Contacts of the strand formed by residues 561 - 564 (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 ILE 561 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475D PRO* 4.4 1.9 - - - +
476D VAL* 3.4 31.4 + - + +
492D PHE* 3.7 24.5 - - + -
495D PHE* 3.9 20.9 - - + -
499D PHE* 6.2 0.7 - - + -
543D LEU* 4.3 25.4 - - + -
544D HIS 3.3 6.7 - - - +
545D HIS* 4.1 17.0 - - + +
555D VAL 4.2 10.1 - - - +
556D TYR 4.3 3.6 - - - -
557D ASP 3.2 23.3 + - - +
558D MET* 3.4 9.6 + - - +
559D ASP 4.9 1.0 - - - +
560D ALA* 1.3 80.4 - - - +
562D SER* 1.3 73.0 + - - +
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Residues in contact with SER 562 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472D LEU* 2.7 32.3 + - - +
473D GLY 4.6 0.4 - - - -
474D SER 3.2 14.1 - - - -
475D PRO* 4.6 2.5 - - - -
476D VAL* 5.3 0.4 - - - -
543D LEU* 3.3 6.1 - - - +
544D HIS* 2.8 51.5 + - - +
546D GLU* 6.1 0.2 - - - +
560D ALA 5.0 1.3 + - - -
561D ILE* 1.3 79.6 - - - +
563D VAL* 1.3 63.1 + - - +
564D VAL 4.0 0.2 - - - -
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Residues in contact with VAL 563 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464D TRP* 3.8 25.4 - - + -
465D LEU* 3.7 22.2 - - + -
468D ALA* 3.6 5.0 - - - +
473D GLY* 3.3 1.0 - - - -
474D SER 2.6 40.8 + - - +
475D PRO 4.9 1.8 - - - +
476D VAL* 5.7 1.8 - - + +
499D PHE* 4.0 10.8 - - + -
500D TRP* 4.0 9.4 - - + -
541D PHE* 3.8 29.4 - - + -
542D GLU 3.5 5.8 - - - +
543D LEU* 3.8 18.6 - - + -
562D SER* 1.3 71.2 - - - +
564D VAL* 1.3 66.8 + - - +
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Residues in contact with VAL 564 (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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468D ALA* 3.1 10.5 - - - +
472D LEU 3.2 35.2 - - - +
473D GLY* 3.5 3.4 - - - -
541D PHE* 3.6 8.0 - - - -
542D GLU 2.8 37.0 + - - +
544D HIS* 4.1 8.3 - - + -
562D SER* 4.2 5.6 - - - +
563D VAL* 1.3 76.7 - - - +
565D THR* 1.3 61.4 + - - +
568D ARG* 4.7 0.7 - - + -
569D HIS* 3.6 44.6 - - + +
572D ILE* 4.1 12.6 - - + -
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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