Contacts of the strand formed by residues 466 - 473 (chain A) in PDB entry 2E4Y
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 TYR 466 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A PRO* 3.3 19.9 + - + +
193A PRO 3.0 26.0 + - - -
194A ASP* 4.5 0.2 - - - -
196A TYR* 3.5 20.4 - - + +
197A GLN* 3.4 41.4 + - + +
200A ALA* 4.7 1.8 - - + -
323A LEU* 4.5 15.7 - - + -
324A GLU 3.2 9.6 - - - +
325A LEU* 3.2 33.9 - - + -
326A ALA* 4.7 0.6 - - - +
464A GLY* 3.5 25.4 - - - -
465A ARG* 1.3 74.7 - - - +
467A ASN* 1.3 62.5 + - - +
485A HIS* 3.1 5.5 - - - +
486A TRP* 2.7 51.7 + + + +
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Residues in contact with ASN 467 (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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323A LEU* 3.2 8.2 - - - +
324A GLU* 2.7 35.1 + - - +
325A LEU 3.7 5.6 + - - +
326A ALA* 3.4 29.2 - - - +
327A SER 4.1 6.5 + - - +
328A HIS* 6.2 0.6 - - - -
466A TYR* 1.3 74.7 - - - +
468A VAL* 1.3 61.6 + - - +
469A PHE* 3.2 27.0 - - + -
482A LYS* 3.4 32.6 + - - +
484A GLY 3.9 3.6 - - - +
485A HIS* 3.6 10.2 - - - +
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Residues in contact with VAL 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ILE* 3.4 31.0 - - + -
321A ILE* 4.1 15.3 - - + -
323A LEU* 3.5 18.6 - - + -
467A ASN* 1.3 69.6 - - - +
469A PHE* 1.3 71.1 + - - +
482A LYS* 3.8 0.5 - - - -
483A VAL* 2.9 37.7 + - + +
484A GLY 2.7 24.3 + - - +
485A HIS* 3.6 21.1 - - - +
486A TRP* 4.5 1.8 - - + +
490A LEU* 4.0 9.9 - - + -
491A SER 4.3 0.4 - - - +
492A LEU* 4.6 7.9 - - + -
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Residues in contact with PHE 469 (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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304A GLY 6.0 0.4 - - - -
305A ALA* 3.8 21.5 - - + -
321A ILE* 3.1 13.9 - - - +
322A THR* 2.8 49.6 + - - +
324A GLU* 4.7 11.2 - - + -
467A ASN* 3.2 40.2 - - + -
468A VAL* 1.3 83.9 - - - +
470A ASN* 1.3 59.6 + - - +
480A TYR* 3.7 31.0 - - + -
481A LEU 3.6 8.3 - - - -
482A LYS* 4.2 21.3 - - + -
483A VAL* 4.0 3.8 - - - -
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Residues in contact with ASN 470 (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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319A GLY 4.0 2.8 - - - -
320A ALA 3.0 17.4 + - - -
321A ILE* 4.5 2.2 - - + +
469A PHE* 1.3 75.1 - - - +
471A LEU* 1.3 68.9 + - - +
472A GLN* 3.2 18.4 + - - +
480A TYR* 3.7 1.7 - - - -
481A LEU 2.9 33.3 + - - +
483A VAL* 3.7 22.2 - - + -
497A ILE* 3.1 18.0 - - + +
498A HIS* 2.6 45.1 + - - +
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Residues in contact with LEU 471 (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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303A TRP* 4.4 5.8 - - + -
310A VAL* 3.3 39.9 - - + -
314A GLU 4.9 1.8 - - - +
317A ALA* 3.4 22.4 - - + +
318A TYR* 4.0 5.0 - - + +
319A GLY* 2.9 27.5 + - - -
320A ALA* 2.9 22.8 + - + +
322A THR* 5.8 1.7 + - + +
469A PHE 4.3 0.2 - - - -
470A ASN* 1.3 69.8 - - - +
472A GLN* 1.3 61.6 + - - +
478A TYR* 4.6 10.8 - - + -
479A SER 3.2 31.0 - - - +
480A TYR* 3.9 28.2 - - + +
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Residues in contact with GLN 472 (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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318A TYR* 3.8 7.0 - - + -
470A ASN* 3.2 30.2 + - - +
471A LEU* 1.3 77.4 - - - +
473A GLN* 1.3 60.9 + - - +
474A THR* 4.2 12.2 - - - +
478A TYR* 4.6 0.9 - - - -
479A SER* 2.9 41.1 + - - +
481A LEU* 3.7 33.1 - - + +
496A SER 3.5 16.8 + - - -
498A HIS* 3.5 42.7 + - + -
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Residues in contact with GLN 473 (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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314A GLU 5.9 1.6 - - - +
318A TYR* 3.5 26.2 + - + -
472A GLN* 1.3 77.5 - - - +
474A THR* 1.3 89.4 + - - +
476A GLY* 2.7 33.9 - - - +
477A LYS 3.2 32.3 - - - +
478A TYR* 3.9 8.7 - - + +
498A HIS* 5.1 1.7 - - - -
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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