Contacts of the helix formed by residues 253 - 263 (chain A) in PDB entry 5HKZ
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 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A HIS* 4.4 2.5 - - - -
250A PRO* 3.0 14.1 + - - +
252A SER* 1.3 80.4 + - - +
254A LEU* 1.3 63.2 + - - +
255A LEU 3.4 2.5 - - - -
256A ARG* 3.0 22.6 + - - +
257A ASN* 2.8 44.7 + - - -
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Residues in contact with LEU 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A LEU* 4.3 9.4 - - + -
213A HIS* 3.7 16.6 - - + +
241A PHE* 5.8 0.9 - - + -
244A PHE* 3.8 33.9 - - + -
245A THR* 4.2 21.1 - - + +
248A PHE* 3.7 24.2 - - + +
250A PRO 3.2 6.0 + - - -
251A TRP* 3.1 49.2 + - + +
252A SER 3.7 0.2 - - - -
253A SER* 1.3 74.9 - - - +
255A LEU* 1.3 68.4 + - + +
257A ASN* 3.3 6.6 + - - +
258A TRP* 3.0 25.1 + - - +
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Residues in contact with LEU 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LEU* 4.3 6.3 - - + -
213A HIS* 3.5 43.2 + - + +
214A PRO 4.0 9.0 - - - +
215A ILE* 3.6 21.3 - - + -
220A GLU* 5.9 1.3 - - - +
224A LEU* 4.0 31.9 - - + -
244A PHE* 4.2 7.2 - - + -
253A SER 3.1 0.8 + - - -
254A LEU* 1.3 96.5 - - + +
256A ARG* 1.3 60.0 + - - +
258A TRP* 3.8 14.4 - - + -
259A ASN* 2.9 28.9 + - - +
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Residues in contact with ARG 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A SER* 3.0 22.4 + - - +
255A LEU* 1.3 75.0 - - - +
257A ASN* 1.3 65.9 + - - +
259A ASN* 3.4 6.1 + - - +
260A SER* 3.0 29.2 + - - +
325A PHE* 5.5 0.4 - - - -
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Residues in contact with ASN 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A PHE 2.8 29.2 + - - +
249A GLN 4.2 0.7 - - - +
250A PRO* 2.9 35.7 + - - +
253A SER* 2.8 35.7 + - - +
254A LEU 3.5 3.8 - - - +
256A ARG* 1.3 75.4 - - - +
258A TRP* 1.3 57.6 - - - +
260A SER* 3.2 1.0 + - - -
261A LEU* 2.9 41.7 + - + +
325A PHE* 3.8 28.0 - - + -
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Residues in contact with TRP 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A GLU* 3.4 46.4 - - + -
223A ALA* 3.6 8.5 - - + -
224A LEU* 3.4 39.9 - - + +
227A THR* 3.2 20.4 + - - +
244A PHE* 3.8 19.5 - + + -
248A PHE* 3.5 32.5 - + + -
254A LEU 3.0 16.3 + - - +
255A LEU* 3.8 19.3 - - + +
256A ARG 3.3 0.2 - - - -
257A ASN* 1.3 75.6 - - - +
259A ASN* 1.3 71.2 + - + +
262A ALA* 2.8 49.1 + - + +
263A VAL* 3.5 29.1 + - + -
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Residues in contact with ASN 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A GLU* 4.2 14.2 - - - +
255A LEU 2.9 18.8 + - - +
256A ARG* 3.8 7.0 - - - +
257A ASN 3.3 0.4 - - - -
258A TRP* 1.3 87.4 - - + +
260A SER* 1.3 60.5 + - - +
263A VAL* 3.2 28.2 + - - +
264A THR* 3.0 46.2 + - - +
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Residues in contact with SER 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A ARG* 3.0 18.4 + - - +
257A ASN 3.8 2.7 - - - -
259A ASN* 1.3 80.3 + - - +
261A LEU* 1.3 59.9 + - - +
264A THR* 3.8 11.9 + - - -
265A HIS* 3.4 23.2 + - - +
325A PHE* 3.8 23.5 - - - -
347A PRO* 5.6 0.7 - - - +
349A LEU* 4.0 11.0 - - - +
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Residues in contact with LEU 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A LEU 5.0 5.2 - - - +
248A PHE* 4.2 21.3 - - + -
249A GLN 5.7 1.3 - - - +
257A ASN* 2.9 23.9 + - + +
260A SER* 1.3 79.5 - - - +
262A ALA* 1.3 56.1 + - - +
265A HIS* 3.5 7.9 - - + +
268A TYR* 3.3 19.5 - - - +
293A PHE* 3.3 13.4 - - + -
303A TRP* 5.2 0.4 - - + -
324A LEU* 3.9 37.0 - - + -
325A PHE* 3.6 36.3 - - + -
328A LEU* 4.0 18.2 - - + -
349A LEU* 4.1 15.7 - - + -
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Residues in contact with ALA 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A THR* 5.2 0.9 - - - +
248A PHE* 4.1 12.1 - - + -
258A TRP* 2.8 39.6 + - + +
261A LEU* 1.3 79.7 - - - +
263A VAL* 1.3 61.0 + - - +
265A HIS 4.6 2.6 - - - +
268A TYR* 3.3 42.2 - - + +
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Residues in contact with VAL 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A GLU* 5.5 4.3 - - + +
223A ALA* 4.8 8.5 - - + -
258A TRP* 3.5 41.7 + - + -
259A ASN* 3.2 30.6 + - - +
262A ALA* 1.3 82.5 - - - +
264A THR* 1.3 68.8 + - + +
265A HIS 3.4 3.2 + - - +
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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