Contacts of the helix formed by residues 283 - 289 (chain B) in PDB entry 4I5L
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 CYS 283 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B ALA* 3.9 4.2 - - - +
215B ALA* 3.8 31.9 - - - +
218B VAL* 3.9 27.8 - - - +
219B HIS* 5.1 7.2 - - - -
227B ASN* 4.6 9.6 + - - -
282B THR* 1.3 69.1 + - - +
284B ALA* 1.3 61.4 + - - +
286B LEU* 3.2 4.9 + - - +
287B ARG* 2.8 51.5 + - - +
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Residues in contact with ALA 284 (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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57A ASP 4.7 12.1 - - - +
59A ILE* 4.6 18.6 - - + -
282B THR* 3.3 12.4 - - + +
283B CYS* 1.3 78.8 - - - +
285B GLU* 1.3 63.2 + - + +
287B ARG* 3.3 19.6 - - - +
288B ARG* 3.1 28.4 + - - +
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Residues in contact with GLU 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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59A ILE* 5.2 14.2 - - + +
273B VAL* 3.4 27.4 - - + +
274B ASN* 2.9 21.4 + - - -
275B ARG* 3.1 21.6 + - + +
276B SER* 3.1 25.7 + - - -
280B ARG 3.4 11.6 - - - +
281B ILE* 3.6 2.3 - - - -
282B THR* 3.0 30.3 + - + +
284B ALA* 1.3 74.8 - - + +
286B LEU* 1.3 63.6 + - - +
288B ARG* 3.0 17.8 + - - +
289B SER* 3.3 13.9 + - - -
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Residues in contact with LEU 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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214B ALA* 3.9 20.9 - - + +
217B PHE* 3.9 23.6 - - + -
218B VAL* 3.9 24.5 - - + -
229B LEU* 4.7 3.8 - - + -
234B PHE* 5.9 3.1 - - + -
269B ILE* 6.3 0.2 - - + -
273B VAL* 4.0 8.9 - - + +
281B ILE* 4.1 14.1 - - + -
282B THR 2.8 13.4 + - - +
283B CYS* 3.2 7.8 + - - +
285B GLU* 1.3 71.3 - - - +
287B ARG* 1.3 62.1 + - - +
289B SER* 2.9 26.8 + - - +
291B PHE* 3.8 36.9 + - + -
292B LEU* 4.3 14.7 + - + +
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Residues in contact with ARG 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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212B ASP* 2.6 43.0 + - - +
214B ALA* 4.1 8.1 - - + +
215B ALA* 4.2 8.3 - - - +
283B CYS* 2.8 36.9 + - - +
284B ALA* 3.3 30.8 - - - +
286B LEU* 1.3 73.2 - - - +
288B ARG* 1.3 62.2 + - + +
289B SER 3.5 5.2 + - - +
292B LEU* 6.3 0.2 - - - -
293B GLN* 5.7 1.2 + - - -
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Residues in contact with ARG 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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59A ILE* 3.4 61.5 + - - +
61A ASP* 2.6 32.1 + - - +
275B ARG* 5.9 5.1 - - - +
284B ALA* 3.1 16.3 + - - +
285B GLU* 3.0 11.6 + - - +
287B ARG* 1.3 77.3 - - + +
289B SER* 1.3 59.1 + - - +
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Residues in contact with SER 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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272B ALA* 5.0 4.5 - - - -
273B VAL* 3.7 26.9 - - - +
285B GLU 3.3 8.2 + - - -
286B LEU* 2.9 22.8 + - - +
287B ARG 3.9 5.2 - - - +
288B ARG* 1.3 82.1 - - - +
290B SER* 1.3 60.9 + - - +
291B PHE* 3.1 19.0 + - - +
293B GLN* 3.6 13.7 + - - +
310B PHE* 5.5 2.0 - - - -
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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