Contacts of the helix formed by residues 383 - 388 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381D TYR 3.6 2.6 + - - -
382D MET* 1.3 75.4 - - - +
384D PRO* 1.3 77.8 - - + +
385D GLU* 3.2 24.7 - - + +
386D VAL* 3.1 9.1 + - + +
387D LEU* 3.0 20.1 + - - +
402D VAL* 4.3 18.3 - - + +
405D TRP* 3.6 24.7 - - + -
485D ARG* 4.2 0.4 - - - +
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Residues in contact with PRO 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D ALA* 1.3 89.8 - - + +
385D GLU* 1.3 65.0 + - - +
387D LEU* 3.1 1.1 + - + -
388D ASP* 2.8 36.4 + - - +
405D TRP* 3.5 37.9 - - + -
448D VAL* 3.7 23.5 - - + +
449D CYS* 3.5 12.6 - - - -
454D ARG* 4.4 8.7 - - - +
480D GLN* 4.5 21.8 - - + +
485D ARG* 3.8 5.4 - - - +
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Residues in contact with GLU 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D ALA* 3.5 14.1 - - + +
384D PRO* 1.3 76.3 - - - +
386D VAL* 1.3 58.7 + - - +
388D ASP* 3.4 9.2 - - - -
389D GLU* 3.1 5.7 + - - -
390D THR* 3.0 37.8 + - - +
391D ILE* 3.0 35.0 + - + +
398D SER* 4.7 1.3 - - - +
401D ARG* 4.6 0.7 - - - +
402D VAL* 3.8 11.9 + - + +
480D GLN 4.4 1.9 - - - +
482D PRO* 3.7 25.5 - - + +
485D ARG* 2.7 46.0 + - - -
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Residues in contact with VAL 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376D VAL* 5.4 5.6 - - + -
382D MET* 4.1 31.2 - - + -
383D ALA* 3.1 17.4 + - + +
385D GLU* 1.3 77.7 - - - +
387D LEU* 1.3 65.6 + - - +
389D GLU* 3.4 12.8 + - - +
391D ILE* 4.0 20.4 - - + -
402D VAL* 3.8 33.2 - - + -
441D PHE* 3.7 11.7 - - + -
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Residues in contact with LEU 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379D LYS* 5.6 0.4 - - - -
382D MET* 3.7 45.1 - - + +
383D ALA 3.0 12.4 + - - +
384D PRO 3.7 5.6 - - - +
386D VAL* 1.3 77.2 - - - +
388D ASP* 1.3 57.3 + - - +
389D GLU* 3.3 2.3 + - - +
441D PHE* 3.4 41.6 - - + +
444D MET* 3.5 47.6 - - + +
445D ARG* 4.2 11.4 - - - +
448D VAL* 3.8 21.1 - - + -
449D CYS* 3.8 9.2 - - - -
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Residues in contact with ASP 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384D PRO* 2.8 24.7 + - - +
385D GLU* 3.2 4.7 - - - +
387D LEU* 1.3 71.6 - - - +
389D GLU* 1.3 70.5 + - - +
390D THR* 2.6 45.1 + - + +
445D ARG* 6.1 0.2 - - - -
449D CYS* 3.9 18.4 - - + +
480D GLN* 5.3 7.4 + - - +
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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