIS* 3.6 24.9 - - + -
389F ILE* 3.9 17.9 - - + +
424F LEU* 2.8 33.4 + - + +
425F VAL 3.6 3.6 - - - +
427F LYS* 1.3 74.0 - - + +
429F ARG* 1.3 59.6 + - - +
431F MET* 4.3 1.8 - - - -
432F ARG* 3.1 2.9 + - - -
433F MET* 2.9 63.7 + - + -
438F LEU* 3.8 21.1 - - + -
441F LEU* 5.9 1.1 - - + -
492F ARG* 6.0 1.6 - - + -
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Residues in contact with ARG 429 (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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389F ILE* 2.3 67.1 + - + +
390F ASP 4.6 0.4 - - - -
391F VAL 3.5 17.8 + - - -
392F ARG* 5.9 1.2 - - - +
393F ASP 6.0 0.8 - - - +
421F LEU* 6.3 0.4 - - - +
425F VAL* 2.9 28.1 + - - +
426F SER* 3.2 23.6 + - - +
428F MET* 1.3 77.0 - - - +
430F ASP* 1.3 68.7 + - - +
432F ARG* 3.0 26.8 + - - +
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Residues in contact with ASP 430 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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426F SER* 3.0 34.2 + - - +
427F LYS* 4.0 7.7 + - + +
429F ARG* 1.3 90.2 + - - +
431F MET* 1.3 61.6 + - - +
432F ARG* 3.1 11.9 + - - +
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Residues in contact with MET 431 (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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427F LYS* 3.0 23.2 + - - +
428F MET* 4.3 0.2 - - - -
430F ASP* 1.3 75.2 - - - +
432F ARG* 1.3 67.3 + - - +
433F MET* 3.8 29.2 - - + +
485F ARG* 2.7 47.9 + - + +
488F LYS* 3.8 44.2 - - + +
489F LEU* 3.4 35.4 - - + +
492F ARG* 5.2 5.6 - - - -
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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