Contacts of the helix formed by residues 278 - 283 (chain E) in PDB entry 4CDC
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 PHE 278 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D ASP* 3.6 34.5 - - + -
63D ILE* 4.4 19.7 - - + -
64D TYR* 3.2 52.5 - + + -
66D GLN* 3.4 29.4 - - + -
80D PHE* 6.2 1.1 - + - -
235E TYR* 4.0 5.6 - - - -
270E TYR 5.2 2.8 + - - -
271E ALA* 5.0 2.8 - - - +
272E GLN* 5.5 0.4 - - - -
277E GLY* 1.3 79.0 - - - -
279E PRO* 1.3 74.2 - - + +
280E TYR* 4.5 4.0 - - + +
281E LEU* 2.9 25.2 + - + +
282E ILE* 3.3 12.0 + - - +
323E TYR* 5.3 0.9 - - - +
379F THR* 4.8 6.3 - - - -
429F ILE* 4.6 12.6 - - + -
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Residues in contact with PRO 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235E TYR* 3.9 18.6 - - + +
238E ALA* 4.8 0.9 - - + -
239E SER* 3.3 17.7 - - - +
277E GLY 4.1 1.6 - - - +
278E PHE* 1.3 87.3 - - + +
280E TYR* 1.3 63.3 + - - +
282E ILE* 3.1 0.4 + - + -
283E ALA* 2.9 27.2 + - + +
284E GLY 3.5 3.1 + - - -
347E ALA* 3.8 29.6 - - + -
348E VAL 5.4 2.2 - - - +
349E ALA* 6.0 3.6 - - + -
382F ALA* 4.0 23.3 - - + -
429F ILE* 6.5 0.2 - - + -
431F VAL* 4.4 12.3 - - + +
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Residues in contact with TYR 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D THR* 3.7 17.4 - - + +
63D ILE* 3.9 33.2 - - + -
69D GLU* 2.6 33.1 + - + -
278E PHE* 3.1 2.3 + - + +
279E PRO* 1.3 78.0 - - - +
281E LEU* 1.3 64.9 + - + +
284E GLY* 3.3 6.8 - - - -
285E LYS* 3.1 20.5 + - + -
321E TYR* 3.6 25.5 + + - -
322E HIS* 4.2 5.8 - - - -
323E TYR* 3.4 68.4 - + + +
431F VAL* 3.8 15.7 - - + +
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Residues in contact with LEU 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D ILE* 4.0 31.6 - - + -
66D GLN* 5.8 0.4 - - + -
78D PHE* 3.5 49.1 - - + -
80D PHE* 3.9 11.9 - - + -
270E TYR* 3.5 32.1 - - + +
278E PHE* 2.9 18.1 + - + +
280E TYR* 1.3 84.1 - - + +
282E ILE* 1.3 57.1 + - - +
285E LYS* 3.9 21.3 - - + -
286E TYR* 2.8 31.1 + - - +
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Residues in contact with ILE 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235E TYR* 3.8 20.9 - - + -
236E SER* 5.0 1.6 - - - +
239E SER* 3.6 12.3 - - - +
240E MET* 3.9 16.4 - - + -
264E VAL* 3.6 38.1 - - + -
268E SER* 3.6 23.1 - - - +
270E TYR* 4.2 5.4 - - + +
271E ALA* 3.9 15.7 - - + -
278E PHE 3.7 11.0 - - - +
279E PRO 3.1 1.4 + - - -
281E LEU* 1.3 85.3 - - - +
283E ALA* 1.3 64.0 + - - +
284E GLY 3.1 0.9 - - - -
286E TYR* 3.5 6.2 - - + +
287E ALA* 2.8 31.2 + - - +
292E LEU* 4.6 2.0 - - + +
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Residues in contact with ALA 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239E SER* 3.3 26.3 + - - +
240E MET* 5.4 0.2 - - - -
242E MET* 3.4 33.0 - - + -
243E LEU* 4.0 13.8 - - + +
279E PRO 2.9 11.9 + - - +
282E ILE* 1.3 75.6 - - - +
284E GLY* 1.3 56.5 + - - +
287E ALA* 3.2 3.2 - - - +
318E SER* 2.8 27.4 + - - -
431F VAL* 5.2 0.9 - - + -
433F ALA* 3.4 8.2 - - + +
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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