Contacts of the helix formed by residues 240 - 245 (chain H) in PDB entry 1I43
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 ALA 240 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208H SER 3.8 1.1 - - - +
209H PRO* 3.7 14.3 - - + +
237H GLY* 3.1 6.9 + - - +
239H PHE* 1.3 80.5 - - - +
241H THR* 1.3 73.8 + - - +
244H ASN* 3.2 28.7 + - + +
245H GLN* 3.2 46.4 - - + +
355H MET* 5.0 2.5 - - + -
358H PHE 6.3 0.4 - - - -
359H GLY* 5.7 0.9 - - - +
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Residues in contact with THR 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237H GLY 2.7 18.3 + - - -
238H THR 3.6 2.0 + - - -
240H ALA* 1.3 82.5 - - - +
242H PRO* 1.3 70.6 - - + +
243H LEU* 2.7 44.1 + - + +
244H ASN 3.1 8.0 + - - +
245H GLN* 3.5 8.6 + - - +
257H HIS* 3.8 5.2 - - - -
262H PHE* 3.3 35.9 - - - +
263H LEU* 5.6 1.0 - - - +
310H LEU* 4.6 4.9 - - + -
314H VAL* 4.2 17.6 - - + +
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Residues in contact with PRO 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H ILE* 5.8 3.8 - - + -
126H LEU* 4.0 31.5 - - + +
127H GLU* 3.3 34.8 - - + +
241H THR* 1.3 88.6 - - + +
243H LEU* 1.3 60.0 + - - +
245H GLN 3.7 11.2 - - - +
246H LYS* 3.0 31.0 + - - -
257H HIS* 3.4 18.1 - - + +
263H LEU* 4.2 21.1 - - + -
310H LEU* 4.7 0.9 - - + -
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Residues in contact with LEU 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57H ASP* 3.4 44.8 - - + +
58H GLY 4.9 0.4 - - - +
61H ALA* 5.5 1.3 - - + -
126H LEU* 4.3 15.5 - - + -
241H THR* 2.7 20.2 + - + +
242H PRO* 1.3 77.9 - - - +
244H ASN* 1.3 63.0 + - - +
245H GLN 3.3 2.3 + - - -
246H LYS* 4.9 2.6 - - - -
310H LEU* 3.6 10.3 - - + -
311H HIS* 3.4 40.2 - - + +
314H VAL* 3.5 25.1 - - + -
356H THR* 3.6 13.7 + - - +
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Residues in contact with ASN 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240H ALA* 3.2 29.5 + - + +
241H THR 3.1 2.2 + - - -
243H LEU* 1.3 79.9 - - - +
245H GLN* 1.3 62.7 + - - +
314H VAL* 4.0 12.5 - - - +
318H ASN* 2.9 42.1 + - - +
355H MET* 3.2 7.9 - - + +
356H THR* 3.0 32.8 + - - +
357H GLY* 3.3 19.3 + - - +
358H PHE* 5.5 0.2 - - - -
359H GLY* 3.4 16.8 - - - +
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Residues in contact with GLN 245 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H GLU* 4.4 1.9 - - - +
208H SER 2.9 23.1 + - - +
219H ILE* 4.3 17.1 - - + +
235H ILE* 4.6 4.8 - - - +
237H GLY* 4.0 10.9 - - - -
240H ALA* 3.2 21.1 - - + +
241H THR 3.5 10.4 + - - +
242H PRO* 3.7 13.9 - - - +
243H LEU 3.3 2.4 + - - -
244H ASN* 1.3 81.8 - - - +
246H LYS* 1.3 66.5 + - - +
247H ALA* 3.9 12.2 + - + +
250H LEU* 5.5 1.1 - - + -
354H GLN* 3.5 24.1 + - - +
355H MET* 3.3 29.0 - - + +
356H THR* 5.5 2.5 - - - -
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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