Contacts of the strand formed by residues 470 - 478 (chain J) in PDB entry 3E20
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 470 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468J PRO* 4.3 10.3 - - + +
469J PHE* 1.3 80.9 - - - +
471J MET* 1.3 60.8 + - - +
472J PRO* 4.2 1.1 - - + -
488J ILE* 3.8 1.1 - - - -
489J GLU* 2.9 27.8 + - + +
490J ALA* 2.9 34.8 + - + +
546J VAL* 3.5 23.3 - - + -
547J LEU 3.4 2.9 - - - -
548J THR* 4.8 0.9 - - - +
554J VAL* 4.3 18.6 - - + -
632J GLU* 4.9 5.8 - - + +
637J TYR* 3.9 33.2 - - + +
640J MET* 3.7 28.0 - - + -
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Residues in contact with MET 471 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469J PHE* 3.7 19.0 - - + -
470J ILE* 1.3 75.3 - - - +
472J PRO* 1.3 69.1 - - - +
473J ILE* 3.3 9.5 + - + -
484J LEU* 4.8 5.4 - - + +
485J GLU 4.2 3.6 - - - -
486J GLY* 3.7 24.0 - - - +
487J LYS 3.6 26.9 - - - +
488J ILE* 3.8 7.0 - - + +
530J VAL* 3.8 20.0 - - - -
532J LEU* 3.8 23.3 - - + -
546J VAL* 3.9 2.7 - - - -
547J LEU* 2.9 46.8 + - + -
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Residues in contact with PRO 472 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470J ILE* 4.1 1.8 - - + +
471J MET* 1.3 84.6 - - - +
473J ILE* 1.3 64.3 + - - +
474J ALA* 3.2 4.7 + - - +
486J GLY* 3.8 12.6 - - - -
487J LYS 3.8 6.9 + - - +
489J GLU* 3.7 24.9 - - + -
545J TYR 3.8 6.1 - - - +
546J VAL* 3.9 7.9 - - + -
584J HIS* 4.1 11.9 - - + -
585J THR* 3.4 28.0 + - + +
639J TYR* 4.4 5.4 - - + -
640J MET* 3.9 29.4 - - + -
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Residues in contact with ILE 473 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471J MET* 4.2 6.7 - - + +
472J PRO* 1.3 68.1 - - - +
474J ALA* 1.3 60.2 + - - +
475J SER 3.6 25.4 - - - +
476J LYS* 4.6 3.1 - - + -
484J LEU* 4.4 14.4 - - + -
485J GLU 4.1 3.1 - - - +
501J VAL* 4.4 0.9 - - + -
541J VAL* 3.3 30.3 - - + -
542J GLN 4.3 1.1 - - - +
543J THR* 3.7 10.4 - - - -
544J GLY 3.0 21.0 + - - +
545J TYR* 2.9 34.3 + - + +
547J LEU* 3.9 34.8 - - + -
585J THR* 2.8 10.1 + - - +
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Residues in contact with ALA 474 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472J PRO 3.2 3.9 + - - +
473J ILE* 1.3 72.6 - - - +
475J SER* 1.3 64.9 + - - +
485J GLU* 2.9 31.7 + - - +
486J GLY* 4.1 7.0 - - - -
529J GLN* 5.6 1.3 - - - +
543J THR* 3.3 16.2 + - - -
585J THR* 3.0 13.8 + - - +
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Residues in contact with SER 475 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473J ILE* 3.6 6.8 - - - +
474J ALA* 1.3 80.9 + - - +
476J LYS* 1.3 62.3 + - - +
477J TYR* 5.1 7.9 - - - -
483J ILE 4.4 0.4 - - - -
484J LEU* 3.5 2.9 - - - -
485J GLU* 2.8 54.2 + - - +
543J THR* 4.9 4.5 - - - -
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Residues in contact with LYS 476 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473J ILE* 4.6 5.2 - - + -
475J SER* 1.3 77.2 - - - +
477J TYR* 1.3 70.3 + - - +
478J LYS* 5.7 4.5 - - - -
482J THR* 3.9 14.4 - - + -
483J ILE 3.3 5.8 - - - -
484J LEU* 3.5 23.3 - - + -
538J ASP* 3.3 33.5 + - - -
539J SER* 4.3 8.7 + - - +
541J VAL* 3.0 31.5 + - - +
542J GLN* 4.8 2.2 - - - -
543J THR* 5.3 9.1 - - - +
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Residues in contact with TYR 477 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480D LEU* 4.5 8.0 - - - +
475J SER* 5.1 6.5 - - - -
476J LYS* 1.3 84.9 - - - +
478J LYS* 1.3 72.4 + - - +
479J ASP* 4.8 9.6 - - + -
481J GLY 4.0 0.5 - - - +
482J THR* 3.7 3.3 - - - -
483J ILE* 2.8 74.8 + - + +
485J GLU* 5.2 8.1 - - + -
531J ARG* 4.1 16.1 + - - -
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Residues in contact with LYS 478 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518D ASP 5.9 2.7 - - - +
519D GLU* 5.5 8.4 + - - +
476J LYS* 5.7 3.6 - - - -
477J TYR* 1.3 82.8 - - - +
479J ASP* 1.3 69.0 - - - +
480J LEU 5.3 0.7 - - - +
481J GLY* 3.5 14.8 - - - +
482J THR* 2.8 38.0 + - + +
538J ASP* 3.5 20.4 + - - +
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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