Contacts of the strand formed by residues 247 - 254 (chain A) in PDB entry 1JBW
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 GLY 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A TYR* 4.0 1.9 - - - +
243A GLU* 3.2 3.5 - - - -
244A ASP* 2.9 35.1 + - - +
245A GLN 3.4 0.8 - - - -
246A ASP* 1.3 82.7 - - - +
248A ARG* 1.3 75.2 + - - -
249A ILE* 5.5 0.8 - - - +
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Residues in contact with ARG 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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229A PRO* 5.4 1.8 - - - -
241A THR* 4.1 16.2 - - + -
242A TYR 3.1 6.5 - - - +
243A GLU* 3.5 38.2 + - + +
247A GLY* 1.3 81.9 - - - -
249A ILE* 1.3 65.6 + - - +
250A SER* 3.9 8.6 + - - +
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Residues in contact with ILE 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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241A THR* 3.5 3.0 - - - -
242A TYR* 2.8 52.7 + - + +
247A GLY 5.5 1.1 - - - +
248A ARG* 1.3 75.3 - - - +
250A SER* 1.3 62.3 + - - +
252A LEU* 3.8 32.1 - - + +
273A LYS* 5.3 5.4 - - + +
285A PRO* 4.0 31.4 - - + +
288A ILE* 3.6 37.5 - - + -
289A ARG* 4.0 14.1 - - - +
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Residues in contact with SER 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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241A THR* 3.9 18.6 + - - +
248A ARG* 3.9 10.3 + - - +
249A ILE* 1.3 73.6 - - - +
251A ASP* 1.3 68.3 + - - +
252A LEU* 3.1 4.9 + - - +
289A ARG* 2.8 30.3 + - - +
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Residues in contact with ASP 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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239A ARG* 4.3 19.1 - - - -
240A PHE 3.8 6.0 + - - -
241A THR* 4.2 3.6 + - - -
250A SER* 1.3 79.1 - - - +
252A LEU* 1.3 62.5 + - - +
253A GLU* 3.8 9.4 + - - +
289A ARG* 2.6 23.6 + - - +
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Residues in contact with LEU 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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239A ARG* 3.2 1.0 - - - -
240A PHE* 2.9 52.3 + - + +
242A TYR* 3.8 29.4 - - + +
249A ILE* 3.8 35.7 - - + +
251A ASP* 1.3 78.2 - - - +
253A GLU* 1.3 66.9 + - - +
269A ILE* 3.8 7.0 - - + -
288A ILE* 4.3 3.1 - - + -
289A ARG* 3.6 41.1 - - + +
292A LEU* 3.6 21.1 - - + -
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Residues in contact with GLU 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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234A HIS* 3.4 27.0 + - - +
238A GLN 3.3 6.5 - - - +
239A ARG* 2.7 44.6 + - + -
240A PHE* 4.5 1.6 - - - -
251A ASP* 3.8 7.0 + - - +
252A LEU* 1.3 82.4 - - - +
254A VAL* 1.3 62.7 + - - +
289A ARG* 4.6 4.1 + - - +
292A LEU* 3.3 6.7 - - - +
293A ALA* 3.3 31.7 + - + +
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Residues in contact with VAL 254 (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* 3.4 1.2 - - - -
238A GLN* 3.0 36.8 + - + +
240A PHE* 4.1 17.9 - - + -
253A GLU* 1.3 74.9 - - - +
255A PRO* 1.3 71.7 - - + +
256A LEU* 2.8 49.6 + - + +
261A GLN* 5.5 1.6 - - + -
262A GLN* 6.5 0.4 - - - -
265A MET* 3.8 24.9 - - + -
292A LEU* 3.6 10.5 - - + +
295A SER* 4.3 2.9 - - - -
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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