Contacts of the strand formed by residues 249 - 253 (chain B) in PDB entry 1X7W
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 CYS 249 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B GLN* 3.9 7.1 + - - +
218B GLU 3.7 6.9 - - - +
219B GLY* 3.6 9.8 - - - -
222B VAL* 3.4 26.7 - - + +
224B LEU* 3.8 19.7 - - + -
238B ALA* 3.8 22.1 + - + +
241B ALA* 3.9 17.5 - - - -
247B VAL* 3.7 4.8 + - - -
248B SER* 1.3 74.1 + - - +
250B GLU* 1.3 60.9 + - - +
251B VAL* 3.7 7.0 + - + +
336B LEU* 3.9 21.5 - - - -
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Residues in contact with GLU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B VAL* 3.8 18.3 - - + +
217B GLN 3.3 8.7 - - - +
218B GLU* 3.3 11.4 - - - +
219B GLY* 3.0 24.9 + - - +
222B VAL 2.7 14.5 + - - +
223B THR* 3.4 2.7 - - - +
224B LEU* 2.8 29.3 + - - +
249B CYS* 1.3 70.5 - - - +
251B VAL* 1.3 61.9 + - - +
252B ILE* 3.9 5.1 + - + +
268B SER* 2.5 37.9 + - - +
271B LYS* 2.8 37.8 + - - -
272B THR* 4.4 2.2 - - + -
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Residues in contact with VAL 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B VAL* 3.6 3.5 - - - -
216B ILE* 2.8 56.4 + - + +
217B GLN* 2.9 26.1 + - + -
224B LEU* 3.7 10.8 - - + -
231B VAL* 4.7 1.3 - - + +
234B ILE* 3.8 31.4 - - + +
235B ARG* 4.1 7.9 - - + -
238B ALA* 3.6 31.0 - - + -
249B CYS 4.2 5.6 - - - +
250B GLU* 1.3 74.1 - - - +
252B ILE* 1.3 62.3 + - - +
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Residues in contact with ILE 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B ALA* 3.7 16.2 - - + -
214B GLU 3.4 11.2 - - - +
215B VAL* 3.9 20.4 - - + +
223B THR* 3.6 27.1 - - + -
224B LEU 2.9 15.4 + - - +
225B VAL* 3.4 7.0 - - + +
226B ALA 3.1 24.9 + - - +
231B VAL* 5.3 0.2 - - - -
234B ILE* 3.9 5.2 - - - +
250B GLU* 4.3 5.8 - - + -
251B VAL* 1.3 81.2 - - - +
253B ASP* 1.3 63.1 - - - +
254B LEU* 3.8 0.8 + - - +
264B THR* 4.4 3.6 - - + +
265B ILE* 3.7 31.9 - - + -
268B SER* 3.6 20.9 - - - +
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Residues in contact with ASP 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B ILE 4.6 1.0 - - - +
165B PRO 5.1 0.2 - - - -
166B ARG* 2.8 48.0 + - - +
170B GLN* 4.5 0.3 - - - +
213B ALA* 3.3 0.7 - - - -
214B GLU* 2.9 40.1 + - + +
216B ILE* 4.6 2.6 - - + +
226B ALA 3.4 5.0 - - - +
227B TRP* 3.7 5.7 - - - +
228B GLY 4.5 1.4 + - - -
231B VAL* 3.6 30.2 - - + +
251B VAL 4.4 0.2 + - - -
252B ILE* 1.3 72.5 - - - +
254B LEU* 1.3 66.3 + - - +
255B ARG* 3.1 28.4 + - + +
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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
------------------------------------------------------------
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