Contacts of the helix formed by residues 219 - 229 (chain B) in PDB entry 5FHK
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 219 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A THR* 4.5 15.9 - - + +
99B TYR* 3.9 21.8 - - + +
100B ASN* 4.2 4.5 - - - +
191B GLY* 4.8 0.4 - - - -
192B HIS 4.5 2.7 - - - -
217B ALA* 3.2 3.0 - - - +
218B ASN* 1.3 81.1 + - - +
220B LEU* 1.3 65.2 + - - +
221B ASN* 3.4 18.8 - - - +
222B VAL* 3.4 21.8 - - + +
223B VAL* 3.5 11.2 - - - +
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Residues in contact with LEU 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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100B ASN* 3.1 39.9 + - + +
191B GLY* 3.6 31.6 - - - +
192B HIS 4.0 5.8 + - - +
193B PRO* 4.8 2.0 - - + -
194B LEU* 4.0 11.4 - - + -
219B ALA* 1.3 71.7 - - - +
221B ASN* 1.3 66.4 + - - +
223B VAL* 3.0 8.7 + - + +
224B ARG* 2.9 22.5 + - - +
234B THR* 5.2 0.2 - - - +
235B LEU 4.1 12.6 - - - +
236B MET* 3.9 22.8 - - + +
237B PRO* 3.5 36.1 - - + -
240B MET* 4.2 7.9 - - + -
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Residues in contact with ASN 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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103A LYS* 4.0 32.4 - - + +
221A ASN* 5.8 3.4 - - - +
100B ASN* 4.6 1.4 + - - -
219B ALA* 3.4 20.6 - - - +
220B LEU* 1.3 78.2 - - - +
222B VAL* 1.3 71.9 + - - +
224B ARG* 3.3 9.3 + - - +
225B SER* 3.2 19.4 + - - -
240B MET* 4.5 13.0 - - + +
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Residues in contact with VAL 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A THR* 3.6 30.5 - - + -
103A LYS* 4.2 12.8 - - + +
107A MET* 3.6 24.6 - - + +
124A LEU* 4.5 5.2 - - + -
126A THR* 5.4 5.4 - - + -
215B PHE* 3.6 13.9 - - + -
217B ALA* 3.6 20.4 - - + -
219B ALA* 3.4 23.3 - - + +
221B ASN* 1.3 90.4 + - - +
223B VAL* 1.3 60.9 + - - +
224B ARG 3.4 0.2 - - - -
225B SER* 3.4 8.8 + - - -
226B ALA 3.2 17.3 + - - -
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Residues in contact with VAL 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B LEU* 3.8 23.6 - - + +
190B LYS 3.8 10.1 - - - +
191B GLY* 3.8 20.2 - - - +
215B PHE* 4.1 13.2 - - + -
217B ALA* 3.9 12.1 - - + -
219B ALA 3.5 16.6 - - - +
220B LEU* 3.0 12.2 + - + +
222B VAL* 1.3 75.0 - - - +
224B ARG* 1.3 59.5 + - - +
226B ALA* 3.2 3.8 + - - +
227B CYS* 2.9 26.7 + - - +
234B THR* 3.3 26.2 - - - +
236B MET* 4.2 3.6 - - + -
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Residues in contact with ARG 224 (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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103A LYS* 4.6 11.3 - - - +
220B LEU 2.9 9.7 + - - +
221B ASN* 3.6 11.7 + - - +
223B VAL* 1.3 75.7 - - - +
225B SER* 1.3 77.3 + - - +
227B CYS* 3.1 4.7 + - + +
228B SER* 1.8 69.9 + - - -
236B MET* 3.6 21.4 - - + +
240B MET* 5.3 2.5 - - + -
241B ILE* 3.8 21.1 - - + -
244B TYR* 3.3 54.7 + - - -
250B LEU* 4.3 7.4 - - + -
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Residues in contact with SER 225 (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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103A LYS* 3.8 33.6 + - - -
107A MET* 4.0 10.5 - - - +
111A ASN* 3.0 19.6 + - - -
221B ASN 3.2 6.2 + - - -
222B VAL* 3.6 9.9 - - - -
223B VAL 3.2 0.2 - - - -
224B ARG* 1.3 93.2 - - - +
226B ALA* 1.3 61.1 + - - +
228B SER* 3.3 2.6 + - - -
229B GLU* 3.1 25.3 + - - +
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Residues in contact with ALA 226 (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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111A ASN* 3.4 23.3 + - - +
114A MET* 4.2 1.8 - - + -
189B LEU* 3.8 9.9 - - + -
215B PHE* 3.8 28.0 - - + -
222B VAL 3.2 4.8 + - - +
223B VAL 3.2 9.0 + - - +
225B SER* 1.3 78.0 + - - +
227B CYS* 1.3 62.8 + - - +
229B GLU* 3.3 11.1 + - - +
230B GLY 3.5 0.2 + - - -
231B LEU* 3.4 28.8 + - + +
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Residues in contact with CYS 227 (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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165B VAL* 3.6 14.4 - - - -
166B ALA* 3.8 9.9 - - - -
167B SER* 3.4 11.6 + - - -
189B LEU* 3.4 12.7 - - + +
223B VAL 2.9 13.6 + - - +
224B ARG* 3.4 10.5 - - + +
226B ALA* 1.3 76.6 - - - +
228B SER* 1.3 58.5 + - - +
230B GLY* 3.0 17.2 + - - -
231B LEU 4.2 0.6 + - - +
232B GLY 3.5 19.0 - - - +
234B THR* 3.5 30.3 - - + -
250B LEU* 4.1 10.8 - - + -
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Residues in contact with SER 228 (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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167B SER* 3.6 10.6 + - - -
169B GLU* 5.1 2.8 - - - +
224B ARG* 1.8 51.1 + - - -
225B SER 3.7 3.8 - - - -
227B CYS* 1.3 76.9 - - - +
229B GLU* 1.3 64.0 + - - +
230B GLY 3.1 1.4 + - - -
244B TYR* 4.3 3.0 - - - -
249B SER* 5.1 2.3 + - - +
250B LEU* 3.6 23.6 - - - +
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Residues in contact with GLU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ASN* 3.4 39.8 - - + +
169B GLU* 3.2 19.9 - - - +
225B SER* 3.1 8.0 + - - +
226B ALA 3.6 9.4 - - - +
227B CYS 3.1 0.6 - - - -
228B SER* 1.3 79.7 - - - +
230B GLY* 1.3 59.1 + - - +
231B LEU* 3.6 10.2 - - + +
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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