Contacts of the strand formed by residues 239 - 247 (chain A) in PDB entry 5IZL
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 THR 239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A CYS* 3.7 12.8 - - - -
232A PHE 3.4 13.0 - - - +
233A SER* 2.7 23.1 + - - +
237A GLN 3.9 0.2 + - - -
238A GLY* 1.3 72.5 - - - -
240A VAL* 1.3 65.2 + - - +
241A MET* 5.0 0.2 - - - +
288A ILE 3.8 0.3 - - - +
289A CYS* 3.7 0.7 - - - -
290A VAL* 2.9 35.7 + - - +
292A GLN* 3.6 2.4 - - - +
293A PHE* 3.2 61.1 + - + +
295A PRO* 4.6 1.8 - - + -
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Residues in contact with VAL 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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230A HIS 3.8 0.2 - - - +
231A CYS* 3.2 8.3 - - - -
232A PHE* 2.7 63.0 + - + -
234A ILE* 3.8 31.9 - - + -
237A GLN* 5.8 0.7 - - - +
239A THR* 1.3 76.0 - - - +
241A MET* 1.3 65.6 + - - +
242A THR* 4.3 11.4 - - + -
287A GLY* 4.7 3.1 - - - -
288A ILE 3.2 15.0 - - - +
289A CYS* 3.8 21.1 - - + -
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Residues in contact with MET 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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226A MET* 3.7 11.5 - - + +
228A VAL* 4.2 15.3 - - + -
230A HIS 3.3 4.9 - - - -
231A CYS* 3.8 18.2 - - - -
239A THR 5.0 0.2 - - - +
240A VAL* 1.3 78.2 - - - +
242A THR* 1.3 63.7 + - - +
256A VAL* 5.0 7.6 - - + -
258A ILE* 4.4 8.5 - - + -
287A GLY* 3.3 0.9 - - - -
288A ILE* 2.8 47.4 + - + +
290A VAL* 3.7 38.6 - - + -
293A PHE* 4.4 9.0 - - + -
298A LEU* 4.1 20.9 - - + -
303A VAL* 4.2 20.4 - - + -
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Residues in contact with THR 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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226A MET* 4.1 1.1 - - - -
228A VAL* 3.7 2.5 - - - -
229A ASP* 2.9 38.7 + - - +
230A HIS* 2.9 22.3 + - - +
232A PHE* 4.3 16.8 - - + -
240A VAL* 4.3 12.3 - - + -
241A MET* 1.3 76.7 - - - +
243A GLY* 1.3 58.6 + - - +
285A ARG* 4.0 10.4 + - - -
286A LEU 3.2 10.1 - - - -
287A GLY* 4.0 11.2 - - - -
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Residues in contact with GLY 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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226A MET* 3.5 16.2 - - - +
227A SER 3.0 15.0 - - - -
229A ASP* 3.1 12.3 + - - -
242A THR* 1.3 76.9 - - - +
244A THR* 1.3 62.2 + - - -
245A ILE 4.2 0.5 + - - -
284A ASP 4.3 0.2 - - - +
285A ARG* 3.5 5.7 - - - +
286A LEU* 2.9 31.4 + - - +
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Residues in contact with THR 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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9A ASN* 3.3 20.7 + - - +
53A PHE* 4.9 2.9 - - - -
109A ILE* 3.1 40.5 - - + +
226A MET* 3.4 1.8 - - - -
227A SER* 2.8 39.4 + - - -
229A ASP* 4.3 4.0 + - - -
243A GLY* 1.3 75.7 - - - -
245A ILE* 1.3 71.7 + - - +
246A LEU* 3.4 4.1 + - + +
283A GLY* 4.5 7.2 - - - +
284A ASP 3.6 12.1 - - - +
285A ARG* 4.0 11.5 + - + +
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Residues in contact with ILE 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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224A PHE* 3.8 24.5 - - + -
225A LEU 3.6 11.7 - - - +
226A MET* 4.3 11.2 - - + +
243A GLY 5.2 0.2 - - - +
244A THR* 1.3 75.8 - - - +
246A LEU* 1.3 60.3 + - - +
247A SER 3.8 12.6 - - - +
248A GLY 4.1 2.9 - - - +
250A ILE* 4.0 7.4 - - + -
280A ALA* 3.7 36.8 - - + +
281A MET 4.0 2.5 - - - +
282A GLN* 3.6 24.6 - - - +
283A GLY* 2.9 28.8 + - - -
284A ASP* 3.0 17.6 + - + +
286A LEU* 4.2 11.7 - - + -
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Residues in contact with LEU 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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108A GLN 3.5 23.6 - - - +
109A ILE* 4.4 19.7 - - + -
225A LEU* 2.9 30.7 + - + +
227A SER* 4.1 17.0 - - - +
244A THR* 4.0 7.9 - - + +
245A ILE* 1.3 77.9 - - - +
247A SER* 1.3 62.1 + - - +
282A GLN* 3.0 26.9 + - - -
302A LEU* 4.6 2.5 - - + -
341A HIS* 3.8 30.1 - - + +
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Residues in contact with SER 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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221A SER 5.3 1.2 + - - -
222A GLY* 5.2 0.2 - - - -
223A PRO* 2.9 38.3 + - - +
224A PHE* 3.2 5.7 - - - -
225A LEU* 3.0 44.3 + - - +
245A ILE* 3.7 3.6 - - - +
246A LEU* 1.3 81.4 - - - +
248A GLY* 1.3 66.3 + - - +
282A GLN* 4.3 5.4 - - - +
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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