Contacts of the helix formed by residues 383 - 388 (chain C) in PDB entry 4BGG
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 ALA 383 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381C TYR 3.6 2.6 + - - -
382C MET* 1.3 76.7 - - - +
384C PRO* 1.4 78.6 - - + +
385C GLU* 3.2 24.7 - - + +
386C VAL* 3.0 16.6 + - + +
387C LEU* 3.0 12.6 + - - +
402C VAL* 4.3 17.8 - - + +
405C TRP* 3.7 24.7 - - + -
485C ARG* 4.2 0.4 - - - +
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Residues in contact with PRO 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383C ALA* 1.4 88.8 - - + +
385C GLU* 1.3 64.6 + - - +
387C LEU* 3.1 1.7 + - + +
388C ASP* 2.8 35.9 + - - +
405C TRP* 3.5 36.6 - - + -
448C VAL* 3.7 24.2 - - + +
449C CYS* 3.4 12.6 - - - -
454C ARG* 4.3 8.7 - - - +
480C GLN* 4.5 21.3 - - + +
485C ARG* 3.8 6.1 - - - +
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Residues in contact with GLU 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C ALA* 3.5 11.2 - - + +
384C PRO* 1.3 77.2 - - - +
386C VAL* 1.3 59.3 + - - +
388C ASP* 3.4 9.2 - - - -
389C GLU* 3.1 5.4 + - - -
390C THR* 2.9 37.5 + - - +
391C ILE* 3.0 34.9 + - + +
398C SER* 4.7 1.1 - - - +
401C ARG* 4.4 0.9 - - - +
402C VAL* 3.7 15.3 + - + +
480C GLN 4.4 1.7 - - - +
482C PRO* 3.7 25.8 - - + +
485C ARG* 2.7 45.6 + - - -
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Residues in contact with VAL 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376C VAL* 5.4 5.8 - - + -
382C MET* 4.0 31.9 - - + -
383C ALA* 3.0 17.6 + - + +
385C GLU* 1.3 76.9 - - - +
387C LEU* 1.3 66.1 + - - +
389C GLU* 3.4 12.8 + - - +
391C ILE* 4.0 20.1 - - + +
402C VAL* 3.8 33.2 - - + -
441C PHE* 3.7 11.9 - - + -
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Residues in contact with LEU 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382C MET* 3.8 46.0 - - + +
383C ALA 3.0 11.5 + - - +
384C PRO 3.7 5.6 - - - +
386C VAL* 1.3 77.3 - - - +
388C ASP* 1.3 57.8 + - - +
389C GLU* 3.3 2.5 + - - +
441C PHE* 3.5 41.3 - - + +
444C MET* 3.5 46.7 - - + +
445C ARG* 3.8 16.6 - - - -
448C VAL* 3.8 22.2 - - + -
449C CYS* 3.9 8.5 - - - -
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Residues in contact with ASP 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A GLN 5.2 0.5 - - - +
384C PRO* 2.8 23.2 + - - +
385C GLU* 3.2 5.0 - - - +
387C LEU* 1.3 71.9 - - - +
389C GLU* 1.3 70.2 + - - +
390C THR* 2.6 44.8 + - + +
445C ARG* 4.9 6.5 - - + +
449C CYS* 3.8 18.7 - - + +
480C GLN* 5.3 6.6 + - - +
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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