Contacts of the helix formed by residues 284 - 291 (chain A) in PDB entry 2I91
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 ASN 284 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A ARG* 3.9 17.3 + - - +
269A TRP* 3.9 32.6 - - + -
276A MET* 5.1 1.4 - - - -
280A ALA* 2.8 27.8 + - - +
281A LEU 3.4 4.0 + - - +
282A LEU 3.2 0.6 - - - -
283A ARG* 1.3 82.2 - - - +
285A LEU* 1.3 63.9 + - - +
286A GLY 3.3 2.0 - - - +
287A LYS* 3.6 13.0 + - + +
288A MET* 3.2 32.1 + - + +
7D G 5.1 10.0 + - - +
12D U 3.4 23.1 + - - +
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Residues in contact with LEU 285 (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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281A LEU* 3.4 25.1 - - + +
282A LEU* 3.6 14.8 - - + +
284A ASN* 1.3 79.1 - - - +
286A GLY* 1.3 63.8 + - - +
288A MET* 3.4 1.6 + - - +
289A THR* 2.9 28.4 + - - -
294A LEU* 4.2 13.8 - - + +
304A VAL* 3.8 28.3 - - + -
308A LEU* 4.2 2.7 - - + -
327A ALA* 5.3 0.4 - - + -
331A TYR* 3.7 13.7 - - + -
349A ILE* 3.7 15.3 - - + -
353A LEU* 3.7 43.1 - - + -
9D U 2.9 10.4 + - - +
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Residues in contact with GLY 286 (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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284A ASN 3.3 0.2 - - - -
285A LEU* 1.3 74.7 - - - +
287A LYS* 1.3 60.0 + - - +
289A THR 3.4 0.2 + - - -
290A ALA* 3.2 17.3 + - - +
331A TYR* 3.7 5.1 - - - -
343A TRP* 3.3 50.9 - - - -
9D U 2.5 20.1 + - - -
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Residues in contact with LYS 287 (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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263A LEU 3.1 27.9 + - - -
264A LYS* 4.7 7.1 - - - +
269A TRP* 3.5 34.5 - - + +
284A ASN* 3.6 18.1 + - - +
285A LEU 3.4 0.2 - - - -
286A GLY* 1.3 75.3 - - - +
288A MET* 1.3 60.2 + - - +
290A ALA* 3.3 5.4 + - - +
291A ASP* 2.6 57.7 + - - +
341A LEU* 4.6 8.0 - - + +
343A TRP* 4.4 2.9 - - - -
6D G 3.4 6.9 + - - -
7D G 3.0 52.7 + - - +
8D C 5.5 3.4 + - - +
9D U 5.7 0.4 - - - -
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Residues in contact with MET 288 (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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269A TRP* 3.3 31.2 - - + -
273A LEU* 3.8 22.7 - - + -
276A MET* 3.2 45.3 - - + -
281A LEU* 4.8 5.2 - - + -
284A ASN* 3.2 22.8 + - + +
285A LEU 3.4 0.4 + - - +
287A LYS* 1.3 75.1 - - - +
289A THR* 1.3 62.2 + - - +
292A SER 3.5 0.7 + - - -
293A VAL* 2.9 61.3 + - + +
294A LEU* 3.0 20.8 + - + -
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Residues in contact with THR 289 (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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285A LEU 2.9 16.2 + - - -
286A GLY 3.8 4.3 - - - -
287A LYS 3.2 0.2 - - - -
288A MET* 1.3 75.9 - - - +
290A ALA* 1.3 65.9 + - - +
292A SER* 3.1 15.1 + - - -
294A LEU* 3.9 27.7 - - - +
295A ALA* 5.6 0.3 - - - -
296A PRO* 6.2 1.6 - - + -
331A TYR* 2.7 27.5 + - - +
343A TRP* 4.1 9.4 - - + -
344A ILE* 3.3 28.0 - - + +
346A ASP* 4.6 4.8 - - + +
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Residues in contact with ALA 290 (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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286A GLY 3.2 12.0 + - - +
287A LYS* 3.3 10.5 + - - +
289A THR* 1.3 80.5 - - - +
291A ASP* 1.3 61.2 + - - +
292A SER* 3.3 4.9 + - - -
341A LEU* 5.2 10.1 - - + -
342A ARG 3.3 24.7 - - - +
343A TRP* 3.7 10.5 - - + +
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Residues in contact with ASP 291 (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 LYS* 4.3 20.8 - - - +
265A SER 6.0 0.2 - - - -
266A LYS* 3.7 18.8 + - - +
269A TRP* 5.6 5.2 + - + -
287A LYS* 2.6 56.4 + - - +
288A MET 3.6 0.2 + - - -
289A THR 3.3 0.4 - - - -
290A ALA* 1.3 80.1 - - - +
292A SER* 1.3 63.9 + - - +
293A VAL* 3.0 28.9 + - + +
341A LEU* 5.1 3.6 - - - +
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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