Contacts of the helix formed by residues 270 - 280 (chain A) in PDB entry 1TQN
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 ASP 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A MET* 3.7 5.8 - - - -
186A SER 4.1 3.8 - - - +
187A THR* 3.2 18.4 - - - +
188A SER 3.6 0.9 - - - -
189A PHE* 2.4 54.9 + - - +
190A GLY 4.1 1.0 + - - -
267A HIS* 4.2 0.4 - - - -
268A ARG* 2.4 21.2 + - + +
269A VAL* 1.3 74.9 - - - +
271A PHE* 1.3 59.4 + - - +
272A LEU* 3.2 1.7 + - - -
273A GLN* 2.4 37.6 + - - +
274A LEU* 2.9 26.0 + - - +
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Residues in contact with PHE 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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136A THR* 3.4 31.9 - - + -
137A PHE* 3.5 32.3 - + - -
145A MET* 3.5 20.4 - - + -
187A THR* 2.8 43.4 + - - +
188A SER* 4.4 8.3 - - - +
270A ASP* 1.3 71.2 - - - +
272A LEU* 1.3 51.9 + - - +
274A LEU* 3.0 6.5 + - - +
275A MET* 2.6 42.2 + - + +
299A SER* 6.4 0.4 - - - -
302A PHE* 4.5 23.8 - + + -
447A PHE* 3.5 35.2 - + - -
508A HEM 4.6 7.4 - - + -
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Residues in contact with LEU 272 (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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188A SER* 3.3 22.1 + - - +
189A PHE* 3.5 20.9 - - + -
253A VAL* 3.9 28.9 - - + +
256A MET* 3.3 39.7 - - + -
257A LYS* 4.9 0.2 - - + -
270A ASP* 3.2 5.5 + - - +
271A PHE* 1.3 77.0 - - - +
273A GLN* 1.3 52.3 + - - +
275A MET* 2.8 11.3 + - - +
276A ILE* 2.5 58.1 + - + +
295A LEU* 4.0 13.7 - - + -
299A SER* 4.9 4.5 + - - +
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Residues in contact with GLN 273 (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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189A PHE* 3.2 29.1 - - + -
261A LEU* 2.9 35.3 - - + +
267A HIS* 3.1 36.2 + - + +
268A ARG 4.2 1.6 - - - +
270A ASP* 2.4 28.0 + - - +
272A LEU* 1.3 72.4 - - - +
274A LEU* 1.3 55.3 + - - +
276A ILE* 4.0 15.7 - - - +
277A ASP* 2.4 78.4 + - - +
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Residues in contact with LEU 274 (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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136A THR* 3.3 47.8 + - + +
141A LYS* 3.8 41.3 - - + +
145A MET* 4.8 4.0 - - + -
267A HIS* 5.9 2.5 - - + +
269A VAL* 4.2 20.0 - - + -
270A ASP 2.9 22.1 + - - +
271A PHE* 3.0 10.3 + - + +
273A GLN* 1.3 76.4 - - - +
275A MET* 1.3 49.1 + - - +
277A ASP* 4.9 3.1 - - + -
278A SER* 2.8 36.4 + - - +
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Residues in contact with MET 275 (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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133A LEU* 3.3 33.9 - - + -
136A THR* 4.9 4.9 - - + +
271A PHE* 2.6 33.0 + - + +
272A LEU* 3.2 7.4 - - - +
274A LEU* 1.3 71.5 - - - +
276A ILE* 1.3 61.1 + - - +
278A SER* 2.4 23.7 + - - -
279A GLN* 3.1 15.6 + - - +
290A LEU* 3.6 17.6 - - + +
295A LEU* 3.9 28.6 - - + +
298A GLN* 3.3 35.4 - - + -
299A SER* 4.1 11.0 - - - -
302A PHE* 4.0 12.3 - - - -
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Residues in contact with ILE 276 (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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189A PHE* 4.3 3.1 - - + -
257A LYS* 3.3 55.4 - - + +
261A LEU* 5.9 0.7 - - + -
272A LEU* 2.5 46.8 + - + +
273A GLN* 3.5 27.1 - - - +
275A MET* 1.3 71.3 - - - +
277A ASP* 1.3 64.5 + - - +
279A GLN* 2.8 32.6 + - - +
280A ASN* 3.0 26.0 + - - +
295A LEU* 4.4 0.7 - - + -
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Residues in contact with ASP 277 (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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267A HIS* 4.5 10.2 + - - -
273A GLN* 2.4 50.8 + - - +
274A LEU* 4.6 3.3 - - + +
276A ILE* 1.3 72.3 - - - +
278A SER* 1.3 65.1 + - - +
279A GLN 3.1 0.5 + - - -
280A ASN* 3.1 33.9 + - - +
281A SER 4.0 3.8 - - - -
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Residues in contact with SER 278 (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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132A LEU* 4.9 20.3 + - - +
136A THR* 5.7 2.0 - - - -
274A LEU 2.8 21.7 + - - -
275A MET* 2.4 32.7 + - - -
277A ASP* 1.3 76.7 - - - +
279A GLN* 1.3 62.2 + - - +
281A SER 4.1 11.1 - - - -
288A LYS* 5.0 6.8 - - - -
290A LEU* 5.0 8.9 - - - +
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Residues in contact with GLN 279 (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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257A LYS* 2.5 45.2 + - - +
275A MET 3.5 4.0 - - - +
276A ILE* 2.8 16.5 + - - +
278A SER* 1.3 85.7 + - - +
280A ASN* 1.3 55.6 + - - +
281A SER* 2.7 16.6 + - - -
288A LYS* 4.5 12.1 + - - -
289A ALA* 5.2 3.3 - - - +
290A LEU* 2.7 42.9 - - + +
292A ASP* 2.8 12.6 + - - +
295A LEU* 3.4 15.3 - - - +
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Residues in contact with ASN 280 (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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276A ILE* 3.0 38.5 + - - +
277A ASP* 3.1 18.5 + - - +
279A GLN* 1.3 75.8 + - - +
281A SER* 1.3 76.7 + - - +
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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