Contacts of the helix formed by residues 259 - 268 (chain X) in PDB entry 4HSC
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 SER 259 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129X GLU* 5.3 3.8 - - - -
258X TYR* 1.3 77.2 - - - +
260X LYS* 1.3 65.3 + - - +
261X SER* 3.6 7.8 + - - -
262X GLN* 3.1 29.6 + - - +
263X ILE* 3.0 24.8 + - - +
282X PHE* 3.3 11.3 - - - -
451X GLU 4.9 0.7 + - - -
452X TYR* 3.7 15.2 - - - +
453X VAL 5.9 0.4 - - - -
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Residues in contact with LYS 260 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259X SER* 1.3 73.8 - - - +
261X SER* 1.3 62.4 + - - +
263X ILE* 3.3 5.9 - - - +
264X GLU* 3.1 27.0 + - - +
271X SER* 3.6 21.8 - - - +
275X ASP* 3.6 24.7 + - + -
282X PHE* 3.3 32.5 - - + -
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Residues in contact with SER 261 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128X GLY* 4.5 6.1 - - - -
129X GLU* 2.7 29.7 + - - -
259X SER* 3.3 5.6 + - - -
260X LYS* 1.3 77.9 - - - +
262X GLN* 1.3 62.7 + - - +
264X GLU* 3.5 11.5 - - - +
265X ALA* 3.0 30.0 + - - +
448X ASN* 5.2 0.9 - - - +
450X THR* 3.0 25.6 + - - +
451X GLU 4.8 0.2 + - - -
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Residues in contact with GLN 262 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156X ILE* 3.4 23.3 - - + +
255X SER* 3.3 13.5 + - - -
256X MET 3.1 21.6 + - - -
257X VAL 3.8 0.2 - - - -
258X TYR* 2.8 39.1 + - - -
259X SER* 3.1 19.3 + - - +
261X SER* 1.3 78.4 + - - +
263X ILE* 1.3 75.0 + - - +
265X ALA 3.2 1.6 + - - -
266X ALA* 2.8 31.7 + - - +
450X THR* 4.1 4.5 - - + -
452X TYR* 3.7 31.8 + - + -
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Residues in contact with ILE 263 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255X SER* 4.0 14.8 - - - +
256X MET 4.0 14.1 - - - +
257X VAL* 3.9 31.2 - - + -
259X SER 3.0 16.1 + - - +
260X LYS* 3.3 16.6 - - - +
262X GLN* 1.3 81.0 + - - +
264X GLU* 1.3 66.4 + - - +
266X ALA* 4.3 0.4 - - - -
267X LEU* 2.9 54.7 + - + +
271X SER* 4.5 4.7 - - - -
274X LEU* 4.0 19.7 - - + -
280X ILE* 4.9 2.2 - - + -
282X PHE* 4.5 10.3 - - + -
294X ILE* 4.6 4.0 - - + -
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Residues in contact with GLU 264 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126X LYS* 3.0 32.1 + - - +
260X LYS 3.1 8.4 + - - +
261X SER* 3.5 11.1 - - - +
263X ILE* 1.3 82.0 - - - +
265X ALA* 1.3 56.8 - - - +
268X ASN* 2.9 32.2 + - - -
269X VAL 3.4 12.9 + - - +
270X ASN* 3.2 21.2 + - - -
271X SER* 2.7 54.2 + - - +
448X ASN* 5.0 3.3 + - - +
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Residues in contact with ALA 265 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156X ILE* 3.5 30.0 - - + +
158X THR* 3.7 16.9 + - - +
261X SER 3.0 15.1 + - - +
262X GLN* 3.2 3.1 + - - +
264X GLU* 1.3 80.3 - - - +
266X ALA* 1.3 62.3 + - - +
268X ASN* 3.8 7.5 + - - +
448X ASN* 3.7 33.5 + - + +
450X THR* 4.8 3.4 - - + -
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Residues in contact with ALA 266 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156X ILE* 4.3 9.6 - - + +
253X THR* 4.0 10.9 - - - +
254X GLU 5.3 1.6 - - - +
255X SER* 3.7 31.2 - - - +
262X GLN* 2.8 22.2 + - - +
263X ILE* 3.2 4.2 + - - +
265X ALA* 1.3 79.1 - - - +
267X LEU* 1.3 64.7 + - - +
268X ASN* 3.8 0.3 + - - +
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Residues in contact with LEU 267 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253X THR* 3.1 34.6 + - - +
254X GLU* 3.6 35.0 - - - +
255X SER* 3.9 4.7 - - - +
263X ILE* 2.9 35.5 + - + +
266X ALA* 1.3 79.8 - - - +
268X ASN* 1.3 72.0 + - - +
269X VAL* 3.6 18.0 - - + +
274X LEU* 4.2 11.7 - - + -
294X ILE* 3.5 36.6 - - + +
296X ALA* 4.7 7.2 - - + -
298X LYS* 4.1 4.3 + - - -
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Residues in contact with ASN 268 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160X PRO* 3.6 32.7 - - + +
162X ASP* 3.1 33.2 + - - +
163X ILE* 4.9 2.8 - - - +
164X SER* 3.1 12.1 + - - -
251X GLN* 5.0 5.7 - - - +
253X THR* 5.5 2.9 - - + -
264X GLU 2.9 11.3 + - - -
265X ALA* 3.8 5.5 + - - +
266X ALA 3.4 2.2 - - - +
267X LEU* 1.3 80.7 - - - +
269X VAL* 1.3 55.8 + - - +
298X LYS* 2.7 40.4 + - - +
448X ASN* 5.5 1.5 + - - +
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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