Contacts of the strand formed by residues 348 - 355 (chain C) in PDB entry 4E52
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 LYS 348 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251C VAL* 3.9 30.1 - - + +
252C LYS 3.5 7.4 - - - -
253C PRO* 3.5 32.0 - - + +
256C GLU* 5.1 1.0 + - - -
346C GLY 4.6 3.4 + - - +
347C GLU* 1.3 76.7 + - - +
349C ARG* 1.3 82.8 + - - +
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Residues in contact with ARG 349 (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 VAL* 3.1 8.9 - - - -
252C LYS 3.0 29.2 + - - +
289C GLU* 6.1 0.7 - - - -
290C ALA* 3.6 21.2 - - - +
292C PHE* 3.4 46.0 - - + +
333C GLU* 2.8 29.5 + - + +
343C ARG* 3.2 43.0 - - + +
347C GLU* 3.8 17.2 + - - +
348C LYS* 1.3 92.8 + - - +
350C LEU* 1.3 64.3 + - - +
351C VAL* 3.4 1.4 + - - +
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Residues in contact with LEU 350 (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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247C THR* 3.4 27.1 - - - +
249C GLY* 4.1 6.1 - - - -
250C PHE 3.7 28.0 - - - +
251C VAL* 3.7 7.6 - - + +
283C LEU 4.4 7.2 - - - +
284C VAL* 4.5 3.4 - - - -
287C LYS* 3.9 25.8 - - + -
289C GLU* 3.6 29.8 - - + +
290C ALA 2.9 20.0 + - - +
291C ALA* 3.2 21.5 - - + +
292C PHE* 3.3 10.7 + - - +
349C ARG* 1.3 72.3 - - - +
351C VAL* 1.3 59.0 + - - +
352C VAL* 3.6 14.7 + - + -
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Residues in contact with VAL 351 (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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234B PHE* 4.1 21.8 - - + -
247C THR* 2.9 19.9 + - - -
248C ALA* 3.0 19.5 + - + -
250C PHE* 3.0 22.6 + - + +
252C LYS* 3.7 38.4 - - + +
257C ALA* 3.8 31.2 - - + +
260C LEU* 4.5 6.3 - - + -
261C CYS* 4.4 1.3 - - - -
268C LEU* 4.8 1.3 - - + -
349C ARG 4.0 0.2 - - - +
350C LEU* 1.3 72.9 - - - +
352C VAL* 1.3 62.3 + - - +
353C CYS* 4.3 8.7 - - - -
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Residues in contact with VAL 352 (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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245C PHE* 4.2 2.2 - - + -
246C LYS 3.6 19.1 - - - +
247C THR* 3.9 14.1 - - - +
261C CYS* 4.2 0.2 - - - -
268C LEU* 3.7 11.6 - - - +
269C ALA* 2.9 27.4 + - + +
280C LEU* 3.6 30.1 - - + -
283C LEU* 4.1 11.4 - - + -
284C VAL* 5.5 0.4 - - + -
291C ALA* 3.7 26.0 - - + -
292C PHE 4.5 2.6 + - - +
350C LEU* 3.6 10.7 + - + -
351C VAL* 1.3 80.3 - - - +
353C CYS* 1.3 70.1 + - - +
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Residues in contact with CYS 353 (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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234B PHE* 3.1 36.1 - - + -
244C ILE 3.8 0.3 - - - +
245C PHE* 3.3 4.8 - - - +
246C LYS 2.9 30.2 + - - -
261C CYS* 2.0 52.0 - - + -
267C GLN 3.2 7.4 - - - +
269C ALA 4.4 1.8 - - - -
351C VAL* 4.3 1.8 - - - -
352C VAL* 1.3 76.3 - - - +
354C GLU* 1.3 61.6 + - - +
355C PHE* 3.8 22.6 - - + -
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Residues in contact with GLU 354 (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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243C LYS* 2.9 40.9 + - + +
244C ILE 3.2 6.5 - - - +
245C PHE* 3.6 15.5 - - + -
266C GLY* 3.5 7.4 - - - -
267C GLN* 2.7 61.3 + - + +
268C LEU 3.6 5.2 - - - +
269C ALA* 4.3 0.9 - - - +
270C SER* 2.7 31.9 + - - -
272C ARG* 5.6 0.9 + - - -
353C CYS* 1.3 73.7 - - - +
355C PHE* 1.3 64.0 + - - +
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Residues in contact with PHE 355 (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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227B GLN* 3.0 32.5 + - + +
230B LYS* 3.9 25.5 - - + +
231B VAL* 3.6 36.1 - - + -
234B PHE* 3.7 37.0 - + + -
242C GLU 4.2 0.3 - - - +
243C LYS* 3.6 9.2 - - - +
244C ILE* 2.8 35.0 + - + +
246C LYS* 4.4 6.7 - - + -
264C ALA* 3.6 26.2 - - + -
265C GLY 4.4 2.2 - - - -
266C GLY* 3.9 20.9 - - - -
353C CYS* 3.8 26.9 - - + -
354C GLU* 1.3 77.6 - - - +
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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