Contacts of the helix formed by residues 243 - 248 (chain F) in PDB entry 4IGM
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 ARG 243 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ARG* 6.2 0.6 - - - +
188A TRP* 3.4 49.5 - - + +
295A PRO* 5.3 12.2 - - + +
239F GLY 2.9 5.8 + - - +
240F PHE 3.7 3.6 - - - -
242F MET* 1.3 85.1 - - + +
244F PRO* 1.4 65.3 - - - +
245F ASP* 3.0 31.6 + - - +
246F LEU* 3.1 41.8 + - + +
247F CYS* 3.3 14.7 + - - +
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Residues in contact with PRO 244 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240F PHE* 3.5 12.1 - - + +
241F SER* 3.7 13.5 - - - +
242F MET 3.4 9.6 - - - +
243F ARG* 1.4 87.6 - - - +
245F ASP* 1.3 59.8 + - - +
248F ALA* 3.0 40.6 + - + +
249F GLN* 3.9 3.3 + - - +
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Residues in contact with ASP 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243F ARG* 3.2 46.3 + - - -
244F PRO* 1.3 78.9 - - - +
246F LEU* 1.3 63.9 + - - +
249F GLN* 3.1 24.8 - - - +
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Residues in contact with LEU 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A TYR* 3.1 24.6 + - - -
188A TRP* 3.6 46.7 - - + +
243F ARG* 3.1 45.8 + - + +
245F ASP* 1.3 87.0 - - - +
247F CYS* 1.3 57.8 + - - +
249F GLN* 4.0 10.2 + - - -
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Residues in contact with CYS 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A TYR* 3.5 31.2 - - - +
188A TRP* 3.8 19.1 - - - -
192A LEU* 4.2 10.5 - - - -
208F MET* 3.9 20.2 - - - +
239F GLY 4.3 4.9 - - - -
240F PHE* 2.9 47.3 - - + +
243F ARG 3.3 15.0 + - - +
246F LEU* 1.3 79.8 - - - +
248F ALA* 1.3 60.9 + - - +
249F GLN* 3.7 5.6 + - - -
251F ASN 4.2 1.0 - - - +
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Residues in contact with ALA 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240F PHE* 3.5 23.8 - - + -
244F PRO* 3.0 27.8 + - + +
247F CYS* 1.3 77.6 - - - +
249F GLN* 1.3 58.4 + - - +
250F ASP 2.7 14.0 + - - -
251F ASN 3.4 19.6 + - - +
252F PRO* 4.1 11.2 - - + +
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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