Contacts of the strand formed by residues 288 - 294 (chain C) in PDB entry 5EG6
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 LEU 288 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273C THR* 3.3 4.9 - - - -
274C VAL* 2.8 42.1 + - + +
276C LEU* 3.6 35.4 - - + +
285C LEU* 4.5 15.7 - - + -
286C PRO* 3.2 19.1 - - + +
287C ARG* 1.3 77.5 - - - +
289C ILE* 1.3 65.0 + - - +
314C PHE* 3.8 33.9 - - + -
315C TYR 3.2 8.7 - - - +
316C LEU* 3.9 30.3 - - + -
324C LEU* 4.6 6.1 - - + -
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Residues in contact with ILE 289 (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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271C GLY* 3.6 32.5 - - - +
272C GLN 3.4 2.7 - - - -
273C THR* 4.0 16.6 - - - +
288C LEU* 1.3 76.2 - - - +
290C ILE* 1.3 63.0 + - - +
291C ARG* 3.5 29.5 + - + +
313C ALA 3.5 0.9 - - - +
314C PHE* 3.6 1.3 - - - -
315C TYR* 2.7 64.4 + - + -
317C LYS* 4.2 22.4 - - + -
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Residues in contact with ILE 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C ILE* 4.5 7.9 - - + -
268C ILE* 4.0 13.0 - - + -
269C HIS 3.7 20.0 - - - +
270C TYR* 3.4 8.6 - - + -
271C GLY 2.7 31.9 + - - -
272C GLN 3.2 11.6 + - - +
274C VAL* 4.4 8.3 - - + -
288C LEU 3.9 2.4 + - - -
289C ILE* 1.3 71.6 - - - +
291C ARG* 1.3 57.9 + - - +
306C VAL* 3.8 22.7 - - + -
312C CYS* 3.9 25.1 - - + -
313C ALA 3.5 3.8 - - - +
314C PHE* 3.7 35.7 - - + -
356C ILE* 4.4 8.1 - - + -
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Residues in contact with ARG 291 (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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270C TYR* 3.4 8.7 - - - -
271C GLY* 4.7 3.1 - - - +
289C ILE* 3.6 27.0 - - + +
290C ILE* 1.3 79.1 - - - +
292C LYS* 1.3 64.4 + - - +
298C ALA* 4.4 8.5 - - + -
299C LEU 4.1 10.1 - - - +
300C LEU* 3.4 40.8 + - - +
312C CYS* 3.3 7.6 - - - +
313C ALA* 2.8 35.0 + - + +
315C TYR* 3.5 40.0 - - - +
323C TYR* 2.8 42.7 + - - -
346C GLU* 3.8 5.7 + - - -
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Residues in contact with LYS 292 (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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197C LYS* 4.3 12.7 - - - +
270C TYR* 3.2 38.4 - - + +
291C ARG* 1.3 74.1 - - - +
293C VAL* 1.3 69.4 + - - +
298C ALA* 3.5 3.1 - - - -
299C LEU* 2.8 45.5 + - + +
302C ALA* 3.8 26.9 - - + -
304C ASP* 2.5 29.3 + - - -
310C HIS* 4.8 10.7 - - - -
311C LYS 4.1 2.0 - - - +
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Residues in contact with VAL 293 (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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292C LYS* 1.3 82.6 - - - +
294C ASP* 1.3 64.2 + - - +
295C LYS 3.4 24.2 + - - +
297C THR 3.3 10.8 - - - +
298C ALA* 4.7 1.1 - - - -
299C LEU* 5.0 0.2 - - - -
311C LYS* 3.2 31.8 + - + +
312C CYS 3.5 30.3 - - - +
313C ALA* 3.6 16.8 - - + +
348C ILE* 4.1 13.5 - - + -
353C SER* 4.2 15.5 - - - +
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Residues in contact with ASP 294 (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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10A G 5.3 6.8 + - - -
292C LYS 4.2 0.6 + - - -
293C VAL* 1.3 72.0 - - - +
295C LYS* 1.3 66.9 + - - +
296C GLN 2.7 18.4 + - - -
297C THR* 2.8 36.9 + - + +
299C LEU* 4.1 23.7 - - + +
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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