Contacts of the strand formed by residues 237 - 244 (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 ARG 237 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A GLY* 5.0 6.1 + - - -
213A ARG* 6.0 1.6 - - - +
235A GLY 4.6 5.8 + - - +
236A PHE* 1.3 74.7 - - - +
238A PRO* 1.4 73.3 - - + +
239A LEU* 4.0 18.1 - - - +
252A TYR* 3.3 4.9 - - - -
253A GLY* 2.7 55.1 + - - +
254A ARG* 2.9 31.7 + - - +
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Residues in contact with PRO 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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232A ALA* 6.4 1.1 - - + -
236A PHE 4.2 4.3 - - - +
237A ARG* 1.4 87.6 + - + +
239A LEU* 1.3 65.8 + - - +
240A GLU 5.3 0.9 - - - +
241A GLU* 6.0 3.6 - - + +
251A ALA 3.9 1.1 - - - +
252A TYR* 3.8 22.0 - - + -
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Residues in contact with LEU 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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117A HIS* 4.3 7.2 - - + -
213A ARG* 3.7 44.2 - - + +
237A ARG* 4.2 19.5 - - - +
238A PRO* 1.3 80.6 - - - +
240A GLU* 1.3 68.4 + - + +
251A ALA* 2.9 15.8 + - + +
252A TYR 3.5 24.9 - - - +
253A GLY* 3.6 17.9 - - - +
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Residues in contact with GLU 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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113A ALA* 5.0 0.2 - - - +
116A ARG* 2.8 40.2 + - - -
117A HIS* 2.7 30.5 + - + +
238A PRO* 5.3 0.8 - - - +
239A LEU* 1.3 80.3 - - - +
241A GLU* 1.3 72.5 + - - +
249A LEU* 5.1 1.6 - - + +
251A ALA* 3.0 41.4 + - + +
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Residues in contact with GLU 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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228A ARG* 2.8 45.7 + - - +
238A PRO* 6.0 3.4 - - + +
240A GLU* 1.3 85.7 - - - +
242A ALA* 1.3 62.8 + - - +
248A VAL* 5.6 3.4 - - + +
249A LEU* 3.4 8.3 - - - +
250A LEU* 3.4 22.9 - - + +
252A TYR* 5.2 1.4 + - - -
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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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109A LEU* 3.9 18.2 - - + +
116A ARG* 4.2 24.2 - - - +
240A GLU* 6.1 0.2 - - - -
241A GLU* 1.3 76.3 - - - +
243A ALA* 1.3 61.1 + - - +
248A VAL* 3.3 5.6 - - - +
249A LEU* 2.7 41.0 + - + +
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Residues in contact with ALA 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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109A LEU* 3.8 7.7 - - - +
221A LYS* 3.6 30.1 - - - +
242A ALA* 1.3 76.6 - - - +
244A GLU* 1.3 64.7 + - - +
245A GLY 5.4 0.4 - - - +
247A TRP 3.4 9.9 - - - +
248A VAL* 4.1 2.5 - - + -
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Residues in contact with GLU 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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105A GLU* 3.7 25.9 - - + +
108A ARG* 2.7 49.7 + - - +
109A LEU* 4.1 15.0 + - + +
112A LYS* 4.8 7.6 + - - +
243A ALA* 1.3 75.3 - - - +
245A GLY* 1.3 67.6 + - - +
246A GLU 3.4 0.5 + - - -
247A TRP* 3.0 30.0 + - - +
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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