Contacts of the helix formed by residues 248 - 259 (chain A) in PDB entry 4LGD
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 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A GLU* 2.7 34.4 + - - -
247A TRP* 1.3 73.6 - - - +
249A ASP* 1.3 63.0 + - - +
250A ASP* 3.6 7.6 + - - +
251A PHE* 3.0 17.7 + - - +
252A THR* 2.8 30.5 + - - -
277A PHE* 4.7 0.3 - - - -
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Residues in contact with ASP 249 (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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247A TRP 5.4 0.3 - - - +
248A SER* 1.3 76.7 - - - +
250A ASP* 1.3 64.7 + - - +
252A THR* 4.0 7.4 - - - +
253A ASP* 2.8 33.1 + - - +
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Residues in contact with ASP 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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248A SER* 3.4 6.6 + - - +
249A ASP* 1.3 78.1 - - - +
251A PHE* 1.3 60.2 + - - +
253A ASP* 4.6 0.4 - - - -
254A PHE* 2.9 26.7 + - - +
275A HIS* 3.0 14.9 - - - -
276A PRO* 3.8 27.7 - - - +
277A PHE* 3.9 23.8 + - + +
280A ASN* 5.1 3.3 + - - -
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Residues in contact with PHE 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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120A GLU* 3.4 27.8 - - + +
123A ILE* 3.8 30.7 - - + -
211A SER* 4.1 18.6 - - - -
215A ALA* 4.2 1.8 - - + -
241A PHE* 3.8 19.5 - + - -
247A TRP* 3.7 28.5 - + + -
248A SER* 3.0 22.3 + - - +
250A ASP* 1.3 78.7 - - - +
252A THR* 1.3 64.1 + - - +
254A PHE* 3.2 3.1 + + - +
255A VAL* 3.1 37.9 + - + +
277A PHE* 3.7 32.6 - + + -
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Residues in contact with THR 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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241A PHE* 3.8 27.2 - - + -
244A PRO* 4.2 10.0 + - + +
247A TRP* 3.9 10.0 + - - +
248A SER 2.8 21.2 + - - -
249A ASP* 4.0 9.6 - - - +
251A PHE* 1.3 79.3 - - - +
253A ASP* 1.3 64.9 + - - +
255A VAL* 3.5 4.3 + - - +
256A LYS* 3.2 20.4 + - + +
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Residues in contact with ASP 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 ASP 2.8 20.6 + - - +
250A ASP* 3.8 2.7 - - - +
252A THR* 1.3 75.9 - - - +
254A PHE* 1.3 68.5 + - - +
256A LYS* 3.0 25.8 + - - +
257A LYS* 3.0 41.1 + - - +
275A HIS* 2.9 24.5 + - + +
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Residues in contact with PHE 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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127A LEU* 3.9 21.8 - - + -
131A LEU* 4.1 16.8 - - + -
207A LEU* 4.6 6.1 - - + -
211A SER* 4.0 11.2 - - - -
250A ASP 2.9 17.7 + - - +
251A PHE* 3.2 5.6 + + - +
253A ASP* 1.3 76.6 - - - +
255A VAL* 1.3 68.3 + - + +
257A LYS* 3.1 14.8 + - - +
258A CYS* 3.2 31.4 + - - -
272A LEU* 3.6 40.6 - - + -
275A HIS* 3.5 32.7 + + + +
277A PHE* 4.1 17.3 - + + -
278A ILE* 3.9 12.1 - - + -
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Residues in contact with VAL 255 (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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208A GLY* 4.7 3.4 - - - +
211A SER* 4.1 16.8 - - - -
212A ILE* 4.5 13.5 - - + -
239A PRO 4.7 4.0 - - - +
240A THR* 5.6 1.6 - - - -
241A PHE* 3.7 26.5 - - + -
251A PHE* 3.1 28.1 + - + +
252A THR 3.7 8.3 - - - +
253A ASP 3.2 0.2 - - - -
254A PHE* 1.3 81.7 - - + +
256A LYS* 1.3 65.6 + - - +
258A CYS* 3.0 7.8 + - - +
259A LEU* 3.0 46.0 + - + +
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Residues in contact with LYS 256 (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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252A THR* 3.2 12.4 + - + +
253A ASP* 3.0 20.1 + - - +
255A VAL* 1.3 81.0 - - - +
257A LYS* 1.3 75.4 + - + +
258A CYS 3.5 0.3 + - - -
259A LEU* 3.6 12.0 - - - +
260A VAL* 3.4 16.0 - - + +
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Residues in contact with LYS 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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253A ASP* 3.0 44.8 + - - +
254A PHE* 3.1 9.6 + - - +
256A LYS* 1.3 89.5 - - + +
258A CYS* 1.3 59.2 + - - +
260A VAL* 3.3 19.8 - - + +
266A ARG* 4.1 0.2 - - - +
267A ALA* 3.7 25.6 + - + +
272A LEU* 4.4 14.6 - - + -
275A HIS* 4.8 9.5 - - + -
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Residues in contact with CYS 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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204A ILE* 3.7 18.4 - - + +
205A TRP* 4.0 3.8 - - - -
207A LEU* 5.0 2.5 - - - -
208A GLY* 3.6 24.5 - - - -
254A PHE* 3.5 32.8 - - - -
255A VAL* 3.0 6.3 + - - +
257A LYS* 1.3 76.0 - - - +
259A LEU* 1.3 59.6 + - - +
260A VAL 2.8 12.3 + - - -
266A ARG* 3.1 23.9 + - - +
272A LEU* 3.4 30.5 - - - -
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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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205A TRP* 3.3 46.9 - - + +
208A GLY* 3.7 5.6 - - - +
209A ILE* 3.6 25.8 - - + +
212A ILE* 4.3 5.6 - - + -
238A PRO* 3.1 30.3 - - + +
239A PRO* 3.4 40.6 - - + +
255A VAL* 3.0 31.4 + - + +
256A LYS* 3.6 9.6 - - - +
258A CYS* 1.3 70.1 - - - +
260A VAL* 1.3 58.6 + - - +
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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