Contacts of the strand formed by residues 205 - 211 (chain B) in PDB entry 5X2L
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 205 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B ASP 2.9 19.6 + - - +
179B ALA* 3.2 5.2 - - + -
180B LEU 2.9 26.3 + - - -
198B LYS* 4.9 1.6 - - - +
203B SER* 3.5 17.2 + - - +
204B VAL* 1.3 78.5 - - - +
206B VAL* 1.3 61.9 + - - +
207B TYR* 3.4 36.8 - - + +
257B ASP* 3.4 25.1 - - + +
305B VAL* 4.5 15.9 - - + +
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Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B LEU* 3.8 4.7 - - + +
182B VAL* 5.1 1.8 - - + -
190B LEU* 3.9 25.1 - - + -
193B ILE* 4.3 16.4 - - + -
194B ALA* 4.3 12.6 - - + -
197B VAL* 3.7 38.1 - - + -
198B LYS* 4.2 11.0 - - - -
205B LYS* 1.3 77.6 - - - +
207B TYR* 1.3 62.2 + - - +
255B LEU 4.3 9.6 - - - +
256B VAL* 3.5 11.2 - - + +
257B ASP* 2.9 38.8 + - - +
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Residues in contact with TYR 207 (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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179B ALA* 3.6 31.2 - - + -
180B LEU 2.8 12.1 + - - +
181B VAL* 3.4 11.9 - - + -
182B VAL* 2.9 29.1 + - - +
190B LEU* 4.6 2.7 - - - -
205B LYS* 3.4 28.7 - - + +
206B VAL* 1.3 79.0 - - - +
208B ALA* 1.3 60.3 + - - +
257B ASP* 4.0 9.2 - - + -
258B ASP* 3.4 31.4 - - + -
260B PHE* 3.7 18.6 - + + -
298B PHE* 3.9 20.6 - + - -
301B VAL* 3.6 34.1 - - + +
305B VAL* 4.2 3.2 - - + +
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Residues in contact with ALA 208 (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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181B VAL* 5.1 1.1 - - - +
182B VAL 3.2 6.5 - - - +
184B VAL* 3.6 15.9 - - + -
190B LEU* 3.6 32.5 - - + -
206B VAL 4.3 0.2 + - - -
207B TYR* 1.3 74.6 - - - +
209B ALA* 1.3 60.3 + - - +
256B VAL* 4.3 2.3 - - + +
258B ASP 3.0 7.5 + - - -
259B ILE* 3.6 19.8 - - + -
260B PHE* 3.0 31.0 + - - -
292B ALA* 5.1 0.2 - - - +
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Residues in contact with ALA 209 (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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181B VAL* 4.1 4.5 - - + -
182B VAL 2.8 13.4 + - - +
183B PRO* 3.2 4.8 - - + +
184B VAL* 2.9 24.9 + - - +
208B ALA* 1.3 73.0 - - - +
210B GLU* 1.3 59.9 + - - +
211B PRO* 4.7 0.2 - - - +
240B VAL* 5.6 0.2 - - - +
260B PHE 3.5 5.8 - - - -
262B VAL* 5.8 0.2 - - + -
288B VAL* 3.4 12.3 - - + +
289B GLY* 3.6 22.0 - - - -
292B ALA* 3.5 27.6 - - + -
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Residues in contact with GLU 210 (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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184B VAL* 3.8 13.4 - - + +
209B ALA* 1.3 74.0 - - - +
211B PRO* 1.4 77.8 - - + +
214B ALA 2.7 15.9 - - - +
215B ASP* 3.3 11.2 - - + +
217B CYS* 3.0 25.7 + - - +
218B TYR* 2.8 31.4 + - - +
259B ILE* 4.0 7.0 - - + +
260B PHE 3.0 9.6 + - - +
261B THR* 3.0 8.8 - - + -
262B VAL* 2.9 28.2 + - - +
288B VAL* 3.8 1.8 - - - +
402B MG 2.1 30.5 - - - -
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Residues in contact with PRO 211 (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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184B VAL 4.6 0.2 - - - +
209B ALA 4.7 0.2 - - - +
210B GLU* 1.4 91.9 - - + +
212B SER* 1.3 65.3 + - - +
213B ASN 4.0 6.7 - - - +
214B ALA* 2.9 35.4 + - + +
215B ASP* 3.3 4.6 + - - +
235B THR* 3.8 20.2 - - - +
237B ALA* 4.0 1.1 - - + -
240B VAL* 3.6 35.0 - - + -
262B VAL* 3.4 7.4 - - - +
264B GLU* 4.3 2.9 - - - +
267B ILE* 3.9 22.9 - - + -
288B VAL* 4.3 5.2 - - + -
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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