Contacts of the helix formed by residues 284 - 291 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B ARG* 3.9 18.4 + - - +
269B TRP* 3.9 31.5 - - + -
276B MET* 5.1 1.8 - - - -
280B ALA* 2.8 28.4 + - - +
281B LEU 3.7 3.6 - - - -
282B LEU 3.2 0.8 - - - -
283B ARG* 1.3 81.7 - - - +
285B LEU* 1.3 65.4 + - - +
286B GLY 3.3 2.2 - - - +
287B LYS* 4.0 13.5 - - + +
288B MET* 3.1 32.5 + - + +
7F G 5.5 7.8 + - - +
12F U 3.5 22.3 + - - +
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B LEU* 3.4 24.9 + - + +
282B LEU* 3.7 13.7 - - + +
284B ASN* 1.3 79.6 - - - +
286B GLY* 1.3 62.1 + - - +
288B MET* 3.3 1.7 + - - +
289B THR* 2.9 28.6 + - - -
294B LEU* 4.2 13.0 - - + +
304B VAL* 3.8 28.3 - - + -
308B LEU* 4.2 4.0 - - + -
327B ALA* 5.3 0.9 - - + -
331B TYR* 3.7 14.8 - - + -
349B ILE* 3.7 14.4 - - + -
353B LEU* 3.7 42.6 - - + -
9F U 3.3 9.6 + - - +
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Residues in contact with GLY 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B ASN 3.3 0.2 - - - -
285B LEU* 1.3 77.5 - - - +
287B LYS* 1.3 59.7 + - - +
289B THR 3.5 0.2 + - - -
290B ALA* 3.2 17.3 + - - +
331B TYR* 3.7 5.6 - - - -
343B TRP* 3.3 49.3 - - - -
8F C 6.0 0.2 - - - -
9F U 2.8 17.2 + - - -
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Residues in contact with LYS 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B LEU 3.0 27.8 + - - -
264B LYS* 4.6 5.9 - - - +
269B TRP* 3.5 35.7 - - + +
284B ASN* 3.6 17.7 + - - +
285B LEU 3.4 0.8 - - - -
286B GLY* 1.3 75.2 - - - +
288B MET* 1.3 60.2 + - - +
290B ALA* 3.3 5.8 + - - +
291B ASP* 2.6 55.9 + - - +
341B LEU* 4.7 7.4 - - + -
343B TRP* 4.6 2.8 - - - -
6F G 3.3 6.5 + - - -
7F G 2.7 47.8 + - - +
8F C 5.2 9.1 + - - +
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Residues in contact with MET 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B TRP* 3.3 31.4 - - + -
273B LEU* 3.8 24.7 - - + -
276B MET* 3.2 45.5 - - + -
281B LEU* 4.8 5.2 - - + -
284B ASN* 3.1 26.6 + - + +
287B LYS* 1.3 73.4 - - - +
289B THR* 1.3 61.8 + - - +
292B SER 3.5 0.7 + - - -
293B VAL* 2.9 60.7 + - + +
294B LEU* 3.0 21.6 + - + -
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Residues in contact with THR 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B LEU 2.9 17.1 + - - -
286B GLY 3.8 4.7 - - - -
287B LYS 3.2 0.2 - - - -
288B MET* 1.3 76.1 - - - +
290B ALA* 1.3 64.8 + - - +
292B SER* 3.0 15.1 + - - -
294B LEU* 3.9 28.4 - - - +
295B ALA* 5.6 0.5 - - - -
296B PRO* 6.2 2.0 - - + -
331B TYR* 2.7 27.8 + - - +
343B TRP* 4.1 9.6 - - + -
344B ILE* 3.3 28.5 - - + +
346B ASP* 4.6 4.4 - - + +
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Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B GLY 3.2 11.5 + - - +
287B LYS* 3.5 10.1 - - - +
289B THR* 1.3 82.3 - - - +
291B ASP* 1.3 61.5 - - - +
292B SER* 3.3 5.4 + - - -
341B LEU* 5.2 10.8 - - + -
342B ARG 3.3 24.5 - - - +
343B TRP* 3.8 9.4 - - + +
344B ILE 5.8 0.2 - - - +
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Residues in contact with ASP 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B LYS* 4.2 21.8 - - - +
265B SER 6.0 0.2 - - - -
266B LYS* 3.7 18.6 - - - +
269B TRP* 5.6 4.0 + - + -
287B LYS* 2.6 56.2 + - + +
289B THR 3.2 0.8 - - - -
290B ALA* 1.3 79.0 - - - +
292B SER* 1.3 63.9 + - - +
293B VAL* 2.9 28.5 + - + +
341B LEU* 5.1 3.1 - - - +
7F G 5.1 0.3 + - - -
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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