Contacts of the strand formed by residues 298 - 306 (chain C) in PDB entry 4ZTZ
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 GLU 298 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92C LEU* 3.6 27.4 - - + +
290C TYR* 3.3 7.9 - - - -
291C TYR* 2.9 33.6 + - - +
293C PHE* 4.5 13.7 - - + -
295C TRP* 4.9 4.3 + - - -
296C GLY* 3.4 15.3 - - - +
297C LYS* 1.3 84.1 - - - +
299C LEU* 1.3 65.1 + - - +
300C ILE* 3.5 6.1 + - + +
344C ARG* 3.4 28.2 + - - +
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Residues in contact with LEU 299 (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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288C LYS* 4.1 20.6 - - + -
289C LEU 4.0 4.0 - - - +
290C TYR* 3.6 20.6 - - + +
298C GLU* 1.3 74.9 - - - +
300C ILE* 1.3 73.2 + - - +
301C GLU 3.6 23.1 - - - +
302C THR* 3.8 24.7 - - + -
341C ASP* 5.4 0.5 - - - +
344C ARG* 3.6 22.3 + - - +
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Residues in contact with ILE 300 (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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263C TRP* 3.6 39.7 - - + +
273C PHE* 5.0 4.9 - - + -
289C LEU* 2.9 20.7 + - + +
290C TYR 5.2 0.9 - - - -
291C TYR* 3.8 30.1 - - + -
293C PHE* 5.5 2.9 - - + -
298C GLU* 4.0 9.2 - - + +
299C LEU* 1.3 84.4 - - - +
301C GLU* 1.3 67.8 + - + +
341C ASP* 2.9 32.7 + - - +
344C ARG* 3.7 39.0 - - + +
345C GLY* 4.4 3.8 - - - +
348C ALA* 4.7 2.0 - - + -
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Residues in contact with GLU 301 (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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259C ARG* 2.6 40.0 + - - +
263C TRP* 2.7 31.9 + - - -
288C LYS* 3.5 2.8 - - - -
289C LEU* 2.7 46.6 + - + +
299C LEU* 3.6 5.2 - - - +
300C ILE* 1.3 90.2 - - + +
302C THR* 1.3 67.0 + - - +
303C LEU* 3.6 10.6 - - + +
338C VAL* 3.3 19.9 - - - +
339C ASN 3.3 17.0 - - - +
340C GLY* 3.6 7.6 - - - -
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Residues in contact with THR 302 (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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287C ASN 3.8 3.1 - - - -
288C LYS* 4.5 8.7 - - + +
299C LEU* 3.8 31.4 - - + -
301C GLU* 1.3 78.9 - - - +
303C LEU* 1.3 64.5 + - - +
304C TRP* 4.1 24.3 - - - +
337C SER* 3.3 4.3 + - - +
339C ASN* 2.9 52.4 + - - +
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Residues in contact with LEU 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C LEU* 3.9 17.5 - - + +
255C TRP* 4.1 5.8 - - + +
256C LEU* 3.6 45.1 - - + +
259C ARG* 4.4 9.2 - - + -
286C GLY* 3.3 2.6 - - - -
287C ASN* 2.7 48.0 + - + +
289C LEU* 4.7 8.7 - - + -
301C GLU* 3.6 25.8 - - + +
302C THR* 1.3 85.4 - - - +
304C TRP* 1.3 64.6 + - - +
337C SER 3.4 2.9 - - - -
338C VAL* 3.7 25.6 - - + -
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Residues in contact with TRP 304 (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 LEU* 3.8 7.8 - - - +
278C CYS* 3.8 25.1 - - + -
279C GLN* 4.8 3.4 - - - -
280C ASP* 3.2 30.1 - - - -
283C GLY* 4.3 11.9 - - - -
285C LYS 4.2 2.0 - - - -
286C GLY* 3.7 28.5 - - - -
287C ASN 5.8 0.2 - - - -
288C LYS* 5.0 11.0 - - + +
302C THR* 4.1 29.4 - - - +
303C LEU* 1.3 76.0 - - - +
305C ASN* 1.3 63.5 + - - +
306C LEU* 3.6 28.0 - - + +
336C LEU* 3.5 4.3 - - - -
337C SER* 2.9 35.5 + - - -
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Residues in contact with ASN 305 (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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248C SER* 3.4 31.1 + - - -
249C ASN* 4.0 9.5 + - - +
252C LEU* 3.8 9.0 - - + +
283C GLY* 4.6 3.1 - - - -
284C ARG* 4.4 16.9 + - - +
285C LYS* 3.2 30.6 + - - +
304C TRP* 1.3 76.4 - - - +
306C LEU* 1.3 62.8 + - - +
307C GLY 3.6 1.2 + - - -
334C CYS* 3.1 24.4 - - - -
335C VAL 3.8 2.2 - - - -
336C LEU* 3.3 16.6 - - - +
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Residues in contact with LEU 306 (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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186C LEU* 5.7 5.2 - - + -
282C GLU* 4.7 15.3 - - + +
283C GLY* 4.9 6.7 - - - -
304C TRP* 3.6 29.8 - - + -
305C ASN* 1.3 75.7 - - - +
307C GLY* 1.3 63.2 + - - +
310C GLU* 4.0 35.2 - - + +
334C CYS* 3.1 4.9 - - - -
335C VAL* 2.8 46.2 + - + +
337C SER* 3.6 21.3 - - - +
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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