Contacts of the strand formed by residues 214 - 221 (chain B) in PDB entry 5H2U
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 VAL 214 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209B LEU* 3.3 4.1 - - - -
210B TRP* 2.7 61.1 + - + +
213B ARG* 1.3 80.3 - - + +
215B GLN* 1.3 71.8 + - - +
216B VAL* 3.5 4.3 + - + +
251B TYR* 3.8 26.0 - - + +
265B GLU* 4.8 10.3 - - + +
407D PRO* 3.9 32.1 - - + -
408D CYS 4.8 1.1 - - - +
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Residues in contact with GLN 215 (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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207B GLU* 4.4 14.0 - - + +
208B GLY 3.5 8.7 - - - +
209B LEU* 3.9 15.0 - - + -
213B ARG 3.6 5.2 + - - +
214B VAL* 1.3 77.9 - - - +
216B VAL* 1.3 65.1 + - - +
265B GLU* 4.0 6.2 - - - +
266B LEU* 3.8 30.1 + - + +
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Residues in contact with VAL 216 (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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191B PHE* 4.5 3.6 - - + -
207B GLU* 3.7 2.8 - - - -
208B GLY 2.9 42.5 + - - +
209B LEU 3.9 13.7 - - - +
210B TRP* 4.0 2.0 - - + +
214B VAL* 4.1 8.5 - - + +
215B GLN* 1.3 80.5 - - - +
217B ALA* 1.3 60.1 + - - +
218B ILE* 3.9 13.5 - - + -
251B TYR* 3.7 34.5 - - + -
263B ILE* 3.5 15.5 - - + -
264B THR 3.2 15.7 - - - +
265B GLU* 4.4 2.0 - - + -
266B LEU* 3.7 12.1 - - - +
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Residues in contact with ALA 217 (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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197B LEU* 5.0 0.4 - - + -
205B VAL* 4.8 1.8 - - + -
206B PHE 3.3 7.9 - - - +
216B VAL* 1.3 72.6 - - - +
218B ILE* 1.3 62.8 + - - +
263B ILE* 3.3 5.5 - - - +
264B THR* 2.8 24.0 + - - +
265B GLU 4.3 0.7 - - - +
266B LEU* 3.8 11.7 - - + +
501B 1N1 2.9 63.2 - - + +
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Residues in contact with ILE 218 (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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191B PHE* 3.9 25.6 - - + -
192B THR 4.2 9.4 - - - +
193B LEU* 3.8 22.9 - - + -
204B GLU 3.7 0.9 - - - +
205B VAL* 3.3 2.5 - - - -
206B PHE* 2.8 49.9 + - + +
207B GLU 5.4 0.2 - - - +
208B GLY* 4.5 3.4 - - - -
216B VAL* 3.9 21.3 - - + +
217B ALA* 1.3 80.8 - - - +
219B LYS* 1.3 66.5 + - - +
220B VAL* 3.9 5.9 + - + -
261B TYR* 3.7 37.2 - - + -
262B ILE 3.5 2.2 - - - -
263B ILE* 3.8 11.0 - - + -
501B 1N1 3.7 2.0 - - - -
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Residues in contact with LYS 219 (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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202B PHE* 3.4 54.3 - - + -
204B GLU 3.4 3.4 - - - +
205B VAL* 4.0 9.5 - - + +
218B ILE* 1.3 72.1 - - - +
220B VAL* 1.3 60.4 + - - +
221B ILE* 4.0 10.8 + - + +
260B VAL 3.5 0.9 - - - +
261B TYR* 3.2 7.1 - - - -
262B ILE* 2.7 39.7 + - + +
317B ASN* 5.2 2.6 - - - +
330B ASP* 2.8 27.7 + - - -
333B LEU* 3.8 12.6 - - + -
501B 1N1 2.8 55.3 + - + +
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Residues in contact with VAL 220 (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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193B LEU* 4.1 9.0 - - + -
203B GLY* 3.6 6.6 - - - -
204B GLU* 2.8 38.2 + - - +
206B PHE* 3.6 35.2 - - + -
218B ILE* 4.2 5.8 - - + +
219B LYS* 1.3 73.9 - - - +
221B ILE* 1.3 60.7 + - - +
222B SER 4.3 0.2 + - - -
259B PRO* 3.7 31.0 - - + -
260B VAL 3.4 3.1 - - - -
261B TYR* 3.9 22.9 - - + -
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Residues in contact with ILE 221 (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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202B PHE* 3.2 31.0 - - + +
219B LYS* 4.4 11.9 - - + +
220B VAL* 1.3 81.4 - - - +
222B SER* 1.3 71.0 + - - +
225B ASN* 4.5 3.4 - - + -
226B LEU* 3.5 31.9 - - + -
259B PRO* 3.4 4.2 - - - +
260B VAL* 2.8 45.5 + - + +
262B ILE* 3.8 31.6 - - + -
333B LEU* 4.5 13.5 - - + -
336B LEU* 5.4 0.7 - - + -
337B ILE* 3.6 15.7 - - + -
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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