Contacts of the helix formed by residues 270 - 279 (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 ASN 270 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126X LYS* 5.5 0.2 - - - +
164X SER* 4.3 6.2 + - - +
166X ILE* 4.5 19.2 - - + +
187X GLU* 4.2 13.9 + - - +
188X ASN* 3.4 30.1 + - - +
264X GLU* 3.2 20.8 + - - -
269X VAL* 1.3 77.4 - - - +
271X SER* 1.3 63.6 + - - +
272X LYS* 3.0 42.8 + - - +
273X ILE* 3.1 17.7 + - + +
274X LEU* 3.2 18.2 + - - +
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Residues in contact with SER 271 (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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260X LYS* 3.6 36.9 + - - +
263X ILE* 4.5 6.3 - - - -
264X GLU* 2.7 39.8 + - - +
269X VAL 4.1 0.7 - - - -
270X ASN* 1.3 68.8 + - - +
272X LYS* 1.3 60.9 + - - +
274X LEU* 3.5 10.2 - - - +
275X ASP* 2.7 38.1 + - - +
280X ILE* 5.2 0.4 - - - +
282X PHE* 5.7 1.1 - - - -
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Residues in contact with LYS 272 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189X LYS* 4.5 19.2 - - - +
270X ASN* 3.0 23.4 + - - +
271X SER* 1.3 81.1 + - - +
273X ILE* 1.3 57.3 + - + +
275X ASP* 4.2 3.5 - - - +
276X GLY* 2.8 26.3 + - - -
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Residues in contact with ILE 273 (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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166X ILE* 4.0 30.1 - - + -
269X VAL* 5.0 2.0 - - + -
270X ASN* 3.1 23.0 + - + +
272X LYS* 1.3 77.4 - - + +
274X LEU* 1.3 54.5 + - - +
276X GLY* 4.8 0.9 - - - -
277X THR* 2.7 49.4 + - + +
349X PHE* 3.6 28.7 - - + -
394X LEU* 4.6 10.1 - - + -
401X HIS* 4.8 15.0 - - + +
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Residues in contact with LEU 274 (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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263X ILE* 4.0 38.8 - - + +
267X LEU* 4.2 9.4 - - + -
269X VAL* 3.7 36.3 - - + +
270X ASN 3.2 13.0 + - - +
271X SER* 3.5 8.5 - - - +
273X ILE* 1.3 75.6 - - - +
275X ASP* 1.3 60.5 + - - +
277X THR* 4.2 2.9 - - - -
278X LEU* 3.0 55.8 + - + +
280X ILE* 4.1 12.4 - - + +
294X ILE* 4.2 11.9 - - + -
349X PHE* 4.2 14.8 - - + -
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Residues in contact with ASP 275 (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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260X LYS* 3.6 26.3 + - - -
271X SER* 2.7 21.1 + - - +
272X LYS* 4.2 3.6 - - - +
274X LEU* 1.3 73.8 - - - +
276X GLY* 1.3 64.1 + - - +
279X GLY* 3.0 18.7 + - - -
280X ILE* 3.0 39.6 + - + +
282X PHE* 4.2 9.6 - - + -
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Residues in contact with GLY 276 (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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272X LYS 2.8 21.6 + - - -
273X ILE* 3.9 0.7 - - - -
275X ASP* 1.3 79.7 - - - +
277X THR* 1.3 62.3 + - - +
279X GLY 4.9 0.3 + - - -
403X LYS* 5.4 1.6 + - - -
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Residues in contact with THR 277 (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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273X ILE* 2.7 30.1 + - + +
274X LEU 3.7 2.1 + - - -
276X GLY* 1.3 80.1 - - - +
278X LEU* 1.3 62.1 + - - +
349X PHE* 3.7 8.5 - - - -
392X VAL* 3.6 29.2 - - + +
394X LEU* 4.4 11.0 - - + -
401X HIS* 4.2 29.4 - - + -
403X LYS* 3.1 33.3 + - - +
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Residues in contact with LEU 278 (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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274X LEU* 3.0 23.8 + - + +
277X THR* 1.3 80.9 - - - +
279X GLY* 1.3 65.2 + - - +
280X ILE* 4.9 2.0 - - + -
294X ILE* 3.7 41.7 - - + -
349X PHE* 3.9 28.0 - - + +
350X VAL 4.8 0.2 - - - +
351X LYS* 3.1 42.3 + - + +
390X THR* 4.1 10.2 + - + +
392X VAL* 3.5 23.3 - - + -
403X LYS* 3.8 17.8 + - - +
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Residues in contact with GLY 279 (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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274X LEU 3.8 0.6 + - - -
275X ASP* 3.0 17.8 + - - -
276X GLY 4.7 0.6 + - - -
277X THR 3.7 0.4 - - - -
278X LEU* 1.3 76.8 - - - +
280X ILE* 1.3 64.5 + - - +
281X ASP 4.1 1.2 + - - -
351X LYS* 2.7 30.5 + - - +
353X GLU* 4.3 0.7 - - - +
403X LYS* 5.3 1.8 - - - -
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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