Contacts of the helix formed by residues 278 - 283 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1G ASP* 3.5 32.8 - - - -
63G ILE* 4.3 20.6 - - + -
64G TYR* 3.2 49.8 - + + -
66G GLN* 3.3 32.5 - - + -
80G PHE* 5.7 2.0 - + - -
235H TYR* 3.8 5.9 - - - +
270H TYR 5.2 2.8 + - - -
271H ALA* 4.9 1.2 - - - +
272H GLN* 5.3 1.1 - - - -
277H GLY* 1.3 80.8 - - - -
279H PRO* 1.3 74.9 - - + +
280H TYR 3.3 2.9 - - - +
281H LEU* 3.0 25.1 + - + +
282H ILE* 3.3 12.1 + - - +
323H TYR* 5.4 1.8 - - - +
379I THR* 5.2 4.7 - - - -
429I ILE* 4.9 10.5 - - + -
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Residues in contact with PRO 279 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235H TYR* 4.0 18.6 - - + +
238H ALA* 4.5 0.7 - - + -
239H SER* 3.3 18.8 - - - +
277H GLY 4.3 1.1 - - - +
278H PHE* 1.3 89.4 - - + +
280H TYR* 1.3 60.0 + - - +
282H ILE* 2.9 0.8 + - + +
283H ALA* 2.7 30.2 + - + +
284H GLY 3.4 2.4 + - - -
347H ALA* 3.7 30.7 - - + -
348H VAL 5.3 2.5 - - - +
349H ALA* 6.2 0.4 - - + -
382I ALA* 4.2 19.7 - - + -
429I ILE* 6.4 1.1 - - + -
431I VAL* 4.2 12.6 - - + -
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Residues in contact with TYR 280 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G THR* 3.7 17.7 - - + +
63G ILE* 4.2 21.3 - - + -
69G GLU* 2.5 42.2 + - + -
278H PHE* 3.2 2.3 + - + +
279H PRO* 1.3 78.3 - - - +
281H LEU* 1.3 65.0 + - + +
284H GLY* 3.2 8.0 - - - +
285H LYS* 3.0 20.5 + - + -
321H TYR* 3.7 25.1 + + - -
322H HIS* 4.2 7.0 - - - -
323H TYR* 3.4 70.7 - + + +
431I VAL* 3.8 15.7 - - + +
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Residues in contact with LEU 281 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63G ILE* 3.9 34.5 - - + -
69G GLU* 6.1 0.2 - - + -
78G PHE* 3.6 45.3 - - + -
80G PHE* 3.9 11.9 - - + -
270H TYR* 3.5 33.8 - - + +
278H PHE* 3.0 19.9 + - + +
280H TYR* 1.3 83.4 - - + +
282H ILE* 1.3 55.9 + - + +
285H LYS* 4.0 16.8 - - + +
286H TYR* 2.7 32.9 + - - +
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Residues in contact with ILE 282 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235H TYR* 3.6 19.5 - - + -
236H SER* 4.7 3.6 - - - -
239H SER* 3.5 24.5 - - - +
240H MET* 4.0 4.5 - - + -
264H VAL* 3.7 35.7 - - + -
268H SER* 3.8 21.5 - - - +
270H TYR* 4.3 4.9 - - + +
271H ALA* 3.9 18.6 - - + -
278H PHE 3.6 13.0 - - - +
279H PRO 2.9 2.8 + - - -
281H LEU* 1.3 85.5 - - + +
283H ALA* 1.3 66.5 + - - +
284H GLY 3.1 0.7 - - - -
286H TYR* 3.6 6.9 - - + +
287H ALA* 3.1 24.3 + - - +
292H LEU* 4.6 2.8 - - - +
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Residues in contact with ALA 283 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239H SER* 3.3 30.0 + - - +
240H MET* 5.3 0.2 - - - -
242H MET* 3.3 33.7 - - + -
243H LEU* 4.0 12.3 - - + +
279H PRO* 2.7 13.1 + - + +
282H ILE* 1.3 75.1 - - - +
284H GLY* 1.3 57.3 + - - +
287H ALA* 3.3 3.6 - - - +
318H SER* 2.9 24.8 + - - -
431I VAL* 5.2 0.7 - - + -
433I ALA* 3.4 8.3 - - + +
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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