Contacts of the strand formed by residues 242 - 249 (chain E) in PDB entry 4JRX
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 242 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131E PRO* 3.6 33.0 - - + +
221E VAL 3.8 0.3 - - - +
222E GLN* 3.1 9.3 + - - +
223E PHE* 2.7 38.9 + - + +
238E LYS 4.3 2.6 + - - -
239E PRO* 4.2 2.4 - - - +
240E VAL* 3.0 36.6 + - + +
241E THR* 1.3 75.8 - - - +
243E ILE* 1.3 60.4 + - - +
244E VAL* 4.0 19.7 - - + +
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Residues in contact with ILE 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218E ARG* 4.8 4.9 - - - +
220E GLN* 3.6 43.5 - - + +
221E VAL 3.4 3.6 - - - +
222E GLN* 3.3 34.5 - - + +
242E GLN* 1.3 77.3 - - - +
244E VAL* 1.3 71.3 + - - +
245E SER* 4.8 2.2 - - - +
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Residues in contact with VAL 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131E PRO* 4.6 2.7 - - + -
132E PRO* 3.6 36.8 - - + +
133E GLU* 5.0 0.7 - - - -
134E VAL* 3.8 28.3 - - + +
220E GLN* 3.7 0.3 - - - -
221E VAL* 2.8 38.6 + - - +
242E GLN* 4.0 25.6 - - + +
243E ILE* 1.3 78.1 - - - +
245E SER* 1.3 66.2 + - - +
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Residues in contact with SER 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E VAL* 4.1 11.0 - - - +
218E ARG* 3.8 35.5 + - - +
219E CYS 3.1 14.4 - - - -
220E GLN* 4.1 1.3 - - - -
243E ILE* 4.2 4.2 + - - +
244E VAL* 1.3 79.7 - - - +
246E ALA* 1.3 62.8 + - - +
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Residues in contact with ALA 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E VAL* 3.6 21.3 - - + +
135E ALA* 3.8 2.9 - - - -
136E VAL* 3.5 34.8 - - + +
218E ARG* 3.5 3.1 - - - +
219E CYS 2.7 32.6 + - - -
245E SER* 1.3 75.0 - - - +
247E GLU* 1.3 60.0 + - - +
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Residues in contact with GLU 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E VAL* 4.2 10.9 - - - +
216E HIS* 3.1 25.2 + - + -
217E PHE 3.2 13.0 - - - +
218E ARG* 4.3 12.2 - - + -
246E ALA* 1.3 77.8 - - - +
248E ALA* 1.3 64.5 + - - +
249E TRP* 3.9 26.4 - - + -
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Residues in contact with ALA 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E VAL* 4.1 18.2 - - + -
138E GLU* 3.9 26.0 - - + +
152E LEU* 4.2 15.0 - - + -
210E TRP* 4.3 2.2 - - + -
216E HIS* 3.7 4.2 + - - -
217E PHE* 2.8 33.0 + - - +
247E GLU* 1.3 76.1 - - - +
249E TRP* 1.3 68.5 + - - +
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Residues in contact with TRP 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E GLU* 4.4 3.3 + - - +
210E TRP* 3.3 21.1 - - - -
213E PRO 3.3 22.4 - - - +
214E ARG 4.3 5.1 + - - -
215E ASN 3.3 19.3 - - - -
216E HIS* 3.3 37.3 - + + +
217E PHE* 4.3 0.4 - - - -
247E GLU* 3.9 27.6 - - + -
248E ALA* 1.3 77.6 - - - +
250E GLY* 1.3 68.2 + - - +
251E ARG* 3.6 5.7 + - - +
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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