Contacts of the strand formed by residues 348 - 355 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B VAL* 4.0 31.4 - - + +
252B LYS* 3.4 7.4 - - - -
253B PRO* 3.9 30.0 - - + +
346B GLY 4.7 3.4 + - - +
347B GLU* 1.3 74.1 + - - +
349B ARG* 1.3 84.9 + - - +
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Residues in contact with ARG 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B VAL* 3.7 8.3 - - - -
252B LYS 3.0 28.1 + - - +
289B GLU* 6.2 0.4 - - - -
290B ALA* 3.6 20.9 - - - +
292B PHE* 3.5 45.5 - - + +
333B GLU* 2.8 30.1 + - + +
343B ARG* 3.2 41.6 - - + +
347B GLU* 3.8 19.0 + - - +
348B LYS* 1.3 101.0 + - - +
350B LEU* 1.3 67.1 + - - +
351B VAL* 3.4 1.9 + - - +
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Residues in contact with LEU 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B THR* 3.4 25.1 - - - +
249B GLY* 4.1 7.0 - - - +
250B PHE* 3.7 26.7 - - - +
251B VAL* 3.7 7.6 - - + +
283B LEU 4.8 0.7 - - - +
284B VAL* 4.6 8.5 - - - +
287B LYS* 4.0 25.8 - - + -
289B GLU* 3.6 30.3 - - + +
290B ALA 2.9 21.0 + - - +
291B ALA* 3.2 20.7 - - + +
292B PHE* 3.3 10.9 + - - +
349B ARG* 1.3 72.9 - - - +
351B VAL* 1.3 59.2 + - - +
352B VAL* 3.6 15.4 + - + -
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Residues in contact with VAL 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A PHE* 4.1 22.2 - - + -
247B THR* 3.0 18.5 + - - -
248B ALA* 3.0 20.2 + - + -
250B PHE* 3.0 22.4 + - + +
252B LYS* 3.7 37.9 - - + +
257B ALA* 3.8 33.7 - - + +
260B LEU* 4.4 6.5 - - + -
261B CYS* 4.4 6.3 - - - -
268B LEU* 4.8 1.3 - - + -
349B ARG 4.0 0.4 - - - +
350B LEU* 1.3 71.8 - - - +
352B VAL* 1.3 60.7 + - - +
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Residues in contact with VAL 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B PHE* 4.2 3.1 - - + -
246B LYS 3.6 16.6 - - - +
247B THR* 3.8 6.3 - - - +
261B CYS* 4.2 0.2 - - - -
268B LEU* 3.7 12.0 - - - +
269B ALA* 3.0 26.3 + - + +
280B LEU* 3.7 28.0 - - + -
283B LEU* 4.1 14.1 - - + -
284B VAL* 5.2 1.8 - - + -
291B ALA* 3.8 25.8 - - + +
292B PHE 4.5 1.8 + - - +
350B LEU* 3.6 19.6 + - + -
351B VAL* 1.3 80.9 - - - +
353B CYS* 1.3 70.3 + - - +
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Residues in contact with CYS 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A PHE* 3.2 33.2 - - - -
245B PHE* 3.3 5.5 - - - -
246B LYS 2.9 32.4 + - - +
261B CYS* 2.0 50.9 - - + -
267B GLN 3.3 7.6 - - - +
269B ALA 4.3 1.3 - - - -
351B VAL* 4.4 1.1 - - - -
352B VAL* 1.3 76.7 - - - +
354B GLU* 1.3 61.9 + - - +
355B PHE* 3.7 23.1 - - + -
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Residues in contact with GLU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B LYS* 2.9 41.5 + - + +
244B ILE 3.2 5.6 - - - +
245B PHE* 3.7 16.6 - - + -
266B GLY* 3.5 6.9 - - - -
267B GLN* 2.8 57.3 + - + +
268B LEU 3.7 5.2 - - - +
269B ALA* 4.3 0.9 - - - +
270B SER* 2.8 31.8 + - - -
272B ARG* 6.0 0.2 - - - -
353B CYS* 1.3 74.8 - - - +
355B PHE* 1.3 62.5 + - - +
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Residues in contact with PHE 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A GLN* 3.0 34.2 + - + +
230A LYS* 4.2 27.3 + - + +
231A VAL* 3.7 33.7 - - + -
234A PHE* 3.8 35.0 - + + -
243B LYS* 3.7 9.4 - - - +
244B ILE 2.8 33.1 + - - +
246B LYS* 4.3 11.2 - - + -
264B ALA* 3.5 27.8 - - + -
265B GLY 4.2 3.8 - - - -
266B GLY* 3.7 21.8 - - - -
353B CYS* 3.7 27.1 - - + -
354B GLU* 1.3 78.9 - - - +
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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