Contacts of the helix formed by residues 240 - 254 (chain A) in PDB entry 5HKE
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 THR 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ASN* 3.3 15.5 - - - +
239A MET* 1.3 89.5 - - + +
241A VAL* 1.3 64.8 + - - +
242A GLU* 3.4 10.1 + - - +
243A GLU* 3.1 31.6 + - - +
244A ASP* 3.0 18.4 + - - +
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Residues in contact with VAL 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASN* 3.9 16.5 - - + +
11A SER* 4.2 10.8 - - - +
13A TYR* 3.6 21.5 - - - +
240A THR* 1.3 74.5 - - - +
242A GLU* 1.3 63.9 + - - +
244A ASP* 3.1 2.6 + - - +
245A ILE* 3.0 37.9 + - + +
279A ASP* 3.7 19.1 - - - +
282A ASN* 5.7 1.8 - - - +
286A TYR* 5.2 2.7 - - - +
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Residues in contact with GLU 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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240A THR* 3.2 10.6 + - - +
241A VAL* 1.3 78.6 - - - +
243A GLU* 1.3 62.1 + - - +
245A ILE* 3.3 11.4 + - + +
246A THR* 3.0 29.1 + - - +
291B GLU* 4.6 3.3 - - - +
316B ARG 4.6 2.3 - - - +
317B LYS* 3.7 26.5 + - - +
318B GLN* 3.1 46.0 + - + +
320B ILE* 5.4 6.5 - - + -
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Residues in contact with GLU 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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238A GLY* 3.5 13.9 - - - -
239A MET* 2.7 39.6 + - - +
240A THR* 3.1 23.8 + - - +
242A GLU* 1.3 81.5 - - + +
244A ASP* 1.3 57.2 + - - +
246A THR* 3.4 9.0 + - - +
247A GLN* 2.9 29.8 + - - +
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Residues in contact with ASP 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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7A LEU* 4.1 9.5 - - + +
9A GLY* 4.4 6.7 - - - -
10A ASN* 2.7 44.1 + - - +
13A TYR* 2.7 37.4 + - + +
238A GLY* 3.7 18.8 + - - +
240A THR 3.0 14.0 + - - +
241A VAL 3.1 2.9 + - - +
243A GLU* 1.3 76.6 - - - +
245A ILE* 1.3 56.9 + - - +
247A GLN* 3.2 7.2 + - - +
248A PHE* 2.8 29.3 + - - +
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Residues in contact with ILE 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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13A TYR* 4.1 16.2 - - + -
241A VAL* 3.0 33.1 + - + +
242A GLU* 3.7 9.9 - - - +
244A ASP* 1.3 71.0 - - - +
246A THR* 1.3 66.8 + - - +
248A PHE* 3.2 7.4 + - - +
249A PHE* 3.1 47.6 + - + -
277A CYS* 4.3 8.3 - - - -
279A ASP* 5.2 0.2 - - - +
286A TYR* 3.4 51.6 - - + +
295A ILE* 4.5 8.7 - - + -
318B GLN* 5.8 0.9 - - + -
320B ILE* 5.2 7.0 - - + -
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Residues in contact with THR 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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242A GLU* 3.0 19.7 + - - +
243A GLU* 3.6 8.0 - - - +
245A ILE* 1.3 80.4 - - - +
247A GLN* 1.3 61.1 + - - +
249A PHE* 3.4 5.7 + - - +
250A HIS* 3.2 34.0 + - + +
295A ILE* 5.6 0.2 - - - -
290B TYR* 3.3 33.4 - - + +
291B GLU* 4.0 8.9 + - - -
318B GLN* 2.9 38.3 + - - +
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Residues in contact with GLN 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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7A LEU* 5.1 5.2 - - + -
235A SER* 3.2 22.8 - - - +
236A SER* 3.9 21.7 - - - +
237A LYS 6.4 0.2 - - - -
243A GLU 2.9 20.0 + - - +
244A ASP* 3.5 7.9 - - - +
246A THR* 1.3 73.6 - - - +
248A PHE* 1.3 52.3 + - - +
250A HIS* 3.0 5.9 + - - +
251A ILE* 2.8 41.5 + - + +
258B ILE* 4.0 7.3 - - - +
259B LYS* 3.0 30.6 + - - +
290B TYR* 2.7 37.2 + - - -
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Residues in contact with PHE 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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5A ILE* 3.4 32.1 - - + -
7A LEU* 3.8 26.6 - - + +
13A TYR* 3.6 27.1 - - + -
14A PHE 3.7 5.8 - - - -
15A GLY* 3.5 21.3 - - - -
244A ASP 2.8 16.4 + - - +
245A ILE 3.4 9.0 - - - +
247A GLN* 1.3 71.8 - - - +
249A PHE* 1.3 63.8 + + - +
251A ILE* 3.1 12.6 + - - +
252A LEU* 3.0 34.6 + - + +
276A ASN 3.3 23.1 - - - -
277A CYS* 3.6 22.7 - - + -
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Residues in contact with PHE 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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245A ILE* 3.1 43.2 + - + +
246A THR* 3.9 4.9 - - - +
247A GLN 3.4 0.2 - - - -
248A PHE* 1.3 72.1 - + - +
250A HIS* 1.3 61.1 + - - +
252A LEU* 3.4 6.5 + - + +
253A GLY* 2.8 26.7 + - - -
275A SER* 3.5 33.7 - - - -
276A ASN* 4.1 2.5 - - - -
277A CYS* 3.9 16.4 - - + -
286A TYR* 3.6 31.0 - - + -
287A TYR* 3.9 4.7 - - - -
288A THR* 3.7 25.1 - - + -
295A ILE* 3.8 22.2 - - + -
293B ARG* 4.1 26.5 + - + +
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Residues in contact with HIS 250 (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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246A THR* 3.2 28.5 + - + +
247A GLN* 3.0 9.3 + - - +
249A PHE* 1.3 75.6 - - - +
251A ILE* 1.3 63.1 + - - +
253A GLY* 3.2 3.8 + - - -
254A THR* 3.2 24.1 + - - +
293A ARG* 6.1 2.2 - - - -
256B GLU* 2.7 38.4 + - - +
258B ILE* 3.7 18.4 - - + +
289B THR 5.0 2.2 - - - -
290B TYR* 2.8 74.2 + + - +
293B ARG* 6.1 5.2 - - + +
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Residues in contact with ILE 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 3.6 23.8 - - + -
7A LEU* 4.2 17.9 - - + -
228A ALA* 4.5 7.4 - - + +
231A SER* 4.6 2.7 - - - -
232A LYS* 4.1 30.1 - - + +
235A SER* 3.6 26.0 - - - +
247A GLN* 2.8 26.1 + - + +
248A PHE* 3.1 11.0 + - - +
250A HIS* 1.3 75.7 - - - +
252A LEU* 1.3 61.4 + - - +
254A THR* 2.7 31.5 + - - -
255A VAL* 4.0 3.6 + - - +
258B ILE* 4.0 17.7 - - + -
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Residues in contact with LEU 252 (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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3A THR* 4.1 24.0 - - + +
5A ILE* 4.0 27.1 - - + -
16A ARG* 3.9 11.7 - - - +
17A ASN* 3.0 46.2 + - - +
248A PHE* 3.0 28.4 + - + +
249A PHE* 3.9 8.3 - - + +
251A ILE* 1.3 76.8 - - + +
253A GLY* 1.3 63.0 + - - +
255A VAL* 3.2 12.5 + - + +
256A GLU* 3.3 1.8 + - - -
275A SER* 4.0 12.3 - - - +
276A ASN 3.5 24.7 - - - +
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Residues in contact with GLY 253 (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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249A PHE 2.8 17.3 + - - -
250A HIS* 3.5 6.7 - - - -
251A ILE 3.2 0.4 - - - -
252A LEU* 1.3 76.1 - - - +
254A THR* 1.3 60.7 + - - +
255A VAL 3.1 1.0 + - - -
256A GLU* 3.2 26.5 + - - +
253B GLY 4.4 13.5 - - - +
254B THR* 5.6 1.7 - - - -
256B GLU* 5.6 4.0 - - - -
293B ARG* 5.8 4.7 - - - -
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Residues in contact with THR 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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227A ARG* 2.7 37.3 + - - -
228A ALA* 4.5 1.4 - - - -
231A SER* 3.4 33.3 + - - +
250A HIS 3.2 14.1 + - - +
251A ILE 2.7 18.0 + - - +
253A GLY* 1.3 77.3 - - - +
255A VAL* 1.3 60.6 + - - +
256A GLU 3.6 0.6 - - - +
254B THR 5.7 1.0 - - - +
256B GLU* 5.5 4.9 - - + +
258B ILE* 3.7 23.8 - - + -
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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