Contacts of the helix formed by residues 241 - 248 (chain D) in PDB entry 1EFU
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 VAL 241 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168D ILE* 4.4 10.1 - - + -
171D HIS* 3.6 29.6 - - + +
228D LEU* 3.3 47.3 - - + +
229D THR* 3.8 0.6 + - - -
231D GLN 3.0 12.6 + - - +
233D PHE* 4.0 14.6 - - + -
240D THR* 1.3 72.9 - - - +
242D GLY* 1.3 61.0 + - - +
244D LEU* 3.1 18.2 + - + +
245D LEU* 2.9 35.0 + - + +
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Residues in contact with GLY 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D THR* 3.0 38.6 + - - +
240D THR* 3.0 3.0 - - - -
241D VAL* 1.3 77.8 - - - +
243D GLN* 1.3 61.0 + - - +
245D LEU* 3.3 4.3 + - - +
246D LYS* 3.0 30.0 + - - +
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Residues in contact with GLN 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D SER 4.4 3.8 + - - +
239D LYS* 3.2 23.0 - - + +
240D THR* 3.0 38.7 + - - +
242D GLY* 1.3 74.1 - - - +
244D LEU* 1.3 57.0 + - - +
246D LYS* 3.1 7.8 + - - +
247D GLU* 2.8 53.4 + - + +
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Residues in contact with LEU 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D LEU* 3.8 25.3 - - + +
167D HIS* 6.2 0.9 - - - +
168D ILE* 4.5 3.1 - - + -
233D PHE* 3.7 52.3 - - + -
239D LYS* 4.5 12.0 - - + +
240D THR 3.2 8.9 + - - +
241D VAL* 3.1 21.3 + - + +
243D GLN* 1.3 80.5 - - - +
245D LEU* 1.3 60.9 + - - +
247D GLU* 3.5 13.2 + - - +
248D HIS* 2.8 49.7 + - + -
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Residues in contact with LEU 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D ALA* 5.5 0.9 - - + -
164D LEU* 4.5 4.3 - - + -
168D ILE* 3.6 24.2 - - + -
228D LEU* 4.9 0.2 - - + -
229D THR* 3.8 26.2 - - + -
241D VAL* 2.9 25.8 + - + +
242D GLY* 3.5 7.4 - - - +
243D GLN 3.2 0.2 - - - -
244D LEU* 1.3 74.7 - - + +
246D LYS* 1.3 56.2 + - - +
248D HIS* 2.8 6.6 + - - -
249D ASN 2.7 30.3 + - - -
250D ALA* 2.9 47.3 + - + +
251D GLU* 4.0 3.4 - - - +
252D VAL* 4.0 27.4 - - + +
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Residues in contact with LYS 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D GLY 3.0 18.8 + - - +
243D GLN* 3.7 9.2 - - - +
245D LEU* 1.3 76.2 - - - +
247D GLU* 1.3 62.9 + - + +
248D HIS 3.1 0.9 + - - -
249D ASN* 3.1 22.4 + - - +
250D ALA 3.8 20.5 + - - +
251D GLU* 5.5 3.2 - - - +
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Residues in contact with GLU 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D LYS* 3.3 31.6 + - - -
243D GLN* 2.8 44.3 + - - +
244D LEU* 3.6 15.5 - - - +
246D LYS* 1.3 75.7 - - + +
248D HIS* 1.3 69.4 + - + +
249D ASN* 3.6 1.9 + - - -
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Residues in contact with HIS 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D GLY 3.5 11.6 - - - +
161D ASP* 4.6 9.4 - - - -
164D LEU* 3.6 36.4 - - + +
244D LEU* 2.8 38.3 + - + +
245D LEU 2.8 6.6 + - - +
247D GLU* 1.3 91.3 - - + +
249D ASN* 1.3 71.3 + - - +
250D ALA* 3.0 1.0 + - + -
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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