Contacts of the strand formed by residues 466 - 473 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192B PRO* 3.5 14.6 + - + +
193B PRO 2.8 26.9 + - - -
196B TYR* 3.3 27.9 - - + +
197B GLN* 3.2 44.3 + - + +
200B ALA* 4.6 3.8 - - + -
323B LEU* 4.8 10.3 - - + -
324B GLU 3.1 12.3 - - - +
325B LEU* 3.2 33.2 - - + -
326B ALA* 4.7 0.6 - - - +
464B GLY 3.6 22.7 - - - -
465B ARG* 1.3 74.0 - - - +
467B ASN* 1.3 67.5 + - - +
485B HIS* 3.1 6.4 - - - +
486B TRP* 2.8 44.7 + + + +
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Residues in contact with ASN 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B LEU* 3.4 7.1 - - - +
324B GLU* 2.7 35.4 + - + +
325B LEU 3.8 5.6 + - - +
326B ALA* 3.6 27.3 - - - +
327B SER 4.2 7.1 + - - +
328B HIS* 6.3 0.4 - - - -
466B TYR* 1.3 75.3 - - - +
468B VAL* 1.3 61.8 + - - +
469B PHE* 3.3 27.2 - - + -
482B LYS* 3.7 24.6 + - - +
484B GLY 3.9 3.8 - - - +
485B HIS* 3.5 17.2 - - - +
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Residues in contact with VAL 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ILE* 3.3 31.0 - - + -
321B ILE* 4.0 14.8 - - + -
323B LEU* 3.5 18.4 - - + -
467B ASN* 1.3 68.6 - - - +
469B PHE* 1.3 72.9 + - - +
482B LYS* 3.8 0.3 - - - -
483B VAL* 3.0 36.9 + - + +
484B GLY 2.8 22.7 + - - +
485B HIS* 3.7 20.9 - - - +
486B TRP* 4.6 2.2 - - + +
490B LEU* 4.0 11.2 - - + -
491B SER 4.3 0.7 - - - +
492B LEU* 4.6 7.4 - - + -
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Residues in contact with PHE 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B GLY 5.9 0.2 - - - -
305B ALA* 3.7 31.4 - - + -
321B ILE* 3.1 31.5 - - - +
322B THR* 2.8 32.3 + - - +
324B GLU* 4.6 12.3 - - + -
467B ASN* 3.3 38.6 - - + -
468B VAL* 1.3 82.8 - - - +
470B ASN* 1.3 61.0 + - - +
480B TYR* 3.7 24.0 - - + -
481B LEU 3.7 9.0 - - - -
482B LYS* 4.3 22.2 - - + -
483B VAL* 3.9 3.8 - - - -
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Residues in contact with ASN 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B GLY* 4.0 3.8 - - - -
320B ALA 3.0 12.3 + - - -
321B ILE* 4.8 1.5 - - + +
469B PHE* 1.3 78.1 - - - +
471B LEU* 1.3 83.0 + - - +
472B GLN* 3.3 18.7 + - - +
480B TYR* 3.7 2.5 - - - -
481B LEU 3.0 31.6 + - - +
483B VAL* 3.7 20.9 - - + -
497B ILE* 3.2 19.1 - - + +
498B HIS* 2.8 40.2 + - - +
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Residues in contact with LEU 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B TRP* 4.5 4.9 - - + -
310B VAL* 3.5 33.4 - - + -
314B GLU 4.7 2.2 - - - +
317B ALA* 3.2 31.4 - - + +
318B TYR* 4.0 6.0 - - + +
319B GLY* 3.0 27.4 + - - -
320B ALA* 2.8 23.0 + - + +
322B THR* 5.6 1.5 + - + +
469B PHE 4.3 0.2 - - - -
470B ASN* 1.3 72.7 + - - +
472B GLN* 1.3 60.6 + - - +
478B TYR* 4.5 11.9 - - + -
479B SER 3.5 27.1 - - - +
480B TYR* 4.2 27.7 - - + +
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Residues in contact with GLN 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B TYR* 3.9 7.2 - - + -
470B ASN* 3.3 30.3 + - - +
471B LEU* 1.3 75.5 - - - +
473B GLN* 1.3 61.1 + - - +
474B THR* 4.2 12.9 - - - +
478B TYR* 4.6 0.9 - - - -
479B SER* 2.8 46.7 + - - +
481B LEU* 3.4 39.8 - - + +
483B VAL* 4.9 0.2 - - - +
496B SER 3.6 12.7 + - - -
498B HIS* 3.9 39.1 + - + -
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Residues in contact with GLN 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B GLU 5.9 1.8 - - - +
318B TYR* 3.6 26.1 + - + -
472B GLN* 1.3 76.6 - - - +
474B THR* 1.3 89.9 + - - +
476B GLY* 2.6 33.6 - - - +
477B LYS 3.2 32.3 - - - +
478B TYR* 4.0 8.7 - - + +
498B HIS* 5.0 2.6 - - - -
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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