Contacts of the helix formed by residues 535 - 542 (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 HIS 535 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369F VAL* 4.7 12.8 - - + +
373F ARG* 3.3 49.5 + - - -
524F GLU* 3.2 40.4 - - + +
525F MET* 4.7 1.3 - - + -
527F GLU 3.7 9.1 + - - -
528F ALA 4.0 14.9 + - - -
533F GLY 3.2 6.5 + - - +
534F SER* 1.3 82.7 + - - +
536F LYS* 1.3 63.3 + - - +
538F LEU* 3.4 9.6 + - + -
539F HIS* 3.2 33.0 + - + -
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Residues in contact with LYS 536 (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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524F GLU* 3.1 6.0 + - - +
533F GLY 4.3 13.2 - - - +
534F SER 2.8 14.2 + - - +
535F HIS* 1.3 73.4 - - - +
537F ILE* 1.3 89.2 + - + +
539F HIS* 3.1 9.3 + - - +
540F ARG* 3.1 22.1 + - - +
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Residues in contact with ILE 537 (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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348F PHE* 4.7 6.1 - - + -
520F THR* 3.6 30.5 - - + +
521F PHE* 3.7 40.8 - - + +
524F GLU* 2.9 20.9 + - + +
536F LYS* 1.3 96.0 - - + +
538F LEU* 1.3 62.5 + - - +
540F ARG* 3.4 25.8 + - - +
541F LEU* 3.2 35.1 + - + +
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Residues in contact with LEU 538 (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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351F VAL* 4.0 19.5 - - + -
369F VAL* 3.8 39.5 - - + +
372F LEU* 4.2 20.9 - - + -
373F ARG* 4.9 2.9 - - + +
521F PHE* 4.0 24.5 - - + -
524F GLU* 3.2 14.7 + - - +
525F MET* 3.9 21.8 - - + -
535F HIS* 3.7 8.3 - - + +
536F LYS 3.3 0.2 - - - -
537F ILE* 1.3 79.4 - - - +
539F HIS* 1.3 62.3 + - - +
541F LEU* 3.5 4.4 + - - +
542F LEU* 3.2 38.5 + - + +
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Residues in contact with HIS 539 (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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365F LEU* 4.1 32.6 - - + +
366F ASP* 4.6 13.7 + - - -
369F VAL* 3.9 22.7 - - + +
533F GLY 4.3 19.1 + - - -
535F HIS* 3.2 23.6 + - + +
536F LYS* 3.1 11.8 + - - +
538F LEU* 1.3 71.9 - - - +
540F ARG* 1.3 67.1 + - - +
541F LEU 3.1 1.3 - - - -
542F LEU* 3.0 16.0 + - - +
543F GLN* 2.7 23.0 + - - +
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Residues in contact with ARG 540 (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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348F PHE* 4.9 11.1 - - - -
536F LYS 3.1 8.7 + - - +
537F ILE* 3.6 32.7 + - - +
539F HIS* 1.3 80.2 - - - +
541F LEU* 1.3 77.1 + - - +
542F LEU 3.4 0.3 + - - -
543F GLN* 3.4 21.6 + - - +
544F ASP 4.3 3.8 + - - +
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Residues in contact with LEU 541 (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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348F PHE* 3.9 26.7 - - + +
351F VAL* 4.1 25.3 - - + +
355F LYS* 3.4 19.4 + - - -
521F PHE* 3.8 31.9 - - + -
537F ILE* 3.2 23.0 + - + +
538F LEU* 3.7 5.6 - - - +
539F HIS 3.1 0.8 - - - -
540F ARG* 1.3 94.5 - - - +
542F LEU* 1.3 56.8 + - - +
543F GLN 3.0 10.7 + - - -
544F ASP 3.4 13.5 - - - +
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Residues in contact with LEU 542 (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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351F VAL* 4.0 19.5 - - + -
355F LYS* 4.2 13.9 - - + +
360F PHE* 4.3 8.5 - - + -
365F LEU* 3.8 22.7 - - + +
368F GLN* 3.8 22.1 - - + +
369F VAL* 3.6 35.9 - - + +
372F LEU* 4.0 17.7 - - + -
538F LEU* 3.2 27.6 + - + +
539F HIS* 3.0 5.4 + - - +
541F LEU* 1.3 75.3 - - - +
543F GLN* 1.3 75.5 + - - +
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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