Contacts of the strand formed by residues 247 - 253 (chain A) in PDB entry 3CJR
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 TRP 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A HIS* 3.4 25.4 + + - -
105A GLU* 3.8 24.0 + - + -
106A THR* 3.5 29.2 - - + -
109A LEU* 4.2 8.1 - - + -
218A GLY* 3.7 27.6 - - - -
219A ILE 3.4 7.4 - - - -
220A LEU* 3.5 31.4 - - + -
243A ALA* 3.4 1.6 - - - +
244A GLU 3.0 39.4 + - - +
245A GLY 3.2 1.2 - - - +
246A GLU* 1.3 92.2 + - + +
248A VAL* 1.3 70.5 + - - +
36B GLU* 5.4 3.2 - - - +
39B ALA* 3.7 9.9 - - + -
40B ALA* 3.8 21.8 - - + -
43B ALA* 3.6 20.9 - - + -
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Residues in contact with VAL 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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109A LEU* 4.0 2.7 - - - -
217A THR* 2.9 24.2 + - - -
219A ILE* 2.8 43.9 + - + +
221A LYS* 3.6 41.5 - - + +
224A ALA* 4.0 16.2 - - + -
228A ARG* 5.9 1.6 - - - +
241A GLU* 5.7 3.4 - - + +
242A ALA 3.3 7.6 - - - +
243A ALA* 4.1 5.4 - - + -
247A TRP* 1.3 79.7 - - - +
249A LEU* 1.3 60.3 + - - +
250A LEU* 4.1 16.6 - - + -
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Residues in contact with LEU 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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109A LEU* 3.6 32.5 - - + +
110A ALA* 3.6 20.0 - - + +
113A ALA* 3.7 22.4 - - + -
116A ARG* 4.5 9.6 - - - +
215A LEU* 4.6 10.5 - - + -
216A LEU 3.2 12.6 - - - +
217A THR* 3.8 17.0 - - + +
240A GLU* 5.1 1.8 - - + +
241A GLU* 3.4 5.0 - - - -
242A ALA* 2.7 42.3 + - + +
248A VAL* 1.3 74.8 - - - +
250A LEU* 1.3 77.1 + - - +
251A ALA* 4.2 11.4 - - + +
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Residues in contact with LEU 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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214A ALA 3.7 2.3 - - - +
216A LEU* 2.8 39.1 + - + +
219A ILE* 3.9 13.9 - - + -
224A ALA* 4.1 15.9 - - + +
227A VAL* 3.7 28.9 - - + -
228A ARG* 4.3 7.2 - - + +
240A GLU 3.9 2.7 - - - +
241A GLU* 3.4 38.6 - - + +
248A VAL* 4.1 15.0 - - + -
249A LEU* 1.3 79.3 - - - +
251A ALA* 1.3 60.4 + - - +
252A TYR* 3.4 32.9 - - + +
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Residues in contact with ALA 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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117A HIS* 4.0 6.1 - - + +
214A ALA 3.3 4.7 - - - -
215A LEU* 3.6 24.5 - - + -
238A PRO* 3.9 0.9 - - - +
239A LEU* 2.9 28.9 + - + -
240A GLU* 3.0 38.5 + - + +
249A LEU* 4.2 5.0 - - + +
250A LEU* 1.3 73.1 - - - +
252A TYR* 1.3 66.9 + - - +
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Residues in contact with TYR 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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213A ARG* 3.1 7.4 - - - +
214A ALA* 2.8 33.6 + - + +
216A LEU* 4.2 5.6 - - + -
228A ARG* 3.3 38.5 - - + +
231A MET* 3.6 47.8 - - + -
232A ALA* 5.2 1.3 - - + -
236A PHE* 3.7 23.5 - - + -
237A ARG 3.3 19.1 - - - -
238A PRO* 3.8 22.0 - - + -
239A LEU* 3.5 6.5 - - - -
241A GLU* 5.2 1.1 + - - -
250A LEU* 3.4 40.7 - - + +
251A ALA* 1.3 77.1 - - - +
253A GLY* 1.3 58.0 + - - +
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Residues in contact with GLY 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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211A GLY 5.4 0.7 - - - -
212A GLY 3.5 8.1 - - - -
213A ARG* 4.3 2.5 - - - -
236A PHE* 3.4 4.2 - - - -
237A ARG* 2.7 62.2 + - - +
239A LEU* 3.6 13.3 - - - +
252A TYR* 1.3 74.1 - - - +
254A ARG* 1.3 59.2 + - - -
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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