Contacts of the helix formed by residues 276 - 281 (chain H) in PDB entry 5GJQ
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 GLU 276 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241H ILE* 4.7 7.2 - - + -
242H GLY* 4.6 2.4 - - - -
275H ASP* 1.3 104.6 + - - +
277H ILE* 1.3 49.4 + - - +
278H ASP* 2.8 15.9 - - - +
279H ALA* 2.6 35.0 + - + +
320H ALA 2.7 14.8 + - - -
321H THR* 5.2 0.2 - - - +
322H ASN* 5.2 9.9 - - - +
310I LEU* 3.3 34.5 - - + +
313I LEU* 2.6 34.4 - - + +
314I ASN* 3.4 27.6 + - - +
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Residues in contact with ILE 277 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213H LEU* 5.6 1.1 - - + -
274H PHE* 3.2 18.2 - - + +
275H ASP 3.3 1.0 + - - -
276H GLU* 1.3 75.9 - - - +
278H ASP* 1.3 101.6 + - - +
279H ALA 2.8 1.9 + - - -
280H ILE* 2.8 29.4 + - + -
281H GLY 3.2 14.4 + - - +
302H LEU* 5.3 1.8 - - + -
319H MET* 1.6 59.0 - - + -
320H ALA 3.5 7.9 - - - +
321H THR* 3.5 20.4 - - + -
327H LEU* 4.1 24.2 - - + -
331H LEU* 5.5 2.5 - - + -
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Residues in contact with ASP 278 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276H GLU* 2.6 18.4 + - - +
277H ILE* 1.3 87.8 - - - +
279H ALA* 1.3 60.1 + - - +
281H GLY* 4.4 5.5 + - - -
282H GLY* 4.8 4.5 + - - +
321H THR* 2.6 26.5 + - - -
322H ASN* 4.8 6.3 - - - +
323H ARG* 3.4 30.8 + - - +
326H THR* 4.1 13.1 + - - +
327H LEU* 5.0 5.4 - - - -
307I ARG* 4.7 4.3 + - - -
310I LEU* 4.7 9.6 - - + -
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Residues in contact with ALA 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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242H GLY 3.8 22.2 - - - +
243H SER* 3.9 2.5 - - - +
246H VAL* 4.7 1.3 - - - +
276H GLU 2.6 16.4 + - - +
278H ASP* 1.3 72.7 - - - +
280H ILE* 1.3 60.3 + - - +
295H VAL* 3.5 0.9 - - - +
307I ARG* 2.6 53.9 + - + +
310I LEU* 3.1 29.1 - - + +
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Residues in contact with ILE 280 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241H ILE 4.7 0.2 - - - -
242H GLY* 2.8 38.4 - - - +
245H LEU* 2.4 48.0 - - + -
246H VAL* 5.0 0.9 - - - -
274H PHE* 4.5 13.9 - - + -
277H ILE* 2.8 30.7 + - + +
279H ALA* 1.3 75.0 - - - +
281H GLY* 1.3 53.6 + - - +
295H VAL* 1.9 42.8 - - - +
298H THR* 4.0 15.5 - - + +
299H MET* 4.5 12.6 - - - +
302H LEU* 4.8 12.6 - - + -
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Residues in contact with GLY 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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277H ILE* 3.2 9.0 + - - +
278H ASP 4.7 2.0 - - - -
279H ALA 4.4 2.0 - - - -
280H ILE* 1.3 85.8 - - - +
282H GLY* 1.3 59.8 + - - -
283H ALA 5.4 0.7 - - - -
292H ASP* 5.2 4.9 - - - -
295H VAL* 4.1 7.0 - - - -
296H GLN* 5.4 1.1 - - - -
299H MET* 3.4 33.0 - - - +
327H LEU* 4.2 0.2 - - - +
331H LEU* 3.5 12.3 - - - +
307I ARG* 5.2 1.3 - - - -
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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