Contacts of the helix formed by residues 240 - 245 (chain A) in PDB entry 1CF5
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 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A LEU* 4.2 1.3 - - - -
37A LEU* 3.1 26.7 + - - +
39A SER* 3.5 23.8 + - - +
67A THR* 2.8 39.9 + - - +
68A ASN* 4.3 2.2 - - - +
238A LEU 3.6 3.2 + - - -
239A LEU* 1.3 74.4 - - - +
241A SER* 1.3 58.2 + - - +
242A ARG* 3.3 7.4 + - - +
243A ALA* 2.8 33.2 + - - +
244A SER 2.9 24.1 + - - -
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Residues in contact with SER 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 4.0 12.5 - - - +
37A LEU 5.1 1.2 + - - -
39A SER* 3.1 15.6 + - - -
198A PHE* 4.2 32.9 - - - -
239A LEU 3.2 3.6 + - - -
240A ASN* 1.3 70.4 - - - +
242A ARG* 1.3 49.8 + - - -
244A SER* 3.5 9.2 + - - -
245A THR* 2.7 39.2 + - - +
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Residues in contact with ARG 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A SER* 3.6 19.2 + - - +
40A THR* 5.3 4.9 - - - -
240A ASN* 3.0 8.3 + - - +
241A SER* 1.3 77.8 + - - +
243A ALA* 1.3 65.7 + - - +
245A THR* 3.7 4.6 - - - +
246A ALA* 3.2 27.9 + - - +
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Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ASN* 5.8 1.1 - - + -
239A LEU* 3.6 17.3 - - + -
240A ASN* 2.8 35.6 + - - +
242A ARG* 1.3 75.6 - - - +
244A SER* 1.3 53.4 + - - +
245A THR 3.4 0.9 + - - -
246A ALA* 3.8 5.5 + - - +
247A ASP* 2.6 30.0 + - - +
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Residues in contact with SER 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A SER* 3.9 4.0 - - - -
194A SER* 4.0 3.8 + - - -
195A LYS* 3.2 44.0 + - - +
198A PHE* 4.8 5.0 - - - +
239A LEU* 3.4 30.9 + - - +
240A ASN 2.9 12.4 + - - -
241A SER* 3.5 13.0 + - - -
242A ARG 3.3 0.2 - - - -
243A ALA* 1.3 76.0 - - - +
245A THR* 1.3 58.8 + - - +
247A ASP* 2.8 21.4 - - - +
249A ASN* 4.0 0.2 - - - +
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Residues in contact with THR 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LYS* 3.9 18.4 + - - +
198A PHE* 6.0 5.2 - - + -
199A LEU* 5.6 6.6 - - - +
241A SER* 2.7 29.0 + - - +
242A ARG* 3.7 7.0 - - - +
244A SER* 1.3 76.4 + - - +
246A ALA* 1.3 70.1 + - - +
247A ASP 2.9 11.7 - - - +
248A GLU* 4.7 3.5 - - - +
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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