Contacts of the helix formed by residues 247 - 259 (chain A) in PDB entry 1EBM
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 GLY 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A CYS* 4.0 8.7 - - - -
246A VAL* 1.3 75.1 - - - +
248A THR* 1.3 65.7 + - - -
251A ALA* 3.0 24.9 + - - +
27C T 3.0 38.6 + - - -
28C C 4.3 2.0 - - - -
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Residues in contact with THR 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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237A HIS* 2.9 42.7 + - + +
241A CYS* 4.3 5.5 - - - -
247A GLY* 1.3 71.1 - - - -
249A GLN* 1.3 61.6 + - - +
252A ASP* 3.0 20.2 + - - +
293A PRO* 5.3 13.4 + - - +
296A ASN* 5.4 15.5 - - + -
297A LYS* 5.6 14.8 - - + +
27C T 3.6 5.6 + - - -
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Residues in contact with GLN 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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147A SER* 5.0 5.9 + - - -
148A SER* 5.5 0.2 - - - +
248A THR* 1.3 78.0 - - - +
250A VAL* 1.3 86.8 + - - +
252A ASP* 3.2 7.3 + - - +
253A CYS* 2.9 33.5 + - - -
266A PRO* 4.3 2.4 - - + +
267A VAL 3.5 39.3 - - - +
268A ASP* 3.9 4.1 - - - +
25C 8OG 3.5 35.4 + - - +
26C G 3.4 30.6 + - - -
27C T 3.0 14.0 + - - +
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Residues in contact with VAL 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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144A PHE* 3.6 38.4 - - + +
145A ILE* 4.4 3.8 - - + +
147A SER* 4.8 1.1 - - - +
148A SER* 4.7 7.6 - - - -
245A GLY 4.1 12.3 - - - +
246A VAL* 3.9 21.1 - - + -
247A GLY 4.0 7.0 - - - +
249A GLN* 1.3 84.4 - - - +
251A ALA* 1.3 64.2 + - - +
253A CYS* 3.1 8.8 + - - +
254A ILE* 3.0 31.8 + - + +
26C G 3.8 5.4 - - - +
27C T 2.5 22.5 + - - +
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Residues in contact with ALA 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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237A HIS* 3.4 31.9 - - + +
240A LEU* 3.7 21.8 - - + +
241A CYS* 4.3 2.0 - - - -
246A VAL* 3.8 14.8 - - + +
247A GLY 3.0 19.7 + - - +
250A VAL* 1.3 77.2 - - - +
252A ASP* 1.3 56.2 + - - +
254A ILE* 3.3 1.8 + - - -
255A CYS* 2.9 33.1 + - - -
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Residues in contact with ASP 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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233A TYR* 2.4 34.0 + - - -
237A HIS* 3.1 16.5 + - - -
248A THR* 3.0 23.7 + - - +
249A GLN* 3.2 9.1 + - - +
251A ALA* 1.3 76.1 - - - +
253A CYS* 1.3 67.8 + - - +
255A CYS* 3.2 3.6 + - - +
256A LEU* 2.9 27.4 + - - +
264A ALA* 3.8 4.2 - - - +
265A VAL 3.9 16.1 - - - +
266A PRO* 3.8 21.3 - - + +
267A VAL 5.2 1.0 + - - -
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Residues in contact with CYS 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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140A CYS* 4.8 1.6 - - - -
144A PHE* 3.8 28.9 - - + -
249A GLN* 2.9 36.5 + - - -
250A VAL* 3.3 10.1 - - - +
252A ASP* 1.3 77.3 - - - +
254A ILE* 1.3 56.8 + - - +
256A LEU* 4.8 0.2 - - - -
257A MET* 2.9 60.7 + - + +
266A PRO* 3.9 16.6 - - - +
25C 8OG 4.6 7.0 - - - -
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Residues in contact with ILE 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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137A PRO 4.9 5.8 - - - +
140A CYS* 4.1 17.0 - - + +
141A LEU* 3.4 47.8 - - + +
144A PHE* 4.8 2.5 - - + -
225A LEU* 5.3 2.9 - - + -
240A LEU* 3.7 27.4 - - + -
246A VAL* 5.0 2.0 - - + -
250A VAL* 3.0 27.3 + - + +
251A ALA* 3.7 6.1 - - - +
253A CYS* 1.3 73.1 - - - +
255A CYS* 1.3 61.7 + - - +
258A ALA* 2.8 37.6 + - + -
259A LEU* 3.2 20.3 + - + -
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Residues in contact with CYS 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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233A TYR* 4.0 6.1 - - + -
236A ALA* 4.0 12.6 - - - -
237A HIS* 3.7 38.4 - - - -
240A LEU* 4.1 6.7 - - - -
251A ALA 2.9 26.0 + - - +
252A ASP 3.6 4.0 - - - +
254A ILE* 1.3 76.4 - - - +
256A LEU* 1.3 61.4 + - - +
259A LEU* 3.3 14.2 + - - -
261A LYS* 2.9 42.9 + - + +
264A ALA* 3.9 8.5 - - + -
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Residues in contact with LEU 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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132A LEU* 3.2 51.5 - - + +
252A ASP 2.9 16.4 + - - +
253A CYS 3.9 1.6 - - - +
255A CYS* 1.3 79.6 - - - +
257A MET* 1.3 67.3 + - + +
258A ALA 3.9 0.2 + - - -
260A ASP* 4.6 4.3 + - - -
261A LYS 3.5 22.1 + - - +
262A PRO* 4.0 3.0 - - + -
264A ALA* 3.8 16.5 - - + +
266A PRO* 3.9 10.3 - - + -
312A GLY* 3.6 24.0 - - - +
313A TRP* 3.8 10.3 + - + -
315A GLN* 3.6 28.3 - - - +
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Residues in contact with MET 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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43A GLN* 3.9 31.0 - - - +
132A LEU* 3.9 19.5 - - + -
133A LEU 3.3 12.2 - - - +
134A ARG* 3.8 2.4 - - - -
135A GLN* 2.9 38.8 + - - +
140A CYS* 4.1 6.7 - - - -
144A PHE* 3.3 35.0 - - + -
253A CYS* 2.9 46.0 + - + +
256A LEU* 1.3 86.8 - - + +
258A ALA* 1.3 58.8 + - - +
259A LEU 4.0 0.2 - - - -
260A ASP 5.3 0.7 - - - -
266A PRO* 4.9 0.7 - - + -
25C 8OG 3.8 14.1 - - + +
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Residues in contact with ALA 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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134A ARG* 5.7 0.4 - - - +
135A GLN 3.6 14.8 - - - +
137A PRO* 3.9 13.5 - - + +
140A CYS* 3.5 29.8 - - + -
229A ARG* 2.7 33.6 + - - -
254A ILE* 2.8 22.4 + - + +
257A MET* 1.3 75.4 - - - +
259A LEU* 1.3 60.1 + - + +
260A ASP* 3.7 3.1 - - - -
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Residues in contact with LEU 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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137A PRO* 4.3 4.9 - - + -
225A LEU* 4.2 22.0 - - + +
228A LEU* 4.0 18.4 - - + -
229A ARG* 3.4 36.3 - - + +
236A ALA* 4.4 8.5 - - + -
240A LEU* 3.9 17.0 - - + -
254A ILE* 3.2 26.4 + - + +
255A CYS* 3.3 15.0 + - - +
258A ALA* 1.3 86.9 - - + +
260A ASP* 1.3 74.4 + - - +
261A LYS* 3.1 29.3 + - - -
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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