Contacts of the strand formed by residues 234 - 241 (chain E) in PDB entry 4NQE
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 234 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123E PRO* 3.6 32.4 - - + +
213E VAL 3.8 0.3 - - - +
214E GLN* 3.6 8.3 - - - +
215E PHE* 2.7 41.4 + - + +
230E LYS 4.6 2.0 + - - -
231E PRO* 4.2 2.0 - - - +
232E VAL* 2.8 37.7 + - + +
233E THR* 1.3 74.9 - - - +
235E ILE* 1.3 61.2 + - - +
236E VAL* 4.0 18.3 - - + +
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Residues in contact with ILE 235 (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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212E GLN* 3.3 45.1 - - + +
213E VAL 3.3 6.7 - - - +
214E GLN* 3.2 33.2 - - + +
234E GLN* 1.3 78.8 - - - +
236E VAL* 1.3 66.7 + - - +
237E SER* 4.3 3.1 - - - -
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Residues in contact with VAL 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E PRO* 4.8 1.8 - - + -
124E PRO* 3.5 39.5 - - + +
125E GLU* 4.7 0.9 - - - -
126E VAL* 3.6 30.2 - - + +
213E VAL* 2.8 32.4 + - - +
234E GLN* 4.0 24.7 - - + +
235E ILE* 1.3 76.7 - - - +
237E SER* 1.3 66.6 + - - +
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Residues in contact with SER 237 (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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126E VAL* 4.1 10.4 - - - +
210E ARG* 4.0 17.7 + - - -
211E CYS 3.2 14.8 - - - -
212E GLN* 3.9 18.5 + - - -
235E ILE* 4.3 3.6 - - - +
236E VAL* 1.3 80.9 - - - +
238E ALA* 1.3 65.3 + - - +
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Residues in contact with ALA 238 (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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126E VAL* 3.8 21.1 - - + +
127E ALA* 3.9 2.5 - - - -
128E VAL* 3.5 30.6 - - + +
210E ARG* 3.5 3.9 - - - +
211E CYS 2.8 30.2 + - - +
237E SER* 1.3 75.1 - - - +
239E GLU* 1.3 62.3 + - - +
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Residues in contact with GLU 239 (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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128E VAL* 4.3 11.6 - - - +
208E HIS* 2.8 31.5 + - - +
209E PHE 3.1 13.2 - - - +
210E ARG* 4.1 12.8 - - + -
238E ALA* 1.3 77.9 - - - +
240E ALA* 1.4 62.4 + - - +
241E TRP* 3.7 18.0 + - + +
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Residues in contact with ALA 240 (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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128E VAL* 4.2 8.3 - - + +
130E GLU* 3.6 31.9 - - + +
144E LEU* 4.2 21.1 - - + -
202E TRP* 4.6 1.3 - - + -
208E HIS* 3.7 5.4 - - - -
209E PHE* 2.7 39.1 + - - +
239E GLU* 1.4 74.2 - - - +
241E TRP* 1.3 65.5 + - - +
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Residues in contact with TRP 241 (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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130E GLU* 4.0 8.0 + - - +
202E TRP* 3.2 20.3 - - - -
205E PRO 3.9 13.2 - - - +
206E ARG* 3.7 18.8 - - - -
207E ASN 3.6 17.7 - - - -
208E HIS* 3.3 33.1 - + + -
209E PHE* 4.3 0.7 - - - -
239E GLU* 3.7 16.6 + - + -
240E ALA* 1.3 80.6 - - - +
242E GLY* 1.3 70.5 + - - +
243E ARG* 4.7 2.6 - - - +
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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