Contacts of the strand formed by residues 467 - 474 (chain B) in PDB entry 5E9W
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 467 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B ASN* 5.6 4.9 - - - -
285B PHE* 3.7 34.7 - + - +
288B HIS* 4.9 3.2 + + - -
317B THR 4.7 0.2 - - - -
318B THR* 3.4 21.8 - - - -
319B PRO* 3.4 27.0 - - + +
320B ASN* 4.3 2.5 - - - +
360B PHE* 4.0 28.2 - + - -
370B GLU* 4.4 8.1 + - - -
394B THR* 3.7 4.7 - - - -
395B PHE* 2.9 49.6 + + + +
463B ALA 4.2 9.6 - - - -
464B THR* 3.1 14.6 + - - +
465B SER 4.0 5.0 - - - +
466B ILE* 1.3 93.2 - - + +
468B LEU* 1.3 60.4 + - - +
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Residues in contact with LEU 468 (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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317B THR* 3.3 4.5 - - - -
318B THR* 2.9 57.9 + - + +
319B PRO 4.5 1.8 - - - +
320B ASN* 3.8 33.6 - - + +
321B SER 5.2 0.7 - - - +
373B VAL 6.1 0.7 - - - +
375B PHE* 4.3 28.7 - - + -
392B LYS* 4.3 16.6 - - + +
393B LYS 3.2 18.2 - - - +
394B THR* 4.1 3.6 - - + -
395B PHE* 3.6 5.5 - - - -
467B TYR* 1.3 74.6 - - - +
469B VAL* 1.3 71.5 + - - +
470B PHE* 3.9 15.7 - - + -
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Residues in contact with VAL 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B MET* 4.0 15.0 - - + +
183B LEU* 4.4 10.3 - - + -
316B GLY 3.3 8.7 - - - +
317B THR* 3.8 8.5 - - + -
391B TYR* 3.8 15.9 - - + -
392B LYS* 3.5 1.7 - - - -
393B LYS* 2.7 45.6 + - + +
395B PHE* 3.4 29.6 - - + -
398B PHE* 3.6 32.8 - - + -
468B LEU* 1.3 76.6 - - - +
470B PHE* 1.3 62.2 + - - +
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Residues in contact with PHE 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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183B LEU* 4.6 4.2 - - - +
287B CYS* 3.9 15.0 - - - -
314B PHE* 3.6 40.2 - + - -
315B ILE* 3.4 5.9 - - - +
316B GLY* 2.9 65.6 + - - +
317B THR 3.7 3.8 - - - -
318B THR* 4.1 19.1 - - + -
375B PHE* 3.7 28.3 - + + -
378B LEU* 4.6 6.3 - - + -
391B TYR* 3.4 12.6 - - - +
468B LEU* 3.9 16.6 - - + -
469B VAL* 1.3 77.5 - - - +
471B ALA* 1.3 65.3 + - - +
472B PHE* 3.7 16.6 - + + -
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Residues in contact with ALA 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B PHE* 3.3 43.3 - - + -
314B PHE 3.2 5.8 - - - -
315B ILE* 3.9 8.1 - - + -
389B LEU* 3.5 5.2 - - - +
390B VAL* 2.7 35.8 + - + +
391B TYR* 3.0 15.5 + - + +
470B PHE* 1.3 77.4 - - - +
472B PHE* 1.3 59.2 + - - +
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Residues in contact with PHE 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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313B TYR* 3.3 9.4 - - - -
314B PHE* 2.8 53.2 + + + +
375B PHE* 3.7 27.8 - + - -
378B LEU* 4.2 14.4 - - + -
379B ASN* 3.4 41.3 - - - -
382B ALA* 4.1 16.6 - - + -
387B MET* 3.6 20.6 - - + -
388B LYS* 3.3 7.4 - - - +
389B LEU* 3.6 24.2 - - + -
390B VAL* 4.0 2.2 - - - -
470B PHE* 3.7 20.6 - + - -
471B ALA* 1.3 76.6 - - - +
473B GLU* 1.3 61.7 + - - +
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Residues in contact with GLU 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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194B LYS* 3.0 26.9 + - - -
311B GLY* 3.8 6.5 - - - +
312B GLY 3.4 9.0 - - - +
313B TYR* 3.9 15.3 + - + -
387B MET* 3.3 6.4 - - - -
388B LYS* 2.7 36.9 + - + +
390B VAL* 3.6 19.8 - - + +
472B PHE* 1.3 73.9 - - - +
474B LYS* 1.3 74.4 + - - +
475B GLN* 3.2 14.5 - - - +
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Residues in contact with LYS 474 (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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305B CYS 3.0 26.1 + - - -
306B GLU* 3.7 12.7 + - - +
308B LEU* 3.2 26.0 - - + +
309B SER 3.4 24.2 - - - +
310B PRO* 3.8 5.6 - - + -
311B GLY* 2.8 28.2 + - - -
312B GLY 2.9 13.4 + - - +
385B TYR* 2.6 31.6 + - - +
386B ASN* 3.9 7.4 - - + +
387B MET* 3.5 12.5 - - - +
473B GLU* 1.3 74.9 - - - +
475B GLN* 1.3 73.5 + - - +
476B GLN 4.0 0.2 + - - -
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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