Contacts of the strand formed by residues 480 - 488 (chain A) in PDB entry 3DF0
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 GLY 480 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389A ILE 3.3 2.8 - - - +
390A LYS* 3.6 3.5 - - - -
391A LEU 2.7 34.3 + - - +
478A PRO 3.4 2.4 + - - -
479A PRO* 1.3 74.3 - - - +
481A GLU* 1.3 65.6 - - - -
482A TYR* 3.4 11.4 - - - -
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Residues in contact with GLU 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A LEU* 3.9 19.0 - - + +
389A ILE 3.6 2.7 - - - -
390A LYS* 3.8 35.9 + - + -
435A GLU* 4.0 2.9 - - - +
436A VAL* 3.2 41.1 + - + +
440A LEU 4.7 0.9 - - - +
441A THR* 3.2 53.5 + - - +
443A GLN 5.3 2.4 - - - +
446A ILE* 4.9 4.3 - - - +
480A GLY* 1.3 74.5 - - - -
482A TYR* 1.3 67.0 + - - +
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Residues in contact with TYR 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387A TYR 3.3 2.8 - - - +
388A LEU* 3.3 3.5 - - - +
389A ILE* 2.7 50.9 + - + +
391A LEU* 4.1 16.8 - - + -
407A PHE* 6.2 0.7 - + + -
433A ILE* 4.1 20.0 - - + -
434A TYR 3.1 19.5 - - - +
435A GLU* 3.3 38.9 + - + -
436A VAL* 3.6 2.4 - - - +
459A ARG* 4.5 6.5 - - + -
477A LEU* 4.0 17.0 - - + -
478A PRO* 2.8 44.7 + - - +
479A PRO 4.7 0.9 + - - -
480A GLY* 3.4 23.8 - - - -
481A GLU* 1.3 75.5 - - - +
483A VAL* 1.3 65.2 + - - +
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Residues in contact with VAL 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A GLN* 3.4 40.2 - - + +
387A TYR 3.4 9.0 - - - +
388A LEU* 3.9 11.0 - - + -
389A ILE* 5.3 0.2 - - - -
432A GLY 3.7 0.7 - - - +
433A ILE* 3.4 8.1 - - - -
434A TYR* 2.8 38.5 + - + +
436A VAL* 3.5 23.1 - - + -
446A ILE* 5.0 7.4 - - + +
448A LEU* 3.6 28.5 - - + -
482A TYR* 1.3 71.8 - - - +
484A LEU* 1.3 68.2 + - - +
485A VAL* 3.8 4.6 + - + -
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Residues in contact with LEU 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A MET* 5.4 1.1 - - - -
386A GLN* 3.5 7.4 - - - -
387A TYR* 2.7 43.9 + - + +
389A ILE* 3.6 21.1 - - + -
409A VAL* 3.9 27.6 - - + -
431A PHE* 3.9 16.8 - - + -
432A GLY 3.8 0.4 - - - -
433A ILE* 3.8 23.3 - - + -
482A TYR 4.0 0.2 + - - -
483A VAL* 1.3 73.6 - - - +
485A VAL* 1.3 63.1 + - - +
486A PRO* 3.5 7.5 - - + +
499A ILE* 3.4 46.0 - - + -
501A VAL* 4.6 1.8 - - + -
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Residues in contact with VAL 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A PHE* 3.7 33.9 - - + +
384A ASN* 4.0 21.5 - - + +
385A PRO 4.1 3.6 - - - +
386A GLN* 4.3 18.6 - - + -
430A GLY 4.1 0.2 - - - +
431A PHE* 3.4 21.5 - - - -
432A GLY 2.9 16.2 + - - +
434A TYR* 4.2 24.9 - - + -
453A PHE* 4.3 10.8 - - + -
483A VAL* 4.3 5.8 - - + +
484A LEU* 1.3 79.4 - - - +
486A PRO* 1.3 64.6 - - - +
487A SER* 4.2 3.1 + - - -
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Residues in contact with PRO 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A TRP* 3.4 8.2 + - + +
384A ASN* 3.4 15.4 - - - +
385A PRO* 3.2 18.6 - - + +
387A TYR* 3.8 22.0 - - + -
411A LEU* 3.7 29.2 - - + -
431A PHE* 3.9 12.8 - - + -
484A LEU* 3.5 8.5 - - + +
485A VAL* 1.3 82.4 - - - +
487A SER* 1.3 66.6 + - - +
497A PHE* 3.8 17.7 - - + -
499A ILE* 4.0 9.0 - - + -
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Residues in contact with SER 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A TRP* 3.4 20.2 - - - +
373A GLY 3.4 18.6 - - - -
374A CYS* 3.6 6.9 - - - +
381A PHE* 4.8 3.1 - - - -
384A ASN* 3.6 9.0 - - - -
411A LEU* 4.4 0.4 - - - +
429A ILE* 3.4 6.1 - - - +
430A GLY 3.0 29.2 + - - +
465A PHE* 3.3 16.3 - - - -
485A VAL 4.2 4.5 + - - -
486A PRO* 1.3 77.4 - - - +
488A THR* 1.3 71.4 + - - +
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Residues in contact with THR 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A TRP* 4.1 22.4 - - - -
373A GLY* 3.1 5.4 - - - +
374A CYS* 2.8 23.7 + - - +
384A ASN* 5.1 0.2 + - - -
427A HIS* 4.2 8.8 - - + +
428A THR* 3.0 29.8 - - - +
429A ILE* 4.3 0.8 - - - +
465A PHE* 4.0 2.7 - - - -
487A SER* 1.3 79.1 + - - +
489A PHE* 1.3 72.0 + - + +
490A GLU* 3.4 24.5 - - + +
493A LYS* 3.9 26.7 + - + +
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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