Contacts of the strand formed by residues 236 - 245 (chain E) in PDB entry 6Q2J
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 LYS 236 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301C GLU* 5.4 5.4 + - - -
305C LYS* 5.4 11.9 - - - +
234E ARG* 3.5 25.2 + - - +
235E GLU* 1.3 103.6 + - + +
237E TYR* 1.3 62.2 + - - +
238E GLU* 3.5 8.3 + - + +
260E VAL 3.6 5.2 - - - +
261E THR* 5.0 14.6 - - + +
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Residues in contact with TYR 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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212E LEU* 3.9 28.3 - - + -
213E PRO* 4.3 8.5 - - + +
214E PHE* 3.7 32.8 - + + -
229E LEU* 3.7 29.6 - - + +
230E ASP 4.9 2.6 + - - -
233E GLN* 5.6 2.8 + - - +
234E ARG* 3.6 58.9 + - + +
236E LYS* 1.3 69.9 - - - +
238E GLU* 1.3 60.4 + - - +
239E LEU* 3.4 10.5 + - + +
258E PHE 3.4 1.7 - - - +
260E VAL* 2.9 40.3 + - + +
262E VAL* 3.9 17.9 - - + -
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Residues in contact with GLU 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234E ARG* 5.2 2.9 - - - +
236E LYS* 3.5 9.1 + - + +
237E TYR* 1.3 69.6 - - - +
239E LEU* 1.3 66.5 + - - +
240E VAL* 4.9 4.1 - - + +
257E PRO* 4.8 12.8 - - + +
258E PHE 3.8 7.6 - - - +
259E PRO* 4.4 14.1 - - + +
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Residues in contact with LEU 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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206E LEU* 4.5 13.5 - - + -
207E LEU 5.8 4.3 - - - +
212E LEU* 3.7 31.6 - - + -
214E PHE* 3.6 45.3 - - + -
237E TYR* 3.4 9.6 + - + +
238E GLU* 1.3 81.0 - - - +
240E VAL* 1.3 69.3 + - - +
257E PRO* 3.6 0.9 - - - +
258E PHE* 2.9 62.9 + - + +
260E VAL* 5.3 0.4 - - + -
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Residues in contact with VAL 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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206E LEU* 4.1 3.9 - - - +
207E LEU* 3.1 53.7 + - + +
238E GLU* 4.9 4.9 - - + +
239E LEU* 1.3 83.9 - - - +
241E ALA* 1.3 63.0 + - - +
242E VAL* 4.7 0.7 - - + -
255E MET* 3.7 32.5 - - + -
256E VAL 3.4 14.4 - - - +
257E PRO* 4.4 11.2 - - + -
258E PHE* 4.7 0.2 - - - -
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Residues in contact with ALA 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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167E PHE* 4.1 11.4 - - + -
188E PHE* 3.7 34.1 - - + -
205E ARG 3.9 4.5 - - - +
206E LEU* 4.3 9.9 - - + -
240E VAL* 1.3 73.6 - - - +
242E VAL* 1.3 63.2 + - - +
243E CYS 4.1 0.3 + - - -
254E VAL 4.0 0.5 - - - +
255E MET* 3.4 1.4 - - - -
256E VAL* 2.9 37.0 + - + +
258E PHE* 4.5 13.9 - - + +
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Residues in contact with VAL 242 (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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167E PHE* 5.2 0.2 - - - -
203E ALA 3.9 0.3 - - - +
204E TYR* 3.4 7.9 - - - +
205E ARG* 2.9 50.8 + - + +
206E LEU 5.3 0.2 - - - -
207E LEU* 4.8 18.6 - - + +
240E VAL* 4.7 5.6 - - + -
241E ALA* 1.3 76.7 - - - +
243E CYS* 1.3 64.0 + - - +
244E THR* 4.5 4.4 + - - +
253E VAL* 3.7 25.8 - - + -
254E VAL 3.3 10.1 - - - +
255E MET* 4.0 20.2 - - + -
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Residues in contact with CYS 243 (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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166E CYS* 2.0 54.7 - - + -
167E PHE* 3.9 7.8 - - + -
202E VAL* 3.6 14.6 - - - -
203E ALA 3.6 4.7 - - - -
204E TYR* 3.6 22.4 - - + -
241E ALA 4.1 1.2 + - - -
242E VAL* 1.3 73.4 - - - +
244E THR* 1.3 80.2 + - - +
252E GLU 4.0 0.7 - - - -
253E VAL* 3.3 1.0 - - - -
254E VAL* 2.8 35.0 + - + +
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Residues in contact with THR 244 (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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201E SER 4.1 0.5 - - - +
202E VAL* 3.2 6.8 - - - -
203E ALA* 2.9 49.4 + - + +
205E ARG* 5.1 9.0 + - - -
242E VAL* 4.5 4.5 + - - +
243E CYS* 1.3 80.0 + - - +
245E VAL* 1.3 74.9 + - - +
246E HIS 4.9 6.1 - - - -
252E GLU* 3.4 6.3 - - - +
253E VAL* 3.6 28.1 - - + +
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Residues in contact with VAL 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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162E PRO* 3.8 29.8 - - + -
165E LEU* 4.3 23.8 - - + -
166E CYS* 3.8 21.8 - - - -
200E ILE* 3.9 20.4 - - + -
202E VAL* 4.2 9.9 - - + -
243E CYS* 4.4 0.7 - - - -
244E THR* 1.3 79.5 - - - +
246E HIS* 1.3 90.3 + - + +
252E GLU 3.0 28.6 + - - +
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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