Contacts of the helix formed by residues 506 - 511 (chain D) in PDB entry 2JBG
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 ASP 506 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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479D ARG* 3.1 52.5 + - - +
480D ILE* 4.3 5.3 - - + +
502D GLU 3.2 8.8 + - - +
503D VAL 3.1 9.3 + - - +
505D LYS* 1.3 75.0 - - - +
507D PRO* 1.3 65.5 - - - +
508D GLU* 3.1 18.0 + - - +
509D LEU* 3.0 15.7 + - + +
510D SER* 2.8 30.2 + - - -
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Residues in contact with PRO 507 (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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70A LYS* 6.3 1.3 - - - +
505D LYS 3.1 11.8 - - - +
506D ASP* 1.3 87.2 - - - +
508D GLU* 1.3 64.0 + - + +
510D SER* 3.4 8.7 + - - +
511D LYS* 3.3 28.7 + - - +
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Residues in contact with GLU 508 (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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460D VAL 5.6 1.2 - - - +
462D ASN* 5.3 0.2 - - - -
479D ARG* 2.8 42.6 + - - +
506D ASP* 3.1 3.4 + - - +
507D PRO* 1.3 79.9 - - + +
509D LEU* 1.3 59.6 + - - +
511D LYS* 3.4 30.0 - - - +
512D GLN* 3.0 17.7 + - - +
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Residues in contact with LEU 509 (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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460D VAL* 3.7 25.6 - - + -
464D TRP* 4.2 15.3 - - + -
477D PRO* 4.0 10.8 - - + -
479D ARG* 3.6 13.7 - - - +
480D ILE* 3.6 38.8 - - + -
503D VAL* 4.1 21.5 - - + +
506D ASP* 3.0 15.6 + - + +
508D GLU* 1.3 75.9 - - - +
510D SER* 1.3 56.4 + - - +
511D LYS 3.2 1.8 - - - -
512D GLN* 2.7 51.7 + - - +
513D PHE* 3.3 11.8 - - + -
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Residues in contact with SER 510 (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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62A ASP* 5.6 1.7 + - - -
503D VAL 3.9 4.8 + - - -
504D SER 3.7 16.2 + - - -
506D ASP 2.8 18.9 + - - -
507D PRO* 3.4 15.4 + - - +
509D LEU* 1.3 72.5 - - - +
511D LYS* 1.3 59.0 + - - +
513D PHE* 2.8 24.0 + - - +
518D ASN* 3.0 41.4 + - - +
521D MET* 4.9 0.4 - - - -
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Residues in contact with LYS 511 (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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462D ASN* 4.9 17.1 - - - +
507D PRO 3.3 16.8 + - - +
508D GLU* 3.4 29.0 - - - +
510D SER* 1.3 81.1 + - - +
512D GLN* 1.3 62.0 + - + +
513D PHE 3.2 7.1 + - - +
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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