Contacts of the strand formed by residues 237 - 243 (chain A) in PDB entry 6EBT
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 GLN 237 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A ARG* 3.3 5.7 - - - -
234A THR* 2.9 32.5 + - - +
235A HIS* 4.2 12.7 - - + +
236A THR* 1.3 86.7 + - - +
238A ASP* 1.3 72.2 + - - +
239A ALA* 4.0 0.3 - - - +
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Residues in contact with ASP 238 (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 ILE* 4.1 10.6 - - + +
232A GLY 3.7 5.8 - - - -
233A ARG* 5.1 7.7 + - - +
234A THR* 4.9 0.9 + - - -
236A THR 4.9 2.3 - - - +
237A GLN* 1.3 80.4 - - - +
239A ALA* 1.3 60.3 + - - +
452A SER* 4.9 7.0 + - - +
453A LEU* 5.5 3.5 + - - +
454A MET* 3.5 27.8 - - + +
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Residues in contact with ALA 239 (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 ILE* 3.2 18.6 - - - +
232A GLY 2.8 18.2 + - - +
234A THR* 3.7 22.4 - - + +
237A GLN 4.0 0.7 - - - +
238A ASP* 1.3 76.1 - - - +
240A VAL* 1.3 68.1 + - - +
454A MET* 3.3 19.1 - - - +
278B ALA* 5.7 2.7 - - + -
279B VAL* 3.7 20.0 - - + -
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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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232A GLY* 3.1 14.6 + - - -
239A ALA* 1.3 81.2 - - - +
241A PRO* 1.3 75.7 - - + +
454A MET* 3.9 23.1 - - + +
457A THR* 5.6 3.6 - - - +
506A MET* 5.4 2.7 - - + -
278B ALA* 4.1 17.9 - - + -
279B VAL* 3.7 32.0 - - + +
281B THR* 4.7 3.4 - - - +
283B LEU* 3.7 29.6 - - + -
284B ASN* 5.7 2.5 - - - +
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Residues in contact with PRO 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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229A ILE* 3.7 19.1 - - + -
230A LYS 3.1 18.2 - - - +
231A ILE* 4.4 2.7 - - + -
232A GLY 4.1 0.9 - - - +
240A VAL* 1.3 94.9 - - + +
242A LEU* 1.3 65.7 + - - +
449A MET* 4.6 6.3 - - + -
454A MET 6.0 0.2 - - - +
455A LEU* 3.6 31.4 - - + -
503A PRO* 4.7 1.8 - - + -
506A MET* 4.0 34.0 - - + +
507A LEU* 4.1 5.2 - - + -
279B VAL* 3.8 3.5 - - - +
281B THR* 3.6 13.7 + - - +
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Residues in contact with LEU 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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229A ILE* 4.6 0.2 - - - -
230A LYS* 3.0 54.7 + - - +
232A GLY* 4.5 4.5 - - - +
241A PRO* 1.3 75.2 - - - +
243A THR* 1.3 91.1 + - - +
246A GLN* 3.4 13.9 - - + +
247A GLU* 3.7 16.8 - - + +
507A LEU* 3.7 9.2 - - - -
279B VAL* 3.7 23.6 - - + +
281B THR* 3.6 8.5 - - + -
312B PHE* 3.8 10.8 - - + -
404B GLU* 3.3 34.3 - - + +
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Residues in contact with THR 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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225A PHE 4.2 0.4 - - - -
226A ALA* 3.3 27.1 + - - +
227A GLN 4.8 0.7 - - - -
228A ILE 3.2 12.8 - - - +
229A ILE* 4.3 9.0 - - + +
242A LEU* 1.3 90.7 - - - +
244A LEU* 1.3 65.4 + - - +
245A GLY* 3.7 3.9 + - - -
246A GLN* 2.8 59.0 + - - +
247A GLU 3.0 0.7 + - - -
507A LEU* 4.0 23.6 - - + -
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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