Contacts of the helix formed by residues 238 - 256 (chain A) in PDB entry 6YB9
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 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A GLU* 3.6 33.5 + - + +
237A VAL* 1.3 78.8 - - - +
239A PRO* 1.4 73.9 - - - +
240A GLU* 3.7 10.5 + - - +
241A GLY* 3.0 21.5 + - - +
242A LEU* 3.1 22.9 + - - +
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Residues in contact with PRO 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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237A VAL 5.1 0.2 - - - +
238A THR* 1.4 89.1 - - - +
240A GLU* 1.3 59.9 + - + +
242A LEU* 3.5 11.7 + - + +
243A GLN* 3.3 29.2 + - - +
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Residues in contact with GLU 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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238A THR* 3.3 7.9 + - - +
239A PRO* 1.3 78.6 - - + +
241A GLY* 1.3 61.3 + - - +
243A GLN* 3.5 7.6 + - - +
244A MET* 3.4 20.1 + - - +
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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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234A LEU* 4.0 25.7 - - - +
236A GLU 5.8 0.2 - - - -
238A THR* 3.0 21.4 + - - -
240A GLU* 1.3 75.9 - - - +
242A LEU* 1.3 60.0 + - - +
244A MET* 3.6 9.3 + - - +
245A VAL* 3.3 25.8 + - - +
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Residues in contact with LEU 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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39A ILE* 4.6 5.4 - - + -
48A ASN* 3.9 29.2 - - + +
49A HIS 4.1 13.0 - - - +
50A LEU* 4.0 22.5 - - + +
231A TYR* 4.1 28.5 - - + -
234A LEU* 4.8 0.4 - - - +
237A VAL* 3.9 14.4 - - + -
238A THR 3.1 9.8 + - - +
239A PRO* 3.8 12.1 - - + +
240A GLU 3.4 0.2 - - - -
241A GLY* 1.3 72.8 - - - +
243A GLN* 1.3 65.6 + - - +
245A VAL* 3.5 6.7 + - + +
246A LYS* 2.9 27.7 + - - +
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Residues in contact with GLN 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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50A LEU* 4.9 4.9 - - - +
239A PRO 3.3 16.5 + - - +
240A GLU* 3.9 7.4 - - - +
241A GLY 3.4 0.4 - - - -
242A LEU* 1.3 80.2 + - - +
244A MET* 1.3 61.1 + - - +
246A LYS* 3.4 26.1 + - - +
247A LYS* 3.0 38.6 + - - +
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Residues in contact with MET 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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230A SER* 3.7 24.2 - - - +
234A LEU* 4.7 10.1 - - + -
240A GLU 3.4 10.5 + - - +
241A GLY* 3.6 11.2 - - - +
243A GLN* 1.3 73.7 - - - +
245A VAL* 1.3 86.5 + - + +
247A LYS* 3.2 8.9 + - - +
248A ASN* 3.0 44.0 + - - +
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Residues in contact with VAL 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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39A ILE* 3.9 17.5 - - + -
50A LEU* 4.4 7.6 - - + -
230A SER* 4.1 3.1 - - - +
231A TYR* 3.6 40.4 - - + +
234A LEU* 4.3 3.6 - - + -
241A GLY 3.3 14.1 + - - +
242A LEU* 3.6 11.0 - - + +
244A MET* 1.3 91.9 - - + +
246A LYS* 1.3 64.1 + - - +
248A ASN* 3.2 7.1 + - - +
249A PHE* 3.0 50.5 + - + -
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Residues in contact with LYS 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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50A LEU* 4.1 24.2 - - + -
51A GLU* 3.0 38.3 + - - +
52A GLY* 5.1 3.3 - - - -
56A ILE* 4.8 8.5 - - + +
242A LEU 2.9 18.0 + - - +
243A GLN* 3.6 25.8 + - - +
244A MET 3.3 0.4 - - - -
245A VAL* 1.3 76.0 - - - +
247A LYS* 1.3 52.6 + - + +
249A PHE* 3.2 9.2 + - - +
250A GLU* 2.9 58.9 + - + +
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Residues in contact with LYS 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 GLN* 3.0 23.6 + - - +
244A MET* 3.2 8.0 + - - +
246A LYS* 1.3 71.7 - - + +
248A ASN* 1.3 57.6 + - - +
250A GLU* 3.2 20.5 + - - +
251A TRP* 2.8 34.9 + - - +
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Residues in contact with ASN 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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225A GLN 3.7 13.9 + - - +
226A LYS* 3.3 41.7 + - - +
230A SER* 3.1 32.8 + - - +
244A MET* 3.0 31.4 + - - +
245A VAL 3.4 8.1 - - - +
247A LYS* 1.3 75.2 - - - +
249A PHE* 1.3 61.0 + - + +
251A TRP* 3.2 5.2 + - - +
252A VAL* 3.2 25.5 + - - +
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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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39A ILE* 3.7 14.4 - - + -
50A LEU* 5.4 3.8 - - + -
53A LYS* 3.7 28.0 - - + -
56A ILE* 3.7 28.0 - - + +
57A SER* 5.4 1.8 - - - -
60A ILE* 4.7 0.2 - - - +
211A ASN* 3.4 36.3 - - + +
212A ASP* 3.6 25.1 - - - -
226A LYS 4.6 0.9 - - - -
227A ASP 4.4 2.9 - - - -
228A LYS* 4.0 21.5 - - + -
230A SER* 5.0 0.2 - - - -
245A VAL* 3.0 45.4 + - + +
246A LYS* 3.5 10.8 - - + +
248A ASN* 1.3 76.6 - - + +
250A GLU* 1.3 57.5 + - - +
252A VAL* 3.3 3.6 + - - +
253A ALA* 3.0 27.2 + - - +
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Residues in contact with GLU 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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56A ILE* 4.1 14.2 - - + +
246A LYS* 2.9 42.4 + - - +
247A LYS* 3.2 30.4 + - - +
249A PHE* 1.3 73.4 - - - +
251A TRP* 1.3 60.9 + - - +
253A ALA* 3.3 7.1 + - + +
254A GLU* 2.9 48.7 + - - +
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Residues in contact with TRP 251 (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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180A TRP* 5.2 1.1 - + - -
183A GLN 5.2 2.9 - - - -
185A CYS* 3.6 31.0 - - - -
216A LEU* 5.0 5.2 - - + -
218A PRO* 4.0 18.2 - - + -
226A LYS* 3.5 46.1 - - + +
247A LYS 2.8 13.0 + - - +
248A ASN* 3.3 11.0 - - - +
250A GLU* 1.3 77.6 - - - +
252A VAL* 1.3 70.3 + - + +
254A GLU* 3.5 2.4 + - - -
255A ARG* 3.2 81.0 + - + +
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Residues in contact with VAL 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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60A ILE* 3.9 16.6 - - + -
180A TRP* 4.0 20.1 - - + -
211A ASN* 3.5 28.3 - - - +
214A TRP* 4.1 11.9 - - + -
216A LEU* 4.2 8.1 - - + -
226A LYS* 3.8 22.7 - - + +
248A ASN 3.2 15.0 + - - +
249A PHE 3.8 5.6 - - - +
250A GLU 3.2 0.2 - - - -
251A TRP* 1.3 82.9 - - + +
253A ALA* 1.3 64.3 + - - +
255A ARG* 3.2 4.3 + - - +
256A VAL* 3.0 23.6 + - + +
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Residues in contact with ALA 253 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ILE* 4.0 27.4 - - + -
59A LYS* 3.3 37.8 + - + +
60A ILE* 4.4 12.0 - - + +
249A PHE 3.0 17.5 + - - +
250A GLU* 3.6 7.9 - - + +
252A VAL* 1.3 75.5 - - - +
254A GLU* 1.3 60.3 + - + +
255A ARG 3.6 0.2 + - - -
256A VAL* 3.8 8.2 + - - +
257A GLU* 4.8 0.7 + - - +
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Residues in contact with GLU 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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59A LYS* 4.9 5.1 + - - +
250A GLU* 2.9 32.7 + - - +
251A TRP* 3.9 6.1 - - - +
252A VAL 3.2 0.2 - - - -
253A ALA* 1.3 77.4 - - + +
255A ARG* 1.3 73.2 + - - +
257A GLU* 5.2 3.4 + - - +
258A LEU* 4.8 8.0 - - - +
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Residues in contact with ARG 255 (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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180A TRP* 4.4 13.5 - - + -
183A GLN* 3.8 22.5 - - - +
251A TRP* 3.2 87.6 + - - +
252A VAL* 3.2 4.1 + - - +
254A GLU* 1.3 92.9 + - - +
256A VAL* 1.3 63.8 + - - +
257A GLU 3.3 2.9 - - - -
258A LEU* 3.2 30.0 + - + +
259A LEU* 4.0 6.4 - - - +
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Residues in contact with VAL 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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59A LYS* 4.5 5.6 - - + -
60A ILE* 4.1 32.5 - - + -
63A CYS* 4.1 22.2 - - + +
64A ILE* 3.8 33.9 - - + -
180A TRP* 4.2 21.1 - - + -
252A VAL* 3.0 13.6 + - + +
253A ALA* 3.8 13.9 - - - +
254A GLU 3.7 0.8 - - - -
255A ARG* 1.3 77.1 - - - +
257A GLU* 1.3 63.6 + - - +
259A LEU* 3.2 20.2 + - + +
260A LEU* 4.5 0.9 + - - +
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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