Contacts of the helix formed by residues 282 - 288 (chain C) in PDB entry 2W4T
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 282 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C ALA 3.6 7.6 - - - +
229C TYR* 4.1 9.2 - + - +
231C ASN 3.1 0.9 - - - +
242C ARG* 2.4 38.4 - - - +
271C ARG* 5.2 0.4 - - - +
272C VAL* 5.3 11.4 - - + -
281C ASN* 1.3 94.7 + - + +
283C HIS* 1.3 61.9 + - - +
284C ILE* 2.6 45.8 - - + +
285C PHE* 2.3 57.3 + - + +
286C TYR* 3.3 2.8 - - - -
311C PHE* 3.9 15.9 - + - -
352C THR* 4.0 9.7 + - - -
355C ILE* 5.5 2.2 - - + +
356C LEU* 3.7 12.1 - - - +
431C TYR* 4.2 22.9 - + + +
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Residues in contact with HIS 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C GLU* 2.9 11.2 - - + +
228C ALA* 3.3 13.1 + - - +
231C ASN* 2.6 59.8 + - + +
232C ALA 3.1 3.0 + - - -
238C ASN 3.9 3.8 - - - -
239C ASN* 2.4 42.6 + - - -
280C ARG* 2.4 33.3 + - - +
282C TYR* 1.3 71.7 - - - +
284C ILE* 1.3 67.1 + - - +
286C TYR* 3.1 15.1 + - - +
287C GLN* 3.2 14.1 + - + +
322C ILE* 4.8 7.5 - - + +
327C GLU* 4.1 12.6 + - - +
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Residues in contact with ILE 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C ALA* 2.3 65.5 + - + +
229C TYR* 2.6 44.2 - - + +
282C TYR* 2.6 25.7 - - + +
283C HIS* 1.3 68.5 - - - +
285C PHE* 1.3 55.5 + - - +
287C GLN* 2.4 36.0 + - + +
288C ILE* 2.8 29.8 + - + -
331C CYS* 6.2 3.6 - - - -
349C PHE* 5.8 6.1 - - + -
352C THR* 4.1 15.3 - - - +
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Residues in contact with PHE 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C ASN* 2.9 15.0 - - - +
282C TYR* 2.3 40.8 - - + +
284C ILE* 1.3 64.8 - - - +
286C TYR* 1.3 59.8 + + - +
288C ILE* 2.7 28.1 - - - +
289C CYS* 3.6 6.0 - - + -
306C SER* 4.0 15.3 - - - -
309C TYR* 3.4 18.6 - + + -
311C PHE* 2.1 30.7 - + - -
312C ILE* 1.8 61.9 - - + -
356C LEU* 2.6 45.8 - - + -
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Residues in contact with TYR 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C ARG* 2.2 45.1 - - + +
281C ASN* 1.6 34.4 + - - -
282C TYR 3.3 4.7 - - - -
283C HIS 3.1 1.7 + - - +
284C ILE 2.7 4.8 + - - -
285C PHE* 1.3 73.9 - - - +
287C GLN* 1.3 64.4 + - - +
289C CYS* 3.4 16.3 + - - -
290C SER* 3.9 4.2 + - - -
306C SER* 4.1 11.7 - - - -
312C ILE* 1.8 47.0 + - + +
314C GLN* 4.2 0.9 + - - -
316C CYS 3.0 9.1 + - - -
317C LEU* 3.1 37.0 - - + -
324C ASP* 3.3 32.7 - - - +
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Residues in contact with GLN 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C ALA* 5.7 0.7 - - + -
283C HIS* 3.2 20.0 + - - +
284C ILE* 2.4 22.5 + - + +
286C TYR* 1.3 72.2 - - - +
288C ILE* 1.3 61.8 + - + +
289C CYS 3.0 1.4 + - - -
290C SER* 2.9 24.3 + - - -
291C ASN 4.6 0.5 + - - -
293C ILE* 5.8 0.2 - - - +
322C ILE* 5.0 5.3 - - - +
324C ASP* 1.6 55.3 + - - +
327C GLU* 2.4 51.1 + - - +
328C PHE* 2.7 34.0 + - + -
331C CYS* 5.2 2.9 - - - -
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Residues in contact with ILE 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282C TYR* 4.9 0.9 - - - +
284C ILE* 2.9 39.3 - - + +
285C PHE* 2.7 23.6 - - - +
287C GLN* 1.3 74.4 - - + +
289C CYS* 1.3 64.7 + - + +
290C SER 3.5 1.1 + - - -
291C ASN 5.1 1.8 + - - -
293C ILE* 5.9 1.8 - - - +
300C MET* 3.7 25.8 - - + +
302C VAL* 3.9 27.8 - - + +
304C PRO* 5.4 0.3 - - - +
309C TYR* 5.7 0.9 - - + -
328C PHE* 3.8 17.6 - - + -
349C PHE* 5.2 2.0 - - + -
352C THR* 4.8 6.7 - - - +
353C ALA* 5.1 1.1 - - + +
356C LEU* 3.1 31.6 - - + -
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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