Contacts of the helix formed by residues 265 - 272 (chain C) in PDB entry 3ZXT
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 THR 265 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197C GLU* 5.9 7.0 - - + -
200C MET* 4.0 4.5 - - - -
263C ARG 4.6 5.6 - - - +
264C MET* 1.3 78.0 - - - +
266C ILE* 1.3 65.9 + - - +
267C GLN* 2.4 35.0 + - - +
268C ASP* 2.8 36.4 + - - +
269C SER* 2.9 10.4 + - - -
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Residues in contact with ILE 266 (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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124C LEU* 3.3 34.3 - - + +
127C VAL* 3.6 20.4 - - + -
128C TYR* 3.7 26.2 - - + +
131C HIS* 3.6 28.5 + - + +
200C MET* 3.1 28.5 - - + +
203C ILE* 4.2 7.6 - - + -
265C THR* 1.3 70.4 - - - +
267C GLN* 1.3 81.1 + - + +
269C SER* 2.6 27.6 + - - +
270C LEU* 3.0 11.9 + - + +
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Residues in contact with GLN 267 (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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128C TYR* 4.4 20.4 - - + -
131C HIS* 5.5 2.8 + - - +
196C LEU* 5.7 4.6 - - - +
265C THR* 2.4 37.2 + - - +
266C ILE* 1.3 89.4 - - + +
268C ASP* 1.3 66.7 + - - +
270C LEU* 2.9 17.6 + - - +
271C GLN* 3.1 23.4 + - - +
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Residues in contact with ASP 268 (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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263C ARG 4.3 2.6 - - - +
264C MET* 3.1 27.1 - - + +
265C THR* 2.8 38.1 + - - +
267C GLN* 1.3 75.6 - - - +
269C SER* 1.3 57.3 + - - +
271C GLN* 2.9 24.9 + - - +
272C HIS* 3.0 12.1 + - - +
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Residues in contact with SER 269 (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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124C LEU* 4.1 11.1 - - - +
200C MET* 4.8 1.8 - - - -
203C ILE* 6.3 0.4 - - - -
251C PHE* 3.8 13.0 - - - -
255C LEU* 4.7 7.6 - - - -
264C MET* 3.6 28.0 - - - +
265C THR 2.9 10.9 + - - -
266C ILE* 2.6 33.5 + - - +
268C ASP* 1.3 76.4 - - - +
270C LEU* 1.3 59.6 + - - +
272C HIS* 3.3 15.8 + - - +
275C ILE* 3.6 14.7 - - - +
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Residues in contact with LEU 270 (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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121C LYS* 5.1 4.9 - - + +
124C LEU* 3.9 34.8 - - + +
125C ASN* 4.2 16.4 - - - +
128C TYR* 3.7 43.3 - - + -
266C ILE* 3.0 13.0 + - + +
267C GLN* 2.9 9.6 + - - +
269C SER* 1.3 77.1 + - - +
271C GLN* 1.3 62.1 + - - +
275C ILE* 4.3 13.0 - - + +
276C LYS* 4.1 18.5 + - - +
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Residues in contact with GLN 271 (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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267C GLN* 3.1 22.1 + - - +
268C ASP* 2.9 14.0 + - - +
270C LEU* 1.3 77.8 - - - +
272C HIS* 1.3 65.2 + - - +
273C PRO* 3.3 6.9 - - - +
276C LYS* 4.4 9.6 - - + +
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Residues in contact with HIS 272 (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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247C LEU* 3.5 28.0 - - + -
250C ASP* 2.5 29.9 + - - -
251C PHE* 3.5 27.2 + + + -
254C ARG* 3.8 10.0 + - - -
264C MET* 4.0 20.9 - - + -
268C ASP 3.0 7.8 + - - +
269C SER* 3.3 19.3 + - - +
271C GLN* 1.3 74.8 - - - +
273C PRO* 1.4 67.9 - - + +
274C TRP* 3.0 34.7 + - + +
275C ILE* 2.8 26.1 + - - +
276C LYS 2.9 11.4 + - - -
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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