Contacts of the helix formed by residues 241 - 251 (chain A) in PDB entry 3DBD
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 CYS 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A THR* 3.2 8.7 - - + +
240A SER* 1.3 78.7 - - - +
242A LEU* 1.3 64.4 + - - +
243A LYS* 3.8 21.5 - - - -
244A GLU* 3.5 22.2 + - + +
245A THR* 3.0 23.8 + - - -
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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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240A SER 3.9 2.6 + - - -
241A CYS* 1.3 71.6 - - - +
243A LYS* 1.3 65.7 + - - +
245A THR* 3.2 21.5 + - + +
246A TYR* 3.2 46.4 - - + +
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Residues in contact with LYS 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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241A CYS* 3.4 13.5 - - - -
242A LEU* 1.3 77.4 - - - +
244A GLU* 1.3 62.1 + - - +
246A TYR* 3.4 16.2 + - - +
247A ILE* 3.3 32.7 + - + +
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Residues in contact with GLU 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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239A THR* 3.7 28.0 - - + +
241A CYS* 3.5 26.4 + - + +
242A LEU 3.2 0.2 - - - -
243A LYS* 1.3 77.4 - - - +
245A THR* 1.3 59.5 + - - +
247A ILE* 3.2 21.1 + - - +
248A ARG* 2.9 59.8 + - + +
253A GLU* 5.0 1.7 - - - +
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Residues in contact with THR 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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237A PHE* 3.4 27.6 + - + +
239A THR* 4.2 10.3 + - - -
241A CYS 3.0 14.8 + - - -
242A LEU* 3.2 18.6 + - + +
244A GLU* 1.3 79.2 - - - +
246A TYR* 1.3 59.7 + - + +
248A ARG* 3.3 8.1 + - - +
249A ILE* 2.9 48.6 + - + +
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Residues in contact with TYR 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 LEU* 3.2 54.4 - - + +
243A LYS* 3.4 10.9 + - - +
244A GLU 3.3 0.6 - - - -
245A THR* 1.3 76.8 - - + +
247A ILE* 1.3 61.5 + - + +
249A ILE* 3.4 18.6 + - + +
250A LYS* 2.9 46.7 + - + +
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Residues in contact with ILE 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 LYS* 3.3 33.0 - - + +
244A GLU* 3.2 24.4 + - - +
246A TYR* 1.3 73.9 - - + +
248A ARG* 1.3 66.2 + - - +
250A LYS* 4.5 12.3 - - - +
251A LYS* 3.0 56.1 + - + +
253A GLU* 5.5 2.0 - - - +
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Residues in contact with ARG 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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236A PRO 5.7 0.4 - - - -
237A PHE* 3.5 22.8 + - + +
238A GLU 4.2 6.9 + - - -
239A THR* 3.0 33.0 + - - +
244A GLU* 2.9 44.8 + - + +
245A THR* 3.3 12.1 - - - +
247A ILE* 1.3 76.8 - - - +
249A ILE* 1.3 58.6 + - - +
252A ASN* 3.2 1.6 + - - -
253A GLU* 2.6 72.2 + - - +
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Residues in contact with ILE 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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221A TRP* 3.7 31.5 - - + +
237A PHE* 4.1 24.2 - - + -
245A THR* 2.9 37.1 + - + +
246A TYR* 3.8 19.5 - - + +
247A ILE 3.3 0.2 - - - -
248A ARG* 1.3 75.1 - - - +
250A LYS* 1.3 68.2 + - + +
252A ASN* 3.0 19.2 + - - +
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Residues in contact with LYS 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 TYR* 2.9 35.3 + - + +
247A ILE* 4.0 12.0 - - - +
249A ILE* 1.3 80.2 - - + +
251A LYS* 1.3 74.6 + - + +
252A ASN* 3.3 2.9 + - - +
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Residues in contact with LYS 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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247A ILE* 3.0 38.8 + - + +
250A LYS* 1.3 87.2 - - - +
252A ASN* 1.3 69.8 + - - +
253A GLU* 3.6 23.6 + - + +
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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