Contacts of the helix formed by residues 276 - 286 (chain C) in PDB entry 3EXG
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274C THR* 3.2 28.7 - - - +
275C ARG* 1.3 79.2 - - - +
277C GLU* 1.3 67.5 + - - +
278C ILE 3.2 0.7 - - - -
279C GLN* 3.1 19.6 + - + +
280C GLU* 3.2 13.2 + - - +
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Residues in contact with GLU 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C ARG* 2.3 37.3 + - - -
258C TYR* 3.3 17.4 + - - +
274C THR* 4.4 5.5 + - - +
276C GLU* 1.3 78.6 - - - +
278C ILE* 1.3 67.2 + - + +
280C GLU* 3.4 6.3 + - + +
281C VAL* 3.2 37.6 + - + +
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Residues in contact with ILE 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C TYR* 3.1 35.2 + - + +
259C ARG 4.9 0.4 - - - +
260C TYR* 4.1 32.1 - - + +
274C THR 3.2 25.4 - - - +
275C ARG* 3.6 16.4 - - + +
277C GLU* 1.3 78.5 - - + +
279C GLN* 1.3 58.3 + - - +
281C VAL* 3.6 2.1 + - - +
282C ARG* 3.2 48.2 + - - +
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Residues in contact with GLN 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275C ARG 3.4 15.8 + - - +
276C GLU* 3.1 16.8 + - + +
278C ILE* 1.3 78.2 - - - +
280C GLU* 1.3 65.0 + - - +
282C ARG* 3.5 31.6 + - - +
283C SER* 3.1 32.9 + - - -
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Residues in contact with GLU 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C GLU 3.2 13.4 + - - +
277C GLU* 3.4 7.1 + - + +
279C GLN* 1.3 74.5 - - - +
281C VAL* 1.3 67.0 + - + +
283C SER* 3.9 3.6 + - - +
284C LYS* 3.1 60.2 + - - +
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Residues in contact with VAL 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C ARG* 4.6 2.0 - - - +
228C MET* 4.8 7.9 - - + -
258C TYR* 3.6 43.3 - - + -
260C TYR* 4.5 6.5 - - + -
277C GLU* 3.2 38.0 + - + +
278C ILE 3.8 3.8 - - - +
280C GLU* 1.3 79.4 - - + +
282C ARG* 1.3 57.6 + - - +
284C LYS* 5.1 0.9 - - - -
285C SER* 3.0 40.5 + - - +
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Residues in contact with ARG 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ARG* 4.6 9.2 - - - +
66C ASP* 4.9 1.8 + - - -
260C TYR* 3.3 60.6 - - + +
261C HIS* 6.1 1.6 - - - -
278C ILE* 3.2 30.2 + - - +
279C GLN* 3.5 24.7 - - - +
280C GLU 3.3 0.2 - - - -
281C VAL* 1.3 77.2 - - - +
283C SER* 1.3 62.5 + - - +
286C ASP* 3.2 34.1 + - + +
289C MET* 4.6 5.1 - - - +
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Residues in contact with SER 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279C GLN* 3.1 24.7 + - - -
280C GLU* 3.9 3.2 + - - +
282C ARG* 1.3 79.7 - - - +
284C LYS* 1.3 59.1 + - - +
285C SER 3.6 0.4 - - - -
289C MET* 5.0 14.3 - - - +
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Residues in contact with LYS 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C GLU* 3.1 51.1 + - - +
281C VAL* 4.3 1.8 - - - +
283C SER* 1.3 79.4 - - - +
285C SER* 1.3 68.1 + - - +
290C LEU* 4.3 8.4 - - - +
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Residues in contact with SER 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C MET* 3.3 34.4 - - - +
260C TYR* 4.4 0.4 + - - -
281C VAL* 3.0 22.2 + - - +
283C SER 3.6 0.8 - - - -
284C LYS* 1.3 85.5 - - - +
286C ASP* 1.3 63.7 + - - +
287C PRO 3.6 0.2 - - - -
289C MET* 6.3 0.2 - - - -
290C LEU* 3.9 26.0 - - - -
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Residues in contact with ASP 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ARG* 2.8 33.3 + - - -
260C TYR* 3.0 20.8 + - - +
282C ARG* 3.2 25.9 + - + +
285C SER* 1.3 73.9 - - - +
287C PRO* 1.3 72.4 - - - +
288C ILE* 3.0 29.6 + - - +
289C MET* 3.1 27.9 + - + +
290C LEU* 3.0 26.3 + - - +
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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