Contacts of the helix formed by residues 256 - 265 (chain A) in PDB entry 4LBD
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 ILE 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A LEU 3.5 1.8 + - - -
255A SER* 1.3 73.2 - - - +
257A ALA* 1.3 66.5 + - + +
259A GLN* 3.8 18.5 - - + +
260A ILE* 3.1 43.3 + - + +
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Residues in contact with ALA 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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255A SER* 3.0 1.4 - - - -
256A ILE* 1.3 85.5 - - + +
258A ASP* 1.3 55.3 + - - +
260A ILE* 3.5 8.3 + - - +
261A THR* 2.7 36.2 + - - +
343A ASP 5.8 1.1 - - - +
345A GLU* 3.5 32.8 - - + +
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Residues in contact with ASP 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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254A LEU* 4.2 16.6 - - + +
255A SER* 3.0 31.2 + - - +
257A ALA* 1.3 75.7 - - - +
259A GLN* 1.3 60.7 + - - +
261A THR* 3.1 5.4 + - - -
262A LEU* 2.8 37.3 + - - +
343A ASP 4.2 0.9 - - - +
344A LEU* 3.4 21.7 - - + +
345A GLU* 3.0 28.6 + - - +
346A GLU* 3.5 29.8 + - - +
350A VAL* 4.6 0.6 - - - +
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Residues in contact with GLN 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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246A LYS* 3.5 27.4 - - - +
251A PHE* 3.1 44.8 + - + +
252A THR* 3.0 25.4 + - - +
254A LEU* 2.9 24.8 + - + -
255A SER 2.9 15.0 + - - +
256A ILE* 3.8 18.6 - - + +
258A ASP* 1.3 77.6 - - - +
260A ILE* 1.3 63.0 + - + +
262A LEU* 3.8 0.8 - - - +
263A LEU* 3.1 31.6 + - + +
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Residues in contact with ILE 260 (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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256A ILE* 3.1 41.4 + - + +
257A ALA* 3.8 6.1 - - - +
258A ASP 3.2 0.4 - - - -
259A GLN* 1.3 76.6 - - + +
261A THR* 1.3 56.0 + - - +
263A LEU* 3.2 8.9 + - + +
264A LYS* 2.8 64.0 + - + +
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Residues in contact with THR 261 (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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257A ALA* 2.7 23.3 + - - +
258A ASP* 3.5 7.9 - - - -
260A ILE* 1.3 77.6 - - - +
262A LEU* 1.3 61.3 + - - +
264A LYS* 3.6 7.7 - - - +
265A ALA* 3.1 25.3 + - + +
341A ARG* 4.6 8.7 - - + +
342A MET 5.2 0.4 - - - +
343A ASP* 4.2 44.5 + - + +
344A LEU* 4.3 12.1 - - + -
418A ASN* 5.4 0.2 + - - -
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Residues in contact with LEU 262 (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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251A PHE* 3.8 19.5 - - + -
254A LEU* 3.7 30.1 - - + -
258A ASP 2.8 19.5 + - - +
259A GLN 3.8 3.8 - - - +
261A THR* 1.3 70.1 - - - +
263A LEU* 1.3 66.7 + - - +
265A ALA* 3.4 3.2 + - - +
266A ALA* 3.0 28.9 + - - +
336A LEU* 3.2 29.1 - - + +
337A ILE* 4.3 4.3 - - + -
338A CYS 3.5 24.2 - - - +
341A ARG* 4.0 12.5 + - + -
344A LEU* 4.2 13.5 - - + -
350A VAL* 4.0 12.6 - - + -
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Residues in contact with LEU 263 (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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241A ILE* 3.9 22.0 - - + -
242A VAL* 3.9 37.0 - - + -
245A ALA* 3.9 14.1 - - + -
246A LYS* 5.6 2.0 - - - -
251A PHE* 4.0 18.6 - - + -
259A GLN* 3.1 20.5 + - + +
260A ILE* 3.6 7.2 - - + +
262A LEU* 1.3 75.1 - - - +
264A LYS* 1.3 67.8 + - - +
266A ALA 3.2 0.5 + - - -
267A CYS* 2.8 34.5 + - + +
336A LEU* 3.8 19.3 - - + -
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Residues in contact with LYS 264 (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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260A ILE* 2.8 48.2 + - + +
261A THR* 3.6 8.7 - - - +
263A LEU* 1.3 74.7 - - + +
265A ALA* 1.3 60.8 + - - +
267A CYS* 4.0 3.0 + - - -
268A LEU 5.1 0.5 + - - -
414A GLU* 2.7 59.8 + - + +
415A MET* 3.5 27.5 - - - +
417A GLU* 3.4 34.6 + - - +
418A ASN* 4.2 9.9 - - - +
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Residues in contact with ALA 265 (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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261A THR* 3.1 15.6 + - + +
262A LEU 4.1 2.0 - - - +
264A LYS* 1.3 80.7 - - - +
266A ALA* 1.3 58.1 + - - +
267A CYS 3.6 0.2 - - - -
268A LEU* 5.1 2.1 + - - +
269A ASP* 4.0 9.7 - - - +
341A ARG* 3.7 43.7 + - + +
418A ASN* 3.5 26.2 - - - +
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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