Contacts of the helix formed by residues 264 - 271 (chain A) in PDB entry 3TIN
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 264 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A ILE* 3.7 26.9 - - + -
203A SER* 5.3 3.8 - - - -
215A LEU* 6.5 2.0 - - + -
217A ARG 3.6 20.2 - - - +
218A GLU* 4.7 11.0 + - - +
219A GLY* 3.2 42.6 + - - +
220A VAL 3.9 0.9 - - - -
221A LEU* 4.5 10.8 - - + -
263A PHE* 1.3 72.3 - - - +
265A GLU* 1.3 55.6 + - - +
267A PHE* 3.9 8.3 - + - -
268A ASN* 3.1 21.1 + - - +
279A LEU* 3.2 32.9 - - + +
283A ILE* 6.1 1.3 - - + -
284A LEU* 3.5 32.3 - - + -
287A ILE* 5.2 6.3 - - + -
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Residues in contact with GLU 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A GLU* 5.4 3.2 + - - +
263A PHE* 2.9 7.5 + - + +
264A PHE* 1.3 75.6 - - - +
266A GLU* 1.3 66.4 + - - +
267A PHE 3.3 0.5 + - - -
268A ASN* 3.3 20.4 + - - +
269A GLN* 3.4 15.3 + - - +
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Residues in contact with GLU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A MET* 3.7 25.8 - - + +
263A PHE* 3.2 11.7 + - + +
265A GLU* 1.3 81.9 - - + +
267A PHE* 1.3 58.6 + - - +
269A GLN* 2.8 30.2 - - + +
270A TYR* 3.6 4.2 + - - +
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Residues in contact with PHE 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A LEU* 6.3 0.4 - - + -
192A LEU* 3.6 20.9 - - + -
199A PHE* 3.7 21.1 - + - -
201A ILE* 4.7 6.7 - - + -
221A LEU* 3.3 42.4 - - + -
262A MET* 3.4 23.0 - - + -
263A PHE 2.9 21.3 + - - +
264A PHE* 4.0 6.1 - + - +
266A GLU* 1.3 74.1 - - - +
268A ASN* 1.3 61.7 + - - +
269A GLN 2.9 5.9 + - - -
270A TYR* 3.0 12.9 + - + +
271A LEU* 3.3 27.8 + - + +
279A LEU* 3.7 20.0 - - + -
283A ILE* 3.9 26.7 - - + -
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Residues in contact with ASN 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A PHE 3.1 18.6 + - - +
265A GLU* 3.3 13.1 + - - +
267A PHE* 1.3 78.5 - - - +
269A GLN* 1.3 62.0 + - - +
271A LEU* 3.3 7.8 + - - +
272A VAL* 3.1 21.2 - - - +
278A ASN* 2.9 25.7 + - - +
279A LEU* 3.5 33.1 + - + -
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Residues in contact with GLN 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A GLU* 3.4 12.9 + - - +
266A GLU* 2.8 28.1 + - + +
268A ASN* 1.3 79.4 - - - +
270A TYR* 1.3 61.2 + - - +
272A VAL* 3.0 13.8 + - - +
273A THR* 3.1 32.7 + - - -
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Residues in contact with TYR 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A LEU* 4.4 11.5 - - + +
191A LEU 3.0 27.5 + - - -
192A LEU* 3.5 22.8 - - + -
193A GLU* 3.3 53.2 + - + +
196A HIS* 6.0 0.2 + - - -
262A MET* 4.9 4.3 - - + -
266A GLU 3.6 3.1 + - - +
267A PHE* 3.0 12.7 + - + +
269A GLN* 1.3 79.6 - - - +
271A LEU* 1.3 70.1 + - + +
272A VAL 3.1 5.8 + - - -
273A THR 5.2 0.4 - - - -
274A SER* 3.4 25.5 - - - -
275A LEU* 3.3 25.1 + - + +
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Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A LEU* 6.0 4.5 - - + -
267A PHE* 3.3 36.5 + - + +
268A ASN* 3.7 10.1 - - - +
269A GLN 3.1 1.8 - - - -
270A TYR* 1.3 86.7 - - + +
272A VAL* 1.3 54.2 + - + +
275A LEU* 3.6 11.0 - - + +
277A ILE* 2.4 52.6 + - + +
278A ASN 4.0 3.6 - - - +
279A LEU* 3.7 36.3 - - + +
283A ILE* 3.4 30.1 - - + -
325A LEU* 6.3 1.8 - - + -
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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