Contacts of the helix formed by residues 240 - 245 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208J SER 3.7 0.7 - - - +
209J PRO* 3.5 16.2 - - + +
237J GLY 3.2 4.3 + - - +
239J PHE* 1.3 80.1 - - - +
241J THR* 1.3 71.5 + - - +
244J ASN* 3.1 31.1 + - + +
245J GLN* 3.1 46.7 - - + +
355J MET* 4.8 3.8 - - + -
359J GLY* 5.2 1.7 - - - +
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Residues in contact with THR 241 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237J GLY 2.8 18.4 + - - -
238J THR 3.7 1.8 + - - -
239J PHE 3.7 0.4 - - - -
240J ALA* 1.3 85.2 - - - +
242J PRO* 1.3 76.4 - - + +
243J LEU* 2.8 38.5 + - + +
244J ASN 3.2 6.3 + - - +
245J GLN* 3.6 9.2 + - - +
257J HIS* 3.8 5.8 - - - -
262J PHE* 3.4 35.7 - - - +
263J LEU* 5.7 0.9 - - - +
310J LEU* 4.7 4.9 - - + +
314J VAL* 4.2 17.2 - - + +
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Residues in contact with PRO 242 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57J ASP* 4.1 0.2 - - - +
123J ILE* 5.8 3.8 - - + -
126J LEU* 4.0 30.4 - - + +
127J GLU* 3.1 36.8 - - + +
241J THR* 1.3 90.5 - - + +
243J LEU* 1.3 59.6 + - - +
245J GLN 3.6 11.0 - - - +
246J LYS* 3.1 30.5 + - - -
257J HIS* 3.6 16.5 - - + +
263J LEU* 4.2 21.5 - - + -
310J LEU* 4.7 1.3 - - + -
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Residues in contact with LEU 243 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57J ASP* 3.3 46.6 - - + +
58J GLY 4.9 0.7 - - - +
61J ALA* 5.4 1.6 - - + -
126J LEU* 4.0 17.0 - - + -
241J THR* 2.8 12.8 + - + +
242J PRO* 1.3 80.1 - - - +
244J ASN* 1.3 65.0 + - - +
245J GLN 3.3 1.6 + - - -
246J LYS* 4.8 3.1 - - - -
310J LEU* 3.6 10.5 - - + -
311J HIS* 3.4 39.5 - - + +
314J VAL* 3.5 26.2 - - + -
356J THR* 3.7 12.8 + - - +
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Residues in contact with ASN 244 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240J ALA* 3.1 29.3 + - + +
241J THR 3.2 1.8 + - - -
243J LEU* 1.3 81.5 - - - +
245J GLN* 1.3 61.6 + - - +
314J VAL* 4.1 11.1 - - - +
318J ASN* 2.9 42.0 + - - +
355J MET* 3.3 6.4 - - + +
356J THR* 3.0 35.3 + - - +
357J GLY* 3.2 20.5 + - - +
359J GLY* 3.2 19.0 - - - +
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Residues in contact with GLN 245 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J GLU* 4.6 1.7 - - - +
208J SER 2.8 25.0 + - - +
219J ILE* 4.2 22.0 - - + +
235J ILE* 4.7 4.0 - - - +
237J GLY* 4.0 10.9 - - - -
240J ALA* 3.1 20.8 - - + +
241J THR 3.6 6.7 + - - +
242J PRO* 3.6 18.5 - - - +
243J LEU 3.3 2.8 + - - -
244J ASN* 1.3 82.0 - - - +
246J LYS* 1.3 66.6 + - - +
247J ALA* 4.0 11.9 + - + +
250J LEU* 5.4 0.9 - - + -
354J GLN* 3.5 19.0 + - - +
355J MET* 3.3 27.9 - - + +
356J THR* 5.3 3.1 - - - -
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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