Contacts of the helix formed by residues 271 - 277 (chain A) in PDB entry 2IHU
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 TYR 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A TYR* 5.2 0.9 - - - -
269A THR* 3.0 7.5 - - - +
270A GLY* 1.3 78.5 - - - +
272A MET* 1.3 58.2 + - - +
273A ASP 3.4 2.0 - - - -
274A GLY* 3.3 4.6 + - - -
275A ILE* 3.0 45.0 + - + +
301A ASP* 6.1 0.9 - - - -
412A PHE* 4.3 9.6 - + - -
415A HIS* 3.2 39.5 - + + -
495A LEU* 3.5 22.7 - - + +
498A LEU* 4.4 4.0 - - + -
499A TYR* 2.4 34.1 + + - -
568A PHE* 3.8 24.9 - + + -
571A LEU* 3.7 26.7 - - + -
603A TAR 2.6 20.8 + - - -
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Residues in contact with MET 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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267A ALA 4.0 9.9 - - - +
268A VAL* 4.0 5.6 - - - -
269A THR* 3.0 36.9 + - + +
270A GLY 3.3 0.6 - - - -
271A TYR* 1.3 77.6 - - - +
273A ASP* 1.3 76.5 + - - +
276A LEU* 3.0 31.2 + - + +
280A ALA* 3.8 21.5 - - + -
281A LEU* 3.6 25.6 - - + -
284A MET* 4.4 8.1 - - + -
364A LEU* 4.3 19.7 - - + -
368A ILE* 5.6 1.6 - - + -
419A LEU* 3.6 41.1 - - + -
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Residues in contact with ASP 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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270A GLY 4.7 1.7 + - - +
271A TYR 3.4 0.6 - - - -
272A MET* 1.3 75.5 - - - +
274A GLY* 1.3 52.4 + - - +
277A ASN* 2.8 31.9 + - - -
278A PHE 3.3 25.7 + - - +
279A PRO* 4.4 4.7 - - - +
280A ALA* 3.1 9.9 + - - +
281A LEU* 2.9 48.9 + - - +
282A GLN* 5.0 1.4 + - - +
309A LYS* 5.7 0.9 + - - -
567A GLY* 4.1 9.9 - - - +
570A ALA* 4.8 10.5 - - + +
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Residues in contact with GLY 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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270A GLY 5.5 0.4 + - - -
271A TYR 3.3 4.4 + - - -
273A ASP* 1.3 81.6 - - - +
275A ILE* 1.3 61.2 + - - +
277A ASN* 3.6 9.1 + - - +
564A GLN* 5.4 6.4 + - - +
567A GLY* 3.3 25.9 + - - -
568A PHE* 3.7 28.4 - - - -
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Residues in contact with ILE 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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271A TYR* 3.0 26.5 + - + +
272A MET 4.1 2.2 - - - +
274A GLY* 1.3 77.3 - - - +
276A LEU* 1.3 61.1 + - - +
277A ASN* 3.6 0.9 + - - +
371A PHE* 3.3 18.6 - - + -
412A PHE* 3.8 27.6 - - + -
415A HIS* 3.7 35.2 - - + +
416A TYR* 3.7 46.1 + - + -
419A LEU* 4.0 20.0 - - + -
420A PHE* 4.4 7.0 - - + -
568A PHE* 4.5 1.1 - - + -
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Residues in contact with LEU 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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272A MET* 3.0 23.1 + - + +
273A ASP* 4.3 0.4 - - - +
275A ILE* 1.3 76.5 - - - +
277A ASN* 1.3 61.7 + - - +
278A PHE* 3.9 12.3 - - + -
280A ALA* 4.0 8.1 - - + -
364A LEU* 3.7 30.5 - - + -
367A ARG* 2.8 41.8 + - + -
368A ILE* 4.0 16.4 - - + -
371A PHE* 3.6 24.8 - - + -
419A LEU* 4.2 15.0 - - + -
420A PHE* 3.8 32.1 - - + -
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Residues in contact with ASN 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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273A ASP 2.8 12.3 + - - -
274A GLY* 3.6 7.0 + - - +
275A ILE 3.4 3.9 - - - +
276A LEU* 1.3 78.6 - - - +
278A PHE* 1.3 56.9 + - - +
367A ARG* 3.0 24.3 + - - +
371A PHE* 5.5 2.5 - - + -
564A GLN* 3.8 26.9 + - - +
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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