Contacts of the helix formed by residues 274 - 285 (chain C) in PDB entry 3T5D
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 HIS 274 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204C TYR* 4.7 1.0 + - - -
218C VAL* 6.3 3.4 - - + -
268C ASN* 3.3 27.1 + - - -
269C MET* 3.3 31.2 - - + +
270C LEU 3.7 2.0 + - - -
272C ARG* 3.4 33.7 + - + -
273C THR* 1.3 75.1 - - - +
275C MET* 1.3 62.6 + - - +
276C GLN 3.2 2.2 - - - -
277C ASP* 3.2 28.2 + - - +
278C LEU* 3.5 10.2 + - - +
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Residues in contact with MET 275 (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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30C PHE* 3.9 24.2 - - + -
32C PHE* 3.5 52.7 - - + -
52C PHE* 4.4 22.2 - - + -
88C LEU* 4.9 17.5 - - + -
90C LEU* 5.3 1.8 - - + -
270C LEU* 3.3 46.9 - - + +
271C ILE* 4.4 4.9 - - - +
273C THR* 4.8 2.9 - - - -
274C HIS* 1.3 78.5 - - - +
276C GLN* 1.3 52.1 + - - +
278C LEU* 3.2 10.3 + - - +
279C LYS* 2.8 33.9 + - - +
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Residues in contact with GLN 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C PHE* 4.3 18.8 - - + -
273C THR* 4.0 23.8 + - + +
274C HIS 3.2 0.4 - - - -
275C MET* 1.3 79.2 - - - +
277C ASP* 1.3 55.6 + - - +
279C LYS* 3.4 19.8 + - - +
280C ASP* 2.9 61.2 + - - +
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Residues in contact with ASP 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C TYR* 2.7 21.7 + - - +
273C THR 5.0 0.2 + - - -
274C HIS* 3.2 19.8 + - + +
276C GLN* 1.3 76.7 - - - +
278C LEU* 1.3 63.2 + - - +
280C ASP* 3.2 9.3 + - - +
281C VAL* 3.1 31.9 + - - +
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Residues in contact with LEU 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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32C PHE* 4.1 22.7 - - + -
140C GLN* 4.0 7.4 - - - +
141C CYS* 4.0 21.8 - - + -
169C ASN* 3.1 30.7 + - + +
171C ILE* 4.6 4.9 - - + -
204C TYR* 3.7 42.2 - - + +
269C MET* 4.5 7.4 - - + +
270C LEU* 4.3 13.0 - - + -
274C HIS 3.5 12.0 + - - +
275C MET* 3.2 10.3 + - - +
277C ASP* 1.3 78.0 - - - +
279C LYS* 1.3 56.9 + - - +
281C VAL 3.6 0.2 + - - -
282C THR* 2.7 31.1 + - - -
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Residues in contact with LYS 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C PHE* 4.6 16.4 - - + -
31C GLU* 2.8 51.6 + - - +
32C PHE* 5.2 1.6 - - + -
136C ASP* 3.5 18.2 + - - +
138C ARG* 5.3 1.4 + - - +
140C GLN* 3.6 30.1 + - + +
275C MET 2.8 16.6 + - - +
276C GLN* 3.4 22.7 - - - +
277C ASP 3.2 0.2 - - - -
278C LEU* 1.3 78.7 - - - +
280C ASP* 1.3 61.0 + - - +
282C THR* 3.8 2.3 + - - -
283C ASN* 3.3 23.7 + - - +
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Residues in contact with ASP 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 GLN* 2.9 47.6 + - - +
277C ASP* 3.2 10.4 + - - +
279C LYS* 1.3 78.3 - - - +
281C VAL* 1.3 60.3 + - + +
283C ASN* 4.6 3.9 + - - +
284C ASN* 2.8 44.8 + - - +
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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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169C ASN* 3.4 28.0 - - - +
204C TYR* 4.1 16.8 - - + -
277C ASP* 3.1 27.6 + - - +
279C LYS 3.5 0.2 - - - -
280C ASP* 1.3 73.5 - - + +
282C THR* 1.3 60.7 + - - +
284C ASN* 5.0 0.7 - - - -
285C VAL* 2.9 46.7 + - + +
286C HIS* 3.4 8.3 + - + +
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Residues in contact with THR 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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119C PHE* 4.4 20.4 - - + -
138C ARG* 4.6 11.2 - - + +
139C VAL 3.4 22.4 - - - +
140C GLN* 2.9 19.2 + - + +
167C LYS 5.4 0.9 - - - +
168C VAL* 5.8 0.4 - - - -
169C ASN* 2.8 14.6 + - - +
278C LEU 2.7 23.8 + - - -
279C LYS 4.0 4.0 - - - -
281C VAL* 1.3 77.9 - - - +
283C ASN* 1.3 56.1 + - - +
286C HIS* 3.5 13.3 + - + +
287C TYR* 2.9 30.8 + - - +
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Residues in contact with ASN 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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122C TYR* 4.2 8.2 + - - -
138C ARG* 2.8 44.4 + - - +
279C LYS 3.3 16.7 + - - +
280C ASP* 3.9 3.3 + - - +
281C VAL 3.3 0.2 - - - -
282C THR* 1.3 80.7 - - - +
284C ASN* 1.3 75.5 + - - +
287C TYR* 3.6 14.4 - - - +
288C GLU* 3.5 17.5 - - - +
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Residues in contact with ASN 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 ASP* 2.8 31.1 + - - +
281C VAL* 5.0 0.2 - - - -
283C ASN* 1.3 94.8 + - - +
285C VAL* 1.3 67.2 + - + +
288C GLU* 3.3 22.9 - - - +
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Residues in contact with VAL 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C VAL* 2.9 32.1 + - + +
284C ASN* 1.3 85.1 - - + +
286C HIS* 1.3 71.0 + - + +
287C TYR 3.4 1.3 - - - -
288C GLU* 3.5 1.2 + - - +
289C ASN* 2.8 53.1 + - - +
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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