Contacts of the helix formed by residues 379 - 383 (chain B) in PDB entry 4M7F
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 379 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B LEU* 3.6 31.0 - - + -
333B VAL* 5.1 0.2 - - + -
347B TYR* 3.4 24.5 - - + +
350B PHE* 5.6 1.6 - - + -
366B LEU* 4.2 15.9 - - + -
368B VAL* 3.9 14.2 - - + +
377B ASP* 2.9 0.6 + - - -
378B SER* 1.3 80.2 - - - +
380B LEU* 1.3 61.3 + - - +
381B LYS 3.2 2.9 - - - -
382B HIS* 2.8 36.6 + - + +
383B SER 3.7 2.8 + - - -
409B TRP* 3.8 21.8 - - + +
410B TRP* 5.0 2.5 - - + -
417B SER* 3.5 18.2 - - - +
437B TRP* 4.0 10.8 - - + -
452B MET* 4.8 8.7 - - + -
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Residues in contact with LEU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B TYR* 3.9 15.9 - - + -
368B VAL* 3.9 10.3 - - + +
369B ALA* 3.6 33.2 - - + +
370B ASP 4.3 1.8 - - - +
371B TYR* 4.2 14.4 - - + +
377B ASP* 3.0 35.6 + - + +
379B LEU* 1.3 77.2 - - - +
381B LYS* 1.3 61.4 + - + +
382B HIS 3.0 0.2 - - - -
383B SER* 3.1 21.0 + - - -
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Residues in contact with LYS 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B ASP* 5.7 1.6 - - - +
378B SER 6.4 0.2 - - - -
379B LEU 3.1 1.6 + - - +
380B LEU* 1.3 78.2 - - + +
382B HIS* 1.3 59.6 + - + +
383B SER 3.3 0.4 - - - -
412B ARG* 3.0 38.0 + - - -
416B THR* 3.9 31.7 - - + +
502B BM3 4.1 15.8 + - - +
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Residues in contact with HIS 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B LEU* 3.7 21.1 - - + +
378B SER 3.5 4.3 - - - -
379B LEU* 2.8 14.8 + - + +
381B LYS* 1.3 78.4 - - + +
383B SER* 1.3 66.2 + - - +
384B GLY 3.3 0.3 + - - -
385B MET* 3.0 25.9 + - - +
409B TRP* 3.6 14.6 - + - -
410B TRP* 2.8 22.6 + - + +
411B TYR* 4.1 1.2 - - - -
412B ARG* 4.2 5.4 + - + +
414B CYS 3.6 7.2 + - - -
415B HIS* 3.3 31.2 - - + -
416B THR* 3.1 32.7 + - - -
417B SER* 3.4 23.9 + - - -
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Residues in contact with SER 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B LEU* 4.0 4.0 + - - -
367B THR* 4.4 1.2 - - - -
368B VAL* 3.3 42.3 + - - -
379B LEU 3.7 3.0 + - - -
380B LEU* 3.1 17.7 + - - -
381B LYS 3.3 0.7 - - - +
382B HIS* 1.3 77.9 - - - +
384B GLY* 1.3 60.2 + - - +
385B MET* 3.4 2.6 + - - +
412B ARG* 3.8 13.7 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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