Contacts of the strand formed by residues 243 - 253 (chain A) 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 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A SER* 3.5 4.0 - - - -
240A VAL* 2.9 38.4 + - + +
241A GLY 4.3 0.3 - - - +
242A GLU* 1.3 80.9 - - - +
244A ILE* 1.3 68.7 + - - +
245A PHE* 3.6 21.3 - - + -
270A SER 3.0 11.3 + - - -
272A ARG* 4.4 10.9 - - - +
276A GLU* 2.9 37.3 + - - +
354A GLU* 2.9 45.0 + - + +
355A PHE 3.7 9.9 - - - +
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Residues in contact with ILE 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A LYS* 3.6 33.0 - - + +
233A LEU* 3.7 27.6 - - + -
238A GLN 3.5 4.5 - - - +
239A SER* 4.4 5.2 - - - -
242A GLU 4.9 1.1 - - - +
243A LYS* 1.3 80.5 - - - +
245A PHE* 1.3 71.4 + - - +
246A LYS* 5.0 0.7 - - + -
353A CYS 3.8 0.3 - - - +
354A GLU* 3.1 3.5 - - - -
355A PHE* 2.8 39.5 + - - +
227C GLN* 3.6 30.3 - - + +
228C TYR* 5.5 5.2 - - + -
231C VAL* 3.9 31.2 - - + -
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Residues in contact with PHE 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A GLY* 3.1 2.8 - - - -
238A GLN* 2.8 38.1 + - + +
240A VAL* 3.9 20.0 - - + -
243A LYS* 3.6 14.6 - - + -
244A ILE* 1.3 77.1 - - - +
246A LYS* 1.3 61.0 + - - +
269A ALA* 3.8 25.8 - - + -
270A SER 4.1 0.7 - - - -
271A PRO* 4.5 9.0 - - + -
276A GLU* 3.4 31.9 - - + -
279A ALA* 4.3 8.3 - - + -
280A LEU* 4.0 24.5 - - + -
283A LEU* 3.7 17.9 - - + -
352A VAL* 4.2 2.7 - - + -
353A CYS 3.3 3.8 - - - -
354A GLU* 3.6 34.5 - - + -
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Residues in contact with LYS 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A GLU* 3.0 23.2 + - - +
233A LEU* 6.1 0.4 - - + -
236A ASN* 3.3 24.0 - - - +
237A GLY* 4.6 2.5 - - - -
244A ILE* 4.1 0.4 + - + -
245A PHE* 1.3 77.1 - - - +
247A THR* 1.3 73.0 + - - +
283A LEU* 4.4 0.2 - - - -
352A VAL* 3.5 4.0 - - - -
353A CYS 2.9 30.2 + - - +
355A PHE* 4.4 14.1 - - + -
231C VAL* 2.9 40.1 + - + +
232C GLU* 3.8 6.5 + - - -
234C PHE* 2.7 38.2 + - + +
235C PRO* 4.6 3.5 - - - +
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Residues in contact with THR 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A ASN* 3.0 46.0 + - + +
246A LYS* 1.3 85.6 - - - +
248A ALA* 1.3 64.1 + - - +
249A GLY 3.1 12.4 + - - +
283A LEU* 4.3 11.2 - - + +
287A LYS* 4.3 16.6 - - + -
350A LEU* 3.4 19.3 - - - +
351A VAL 3.0 14.2 + - - -
352A VAL* 3.8 13.7 - - - +
234C PHE* 4.1 3.0 - - - -
235C PRO* 4.9 1.6 - - - +
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Residues in contact with ALA 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A ASN* 6.1 0.4 - - - -
247A THR* 1.3 73.0 - - - +
249A GLY* 1.3 60.6 + - - +
250A PHE* 3.3 43.9 - - + -
351A VAL* 2.9 18.6 + - + +
234C PHE* 3.7 24.0 - - + -
235C PRO* 4.0 20.3 - - + +
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Residues in contact with GLY 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A ASN* 5.5 3.4 - - - -
247A THR* 3.1 14.5 + - - -
248A ALA* 1.3 78.4 - - - +
250A PHE* 1.3 60.4 + - - +
287A LYS* 3.4 36.5 + - - -
350A LEU* 4.0 6.0 - - - +
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Residues in contact with PHE 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A ALA* 3.3 34.1 - - + -
249A GLY* 1.3 80.7 - - - +
251A VAL* 1.3 67.6 + - - +
252A LYS* 3.7 36.6 - - + -
260A LEU* 3.7 22.2 - - + -
350A LEU* 3.7 3.1 - - - -
351A VAL* 3.1 26.5 + - + +
235C PRO* 4.5 13.5 - - + -
286C ALA 6.0 2.7 - - - -
287C LYS* 5.7 10.1 - - + -
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Residues in contact with VAL 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A PHE* 1.3 79.7 - - - +
252A LYS* 1.3 77.3 + - - +
289A GLU* 4.0 25.1 - - + +
348A LYS* 4.0 25.4 - - + +
349A ARG* 3.2 16.2 - - - +
350A LEU* 3.6 22.9 - - + +
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Residues in contact with LYS 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A PHE* 3.7 33.0 - - + -
251A VAL* 1.3 84.4 - - - +
253A PRO* 1.3 79.0 - - + +
256A GLU* 3.8 23.1 + - + +
257A ALA* 4.2 8.5 - - - +
260A LEU* 4.3 11.0 - - + -
292A PHE* 3.5 5.5 - - - -
348A LYS* 3.8 7.6 - - - -
349A ARG 3.0 26.4 + - - +
351A VAL* 3.7 13.9 - - + +
286C ALA 5.4 6.6 + - - -
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Residues in contact with PRO 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A LYS* 1.3 92.8 - - + +
254A PHE* 1.3 67.2 + - - +
255A THR* 3.5 3.8 - - - +
256A GLU* 3.2 35.7 + - + +
257A ALA* 2.9 18.7 + - - +
292A PHE* 4.4 0.2 - - - -
345A CYS 4.2 3.4 - - - +
346A GLY* 3.9 17.0 - - - +
347A GLU 3.2 11.7 - - - +
348A LYS* 4.0 25.4 - - + -
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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