Contacts of the strand formed by residues 276 - 282 (chain C) in PDB entry 4L28
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 ARG 276 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249C ASP 3.0 14.7 + - - +
250C MET* 3.4 21.0 - - + +
251C LEU 2.9 26.5 + - - +
274C GLY 4.2 8.1 - - - +
275C CYS* 1.3 75.9 - - - +
277C ILE* 1.3 61.6 + - - +
278C ILE* 3.8 12.2 + - + +
321C ASP* 3.5 21.4 + - - +
322C LYS* 4.1 30.5 - - - +
360C ALA 5.6 0.2 + - - -
363C GLU* 2.9 39.3 + - - -
364C LEU* 6.0 0.9 - - + -
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Residues in contact with ILE 277 (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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251C LEU* 3.8 13.5 - - + +
261C ILE* 3.7 33.2 - - + -
265C ALA* 3.8 27.1 - - + +
268C LEU* 4.2 24.2 - - + -
269C LYS* 4.2 10.5 - - + -
275C CYS* 4.5 4.7 - - - +
276C ARG* 1.3 76.5 - - - +
278C ILE* 1.3 63.5 + - - +
319C VAL 3.5 26.9 - - - +
320C VAL* 3.8 3.6 - - - +
321C ASP* 3.0 31.8 + - - +
322C LYS 3.3 9.4 + - - +
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Residues in contact with ILE 278 (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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250C MET* 3.9 41.5 - - + -
251C LEU 2.9 12.4 + - - +
252C VAL* 3.4 10.3 - - + +
253C ALA* 3.0 26.0 + - - +
261C ILE* 4.1 4.5 - - - +
276C ARG* 4.4 15.7 - - + +
277C ILE* 1.3 79.9 - - - +
279C GLY* 1.3 61.3 + - - +
321C ASP* 5.5 0.2 - - + -
322C LYS* 3.5 22.7 - - + +
324C PHE* 3.7 32.8 - - + -
356C VAL* 4.1 14.8 - - + -
360C ALA* 4.2 5.2 - - + -
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Residues in contact with GLY 279 (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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253C ALA 3.4 6.1 - - - -
255C VAL* 4.4 0.2 - - - -
261C ILE* 3.7 14.4 - - - -
278C ILE* 1.3 74.4 - - - +
280C VAL* 1.3 63.8 + - - +
320C VAL* 3.7 9.9 - - - +
322C LYS 2.9 11.4 + - - -
323C TRP* 3.4 13.8 - - - -
324C PHE* 2.9 26.3 + - - +
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Residues in contact with VAL 280 (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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252C VAL* 3.9 17.3 - - + -
253C ALA 3.0 11.9 + - - +
254C SER* 3.6 12.7 - - - -
255C VAL* 3.1 27.4 + - - +
278C ILE* 5.1 0.2 - - + -
279C GLY* 1.3 77.6 - - - +
281C ASP* 1.3 62.6 + - - +
282C PRO* 4.3 1.9 - - - +
306C ILE* 5.0 1.6 - - + +
323C TRP* 4.6 1.6 - - - -
324C PHE 3.5 2.5 - - - +
326C SER* 3.8 20.6 - - - +
352C SER* 4.1 14.4 - - - +
353C THR* 4.4 5.4 - - - -
356C VAL* 3.6 44.9 - - + -
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Residues in contact with ASP 281 (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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255C VAL 4.4 0.9 - - - +
279C GLY 4.2 0.2 + - - -
280C VAL* 1.3 75.4 - - - +
282C PRO* 1.3 74.7 - - - +
285C SER* 2.8 28.2 + - - -
287C LEU* 3.3 34.3 + - - +
288C ALA* 3.3 20.3 + - + -
307C GLY* 3.8 0.3 + - - -
323C TRP* 4.1 8.5 - - + -
324C PHE 2.9 7.9 + - - +
325C LYS* 2.9 30.2 + - - +
326C SER* 2.9 22.9 + - - -
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Residues in contact with PRO 282 (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 VAL 4.3 1.1 - - - +
281C ASP* 1.3 99.4 - - - +
283C GLU* 1.3 66.6 + - - +
285C SER* 3.2 17.5 + - - -
301C TYR* 3.6 30.5 - - + +
303C VAL* 5.7 2.2 - - + -
306C ILE* 3.8 27.4 - - + +
307C GLY* 3.6 26.0 - - - +
325C LYS* 3.3 6.2 + - - -
326C SER* 3.3 14.3 - - - +
327C ASN* 6.1 0.4 - - - -
328C ASP* 6.0 1.1 - - - +
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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