Contacts of the strand formed by residues 239 - 244 (chain A) in PDB entry 2IAU
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 239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A ALA* 4.0 10.3 - - + -
191A ILE* 3.7 24.7 - - + -
200A LEU* 4.1 1.6 - - + -
217A TRP* 3.6 36.1 - - + -
231A MET* 4.0 9.4 - - + -
232A ASP 3.7 30.1 - - - +
233A PHE* 3.8 26.0 - - + -
237A ASN 3.7 1.6 + - - -
238A ASN* 1.3 71.2 - - - +
240A LEU* 1.3 61.4 + - - +
241A VAL* 3.7 21.8 + - + -
250A GLU 3.4 3.1 - - - +
251A VAL* 3.5 0.4 - - - -
252A PHE* 2.9 39.6 + - + -
253A GLY 5.1 0.4 + - - -
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Residues in contact with LEU 240 (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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231A MET* 3.3 5.0 - - - +
232A ASP 2.9 36.4 + - - +
234A ASP* 4.2 9.9 - - + +
238A ASN* 3.6 20.2 - - + +
239A LEU* 1.3 73.2 - - - +
241A VAL* 1.3 59.7 + - - +
242A ALA 4.3 0.2 - - - -
249A ILE* 4.0 11.4 - - + -
250A GLU 3.2 3.8 - - - -
251A VAL* 3.9 12.8 - - + -
263A ILE* 3.7 25.4 - - + -
273A LEU* 4.0 12.6 - - + +
275A PHE* 4.7 2.7 - - + -
282A ILE* 3.6 29.6 - - + -
297A TRP* 3.9 29.4 - - + +
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Residues in contact with VAL 241 (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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200A LEU* 4.0 9.2 - - + -
220A ILE* 4.9 4.0 - - + -
228A ALA* 3.5 33.0 - - + -
229A ASP 4.3 0.7 - - - +
230A GLY 3.5 9.4 - - - +
231A MET* 4.0 9.0 - - + -
239A LEU* 3.7 28.9 - - + -
240A LEU* 1.3 78.0 - - - +
242A ALA* 1.3 68.1 + - - +
243A ASN* 3.1 2.1 + - - +
249A ILE* 3.3 3.7 - - - +
250A GLU* 2.8 39.9 + - + +
252A PHE* 4.0 24.7 - - + -
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Residues in contact with ALA 242 (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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228A ALA* 3.6 1.2 - - - -
229A ASP* 2.8 31.0 + - - +
230A GLY 2.9 14.1 + - - +
240A LEU 4.3 0.6 - - - -
241A VAL* 1.3 68.9 - - - +
243A ASN* 1.3 58.5 + - - +
244A TYR 3.3 2.3 + - - -
249A ILE* 4.3 14.6 - - + +
270A PRO* 3.8 17.0 - - + +
271A SER 3.5 32.5 - - - +
272A ASN* 4.1 5.4 - - - +
273A LEU* 4.4 6.3 - - + +
284A VAL* 5.9 0.4 - - + -
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Residues in contact with ASN 243 (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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220A ILE* 3.1 15.3 - - + +
221A PRO* 3.1 20.1 - - - +
224A HIS* 3.0 20.4 + - - -
227A GLY* 3.2 21.1 - - - -
228A ALA* 4.6 1.3 - - - +
241A VAL* 3.1 2.4 + - + -
242A ALA* 1.3 68.7 - - - +
244A TYR* 1.3 61.8 + - - +
245A GLY 3.2 0.3 + - - -
246A SER* 2.7 44.1 + - - +
248A HIS 3.1 16.8 + - - +
250A GLU* 2.8 30.8 - - + +
270A PRO* 3.7 6.6 - - - +
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Residues in contact with TYR 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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195A THR* 5.4 2.9 - - + -
224A HIS* 3.0 9.9 + - - -
225A GLU 4.6 2.7 - - - -
226A GLY* 3.4 15.7 - - - -
227A GLY 2.8 40.2 + - - +
229A ASP* 3.7 22.4 - - + +
242A ALA 3.3 3.2 + - - -
243A ASN* 1.3 69.6 - - - +
245A GLY* 1.3 60.4 + - - +
269A LYS* 3.5 42.8 + - + +
270A PRO* 3.4 27.6 - - - +
271A SER* 4.2 0.7 - - - -
287A HIS* 3.4 44.3 + + - +
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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