Contacts of the strand formed by residues 389 - 395 (chain B) in PDB entry 2W27
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 MET 389 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B ARG* 6.0 3.4 - - - -
294B ASP* 4.1 18.2 - - - +
314B MET* 4.3 7.0 - - + -
315B CYS 3.7 4.3 - - - +
316B ASP* 4.9 1.6 - - + -
322B LEU* 3.5 30.7 - - + -
385B MET* 3.0 41.9 + - + +
386B ASP 3.7 9.9 + - - +
387B ASP* 3.1 33.4 - - + +
388B GLN* 1.3 78.2 - - - +
390B TYR* 1.3 68.8 + - - +
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Residues in contact with TYR 390 (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 MET* 3.5 2.4 - - - -
315B CYS 2.9 39.1 + - - +
316B ASP 4.0 9.0 - - - +
317B GLU* 3.7 21.9 - - - +
354B ILE* 3.8 31.3 - - + +
357B MET* 3.5 36.3 - - + -
358B ARG* 3.2 30.6 - - + +
383B TYR 3.7 3.1 - - - +
384B PRO* 4.2 11.4 - - + -
385B MET* 3.4 4.7 - - - +
388B GLN* 3.5 32.8 - - - +
389B MET* 1.3 80.8 - - - +
391B LEU* 1.3 60.8 + - - +
392B PHE* 3.5 21.1 - - + -
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Residues in contact with LEU 391 (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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279B VAL* 4.7 0.2 - - + -
283B VAL* 4.0 16.4 - - + -
297B PHE* 4.4 6.5 - - + -
298B ILE* 4.3 6.7 - - + -
301B LEU* 3.6 25.8 - - + -
312B ILE* 3.6 22.0 - - + -
313B TYR 3.4 18.6 - - - +
314B MET* 3.9 13.0 - - + -
381B PHE 3.8 0.9 - - - +
382B SER* 3.5 4.2 - - - -
383B TYR* 2.7 53.3 + - + +
385B MET* 3.4 17.2 - - + +
390B TYR* 1.3 73.3 - - - +
392B PHE* 1.3 64.1 + - - +
393B ILE* 4.2 16.4 - - + -
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Residues in contact with PHE 392 (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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311B ARG 4.0 0.2 - - - +
312B ILE* 3.4 8.7 - - - +
313B TYR* 2.9 70.9 + + + +
315B CYS* 3.9 19.1 - - + -
350B PHE* 3.6 30.1 - + - -
353B ASN* 5.9 4.9 - - + -
354B ILE* 5.0 2.9 - - + -
357B MET* 4.1 17.7 - - + -
380B THR* 4.2 13.2 - - + -
381B PHE 3.6 1.3 - - - -
382B SER* 4.0 26.9 - - - -
390B TYR* 3.5 29.8 - - + -
391B LEU* 1.3 74.7 - - - +
393B ILE* 1.3 63.3 + - - +
394B ASP* 4.6 1.6 - - - -
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Residues in contact with ILE 393 (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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275B PHE* 4.9 11.9 - - + -
279B VAL* 4.1 21.1 - - + -
301B LEU* 4.5 2.2 - - + -
305B LEU* 3.8 26.0 - - + -
309B SER* 3.0 34.1 - - - +
311B ARG 3.6 2.7 - - - +
312B ILE* 3.8 13.5 - - + -
380B THR* 3.2 3.2 - - - +
381B PHE* 2.6 54.9 + - + +
383B TYR* 5.6 0.7 - - + -
391B LEU* 4.2 22.0 - - + -
392B PHE* 1.3 79.3 - - - +
394B ASP* 1.3 64.6 + - - +
395B LEU* 4.0 2.0 + - + +
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Residues in contact with ASP 394 (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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309B SER* 3.5 4.1 + - - -
310B PHE* 2.9 48.6 + - + -
311B ARG* 2.8 55.0 + - + +
313B TYR* 4.2 14.2 + - - -
369B TYR* 4.9 1.1 + - - -
371B ASP* 4.6 0.7 - - - +
378B ILE* 4.5 5.2 - - + -
379B ARG 3.6 4.5 - - - +
380B THR* 2.7 30.2 + - - +
393B ILE* 1.3 79.0 + - - +
395B LEU* 1.3 59.8 + - - +
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Residues in contact with LEU 395 (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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271B HIS* 5.2 5.6 - - - +
275B PHE* 3.4 39.0 - - + -
308B CYS* 2.9 32.5 - - + +
309B SER* 5.0 0.4 - - - -
310B PHE* 4.2 2.8 - - - -
365B PHE* 3.9 23.3 - - + -
378B ILE* 3.5 3.2 - - - +
379B ARG* 2.8 45.1 + - + +
381B PHE* 5.8 1.1 - - + +
393B ILE* 5.1 3.6 - - + +
394B ASP* 1.3 73.6 - - - +
396B PRO* 1.3 77.9 - - + +
397B TYR 3.7 10.5 + - - +
398B SER* 5.1 7.4 - - - -
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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