Contacts of the strand formed by residues 215 - 222 (chain H) in PDB entry 5FHX
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 ALA 215 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162H ARG* 4.0 13.9 - - - -
163H GLN 3.4 28.3 - - - +
164H PRO* 3.5 5.6 - - + -
165H PRO* 4.1 5.6 - - - -
212H ASP 5.5 0.2 - - - +
213H ASP 3.0 12.0 + - - +
214H THR* 1.3 75.7 - - - +
216H THR* 1.3 61.2 + - - +
217H TYR* 3.2 19.2 - - + -
237H SER* 4.8 2.0 - - - -
238H VAL 3.0 28.5 + - - +
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Residues in contact with THR 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162H ARG* 3.3 4.3 - - - -
163H GLN* 2.8 40.1 + - - -
165H PRO* 5.1 3.7 - - - +
215H ALA* 1.3 71.7 - - - +
217H TYR* 1.3 61.6 + - - +
218H TYR* 3.6 35.4 + - + +
234H GLN 4.6 2.0 - - - +
235H GLY* 3.9 18.4 - - - -
236H THR 3.5 9.6 - - - +
237H SER* 4.2 13.7 + - - +
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Residues in contact with TYR 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H GLU* 3.6 8.3 - - - +
142H LEU* 4.7 9.8 - - + +
144H ILE* 3.5 28.9 - - + -
160H TRP* 5.2 5.2 - + + -
161H VAL 3.9 1.8 - - - -
162H ARG* 3.0 44.5 + - + -
172H LEU* 3.7 18.8 - - + -
204H LEU* 4.6 7.9 - - + -
206H MET* 3.7 12.9 - - + +
213H ASP* 2.6 32.1 + - - +
215H ALA* 3.2 24.5 - - + -
216H THR* 1.3 73.4 - - - +
218H TYR* 1.4 61.1 + - - +
235H GLY* 3.2 2.9 - - - -
236H THR* 2.8 36.8 + - + +
238H VAL* 3.8 22.7 - - + -
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Residues in contact with TYR 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130H GLU* 3.2 5.8 - - - +
160H TRP* 3.3 15.5 - - - -
161H VAL* 2.8 41.0 + - + +
163H GLN* 3.8 25.3 + - + -
169H LEU* 4.4 8.5 - - + -
216H THR* 3.6 25.6 - - + +
217H TYR* 1.4 72.0 - - - +
219H CYS* 1.3 59.5 + - - +
232H TRP* 3.8 30.5 - + + -
233H GLY 3.4 20.2 - - - -
234H GLN 3.4 23.6 + - - -
235H GLY* 3.6 8.1 - - - -
42L GLN* 3.4 16.6 + - - -
45L GLY 5.4 1.9 - - - -
46L GLN 3.7 8.8 + - - -
47L PRO* 3.8 18.6 - - + -
48L PRO* 4.5 0.9 - - + -
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Residues in contact with CYS 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H LEU* 4.2 10.2 - - - +
130H GLU* 3.0 28.1 + - - -
146H CYS* 2.0 52.7 - - + -
158H ILE* 3.8 9.0 - - + -
159H ASN 3.1 10.5 - - - +
160H TRP* 3.9 9.0 - - + -
218H TYR* 1.3 73.9 - - - +
220H ALA* 1.3 61.2 + - - +
221H ARG 4.4 0.2 - - - -
232H TRP* 3.5 2.6 - - - +
233H GLY 3.1 24.8 + - - -
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Residues in contact with ALA 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H LEU* 4.9 0.2 - - - -
158H ILE* 4.4 3.5 - - - +
159H ASN* 2.9 48.7 + - + +
161H VAL* 5.5 1.8 - - + +
219H CYS* 1.3 75.2 - - - +
221H ARG* 1.3 59.6 + - - +
229H MET* 3.8 24.7 - - + -
231H PHE 3.2 13.5 - - - +
232H TRP* 3.6 27.6 - - + -
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Residues in contact with ARG 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H VAL* 3.5 22.3 - - - +
128H LEU* 4.2 10.0 - - + +
151H PHE* 3.5 49.9 - - + +
156H SER* 4.1 11.3 + - - -
157H SER 3.6 11.0 - - - +
158H ILE* 3.8 12.1 - - + +
220H ALA* 1.3 73.5 - - - +
222H ASP* 1.3 76.4 + - - +
223H GLY* 4.0 6.3 - - - -
224H TYR* 5.3 10.7 - - - -
229H MET* 3.5 4.2 - - - -
230H ASP* 3.0 54.0 + - - +
231H PHE* 2.9 31.4 + - + +
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Residues in contact with ASP 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156H SER* 4.9 5.4 + - - -
157H SER* 3.0 35.1 + - - +
159H ASN* 3.2 13.2 + - - -
174H MET* 3.3 4.0 - - - +
176H TRP* 4.3 1.0 - - - -
220H ALA 3.8 0.2 + - - -
221H ARG* 1.3 86.6 + - - +
223H GLY* 1.3 66.1 + - - +
227H TYR* 3.0 21.8 - - + +
228H ALA 3.4 5.4 - - - +
229H MET* 3.8 5.0 - - - +
230H ASP* 3.8 1.1 - - - -
100L ARG* 2.8 44.5 + - - -
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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