Contacts of the helix formed by residues 235 - 249 (chain A) in PDB entry 4KZK
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 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A GLN* 5.4 3.2 + - - -
44A ASP* 3.8 8.5 + - - -
181A ARG* 4.6 0.4 - - - +
207A ALA 5.0 8.1 + - - -
233A GLY 3.5 0.8 - - - -
234A SER* 1.3 85.2 + - - +
236A ASP* 1.3 63.6 + - - +
237A ASP* 3.6 15.0 + - - +
238A THR* 2.8 40.8 + - - +
239A THR* 2.8 20.1 + - - -
261A ILE 3.2 23.1 - - - +
262A ASN* 3.7 2.7 - - - +
600A GAL 3.0 39.4 + - - +
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Residues in contact with ASP 236 (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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235A ASN* 1.3 74.7 - - - +
237A ASP* 1.3 60.4 + - - +
239A THR* 3.3 1.0 + - - -
240A VAL* 2.8 35.3 + - - +
260A GLY* 3.4 6.6 - - - -
261A ILE 2.8 24.3 + - - +
262A ASN* 3.4 7.4 - - + +
263A GLY 2.9 23.4 + - - -
264A SER* 3.6 4.2 + - - +
266A VAL* 3.8 22.4 - - + -
267A ALA* 3.5 12.8 + - - +
279A PHE* 3.4 18.2 - - + -
282A SER* 2.7 20.9 + - - -
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Residues in contact with ASP 237 (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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41A GLN* 5.1 3.7 - - - +
43A ASP 4.4 3.3 - - - +
44A ASP* 3.7 34.8 - - - +
45A PRO* 4.6 0.2 - - - +
208A ASP* 4.9 4.5 - - - -
209A THR* 2.9 36.9 + - - +
235A ASN* 3.3 19.0 + - - +
236A ASP* 1.3 80.6 + - - +
238A THR* 1.3 62.7 + - - +
240A VAL* 3.5 1.2 + - - +
241A GLY 3.3 14.0 + - - -
262A ASN* 4.6 2.1 + - - -
266A VAL* 3.5 29.1 - - - +
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Residues in contact with THR 238 (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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170A LEU* 3.2 10.6 - - - +
204A GLU* 3.4 28.7 - - - +
207A ALA 3.7 7.4 - - - +
208A ASP* 3.6 29.6 - - - +
212A ALA* 3.0 18.4 - - - +
233A GLY* 3.8 1.0 - - - -
234A SER* 3.2 17.7 + - - +
235A ASN* 2.8 38.4 + - - +
237A ASP* 1.3 70.9 - - - +
239A THR* 1.3 65.7 + - - +
241A GLY 2.9 10.9 + - - -
242A ALA 3.4 0.3 + - - -
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Residues in contact with THR 239 (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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170A LEU* 3.9 8.7 - - - +
231A ALA 4.3 5.2 - - - +
232A PHE* 4.4 1.6 - - - -
233A GLY 3.2 18.4 + - - -
235A ASN 2.8 22.7 + - - -
236A ASP 3.7 3.6 - - - -
238A THR* 1.3 76.3 + - - +
240A VAL* 1.3 61.3 + - - +
242A ALA* 3.1 15.6 + - - +
243A VAL* 3.2 11.5 + - - +
258A ALA* 3.8 26.0 - - + -
259A VAL 3.7 19.2 + - - +
260A GLY* 3.6 13.4 - - - -
279A PHE* 3.9 11.0 - - + -
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Residues in contact with VAL 240 (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 THR* 4.4 10.5 - - + +
236A ASP 2.8 20.9 + - - +
237A ASP 3.8 3.8 - - - +
239A THR* 1.3 73.2 - - - +
241A GLY* 1.3 67.1 + - - +
243A VAL* 3.1 7.5 + - - +
244A ARG* 2.9 51.8 + - + +
266A VAL* 3.5 23.1 - - + -
270A GLU* 3.9 15.9 - - + +
279A PHE* 3.5 21.8 - - + -
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Residues in contact with GLY 241 (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 THR* 3.7 30.0 - - - +
212A ALA* 4.0 0.2 - - - -
213A PHE* 3.5 18.8 - - - -
237A ASP 3.3 4.9 + - - -
238A THR 2.9 10.1 + - - -
240A VAL* 1.3 80.3 - - - +
242A ALA* 1.3 54.7 + - - +
244A ARG* 3.5 2.4 + - - -
245A ALA* 3.0 28.1 + - - +
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Residues in contact with ALA 242 (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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168A LEU* 3.8 24.7 - - + -
170A LEU* 3.8 21.3 - - + -
212A ALA* 4.4 1.8 - - - +
216A ALA* 3.7 13.2 - - + -
220A PHE* 3.8 6.8 - - + -
231A ALA* 4.2 12.1 - - + -
238A THR 3.4 3.6 + - - -
239A THR 3.1 10.3 + - - +
241A GLY* 1.3 72.4 - - - +
243A VAL* 1.3 59.8 + - - +
245A ALA* 3.3 1.6 + - - +
246A GLY* 2.9 27.0 + - - -
256A MET* 4.5 3.6 - - - +
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Residues in contact with VAL 243 (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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239A THR 3.2 10.0 + - - +
240A VAL* 3.1 12.2 + - + +
242A ALA* 1.3 76.9 - - + +
244A ARG* 1.3 74.0 + - - +
246A GLY* 3.3 2.2 + - - -
247A GLU* 3.0 46.3 + - + +
251A ILE 4.8 0.9 - - - +
256A MET* 4.6 10.3 - - + -
258A ALA* 3.5 31.9 - - + -
277A THR* 4.4 1.1 - - - +
278A GLY* 4.0 11.2 - - - +
279A PHE* 3.8 31.4 - - + +
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Residues in contact with ARG 244 (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 THR* 5.6 3.4 - - + -
213A PHE* 3.9 18.9 - - + -
240A VAL* 2.9 33.3 + - + +
241A GLY* 3.7 5.6 - - - +
243A VAL* 1.3 84.9 - - - +
245A ALA* 1.3 62.1 + - - +
247A GLU* 2.8 44.1 + - - +
248A GLY* 3.2 17.8 + - - -
270A GLU* 2.8 42.2 + - - -
273A LYS* 3.5 15.0 - - - +
277A THR* 3.7 5.1 - - - +
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Residues in contact with ALA 245 (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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213A PHE* 3.6 17.0 - - + +
216A ALA* 3.7 20.6 - - + -
217A ASN* 3.5 25.5 - - - +
220A PHE* 3.9 4.7 - - + -
241A GLY 3.0 17.6 + - - +
242A ALA 3.7 4.7 - - - +
243A VAL 3.3 0.2 - - - -
244A ARG* 1.3 74.2 - - - +
246A GLY* 1.3 63.8 + - - +
248A GLY* 3.1 12.1 + - - -
249A ARG* 3.3 17.0 + - - +
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Residues in contact with GLY 246 (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 PHE* 3.4 19.6 - - - -
242A ALA 2.9 13.3 + - - -
243A VAL* 3.7 3.4 - - - -
245A ALA* 1.3 75.3 - - - +
247A GLU* 1.3 62.9 + - - +
249A ARG* 2.9 9.2 + - - -
251A ILE* 2.9 42.7 + - - +
256A MET* 5.2 2.0 - - - -
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Residues in contact with GLU 247 (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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243A VAL* 3.0 25.4 + - + +
244A ARG* 2.8 51.8 + - - +
245A ALA 3.3 0.2 - - - -
246A GLY* 1.3 75.1 - - - +
248A GLY* 1.3 62.0 + - - +
249A ARG 3.2 0.9 + - - -
250A GLY* 3.3 11.4 + - - -
251A ILE 3.4 12.7 + - - +
252A GLY* 4.9 7.6 - - - -
277A THR* 3.9 13.9 - - - +
278A GLY 4.7 1.0 + - - +
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Residues in contact with GLY 248 (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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213A PHE* 6.4 0.4 - - - -
244A ARG 3.2 6.6 + - - -
245A ALA* 3.1 9.5 + - - -
247A GLU* 1.3 78.5 - - - +
249A ARG* 1.3 60.6 + - - +
250A GLY 3.6 0.4 + - - -
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Residues in contact with ARG 249 (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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217A ASN* 3.3 29.4 + - - +
220A PHE* 3.1 35.4 + - - +
221A THR* 2.9 43.6 + - - +
245A ALA 3.3 13.0 - - - +
246A GLY 2.9 7.1 + - - +
248A GLY* 1.3 79.4 - - - +
250A GLY* 1.3 60.0 + - - +
251A ILE* 3.3 13.5 + - + +
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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