Contacts of the helix formed by residues 239 - 247 (chain I) in PDB entry 5U0A
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 LEU 239 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2I THR* 2.7 37.6 + - - +
4I VAL* 3.7 18.2 - - + -
237I VAL* 3.3 9.2 + - + +
238I ASN* 1.3 71.4 - - - +
240I ASP* 1.3 63.1 + - - +
242I LEU* 4.4 4.9 - - + +
243I VAL* 2.9 36.6 + - + +
252I ALA* 6.0 1.6 - - + -
256I VAL* 3.5 32.1 - - + -
367I ALA* 3.7 35.7 - - + +
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Residues in contact with ASP 240 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I THR* 3.6 34.2 + - - +
3I PHE* 5.8 1.0 - - - -
238I ASN* 3.2 10.1 + - - +
239I LEU* 1.3 79.1 - - - +
241I ARG* 1.3 58.1 + - + +
243I VAL* 3.8 4.5 - - - +
244I GLU* 2.9 30.2 + - - +
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Residues in contact with ARG 241 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273E ASN* 5.0 10.1 + - - +
183I ASP* 4.4 25.5 + - - +
184I GLY 3.4 24.3 + - - +
185I ALA* 4.1 9.0 - - + -
187I GLN* 6.0 2.2 - - - +
238I ASN* 3.1 32.9 + - + +
240I ASP* 1.3 77.3 - - + +
242I LEU* 1.3 61.6 + - - +
244I GLU* 3.6 15.3 - - - +
245I ASN* 2.9 38.2 + - - +
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Residues in contact with LEU 242 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168I ASN* 3.5 34.1 - - + +
169I LEU* 3.6 29.8 - - + -
185I ALA* 3.8 8.7 - - + +
237I VAL* 4.4 3.8 - - + -
238I ASN 3.0 15.8 + - - +
239I LEU* 4.0 6.1 - - + +
241I ARG* 1.3 76.7 - - - +
243I VAL* 1.3 58.2 + - - +
245I ASN* 4.4 0.7 - - - +
246I THR* 2.9 38.4 + - + -
252I ALA* 3.9 18.6 - - + +
255I ALA* 4.0 8.5 - - + -
256I VAL* 3.4 31.9 - - + -
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Residues in contact with VAL 243 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239I LEU* 2.9 28.5 + - + +
240I ASP* 3.9 4.5 - - - +
242I LEU* 1.3 74.6 - - - +
244I GLU* 1.3 59.5 + - - +
246I THR* 4.0 5.8 - - - -
247I GLY* 2.9 38.1 + - - +
249I ALA* 4.6 20.6 - - + +
252I ALA* 3.7 18.8 - - + -
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Residues in contact with GLU 244 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183I ASP* 4.7 12.7 - - - +
240I ASP 2.9 20.1 + - - +
241I ARG* 3.6 16.9 - - - +
242I LEU 3.2 0.2 - - - -
243I VAL* 1.3 80.5 - - - +
245I ASN* 1.3 67.4 + - - +
247I GLY* 3.8 5.7 + - - -
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Residues in contact with ASN 245 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163I ARG* 4.2 21.9 + - - +
168I ASN* 2.9 47.1 + - + +
182I VAL* 3.7 18.4 - - - +
183I ASP* 3.2 29.6 + - - +
185I ALA* 4.4 2.0 - - - +
241I ARG* 2.9 25.2 + - - +
242I LEU* 3.3 3.5 + - - +
244I GLU* 1.3 83.4 - - - +
246I THR* 1.3 66.0 + - - +
247I GLY* 3.3 0.7 + - - -
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Residues in contact with THR 246 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165I VAL* 5.9 2.0 - - + -
168I ASN* 3.5 33.4 - - + +
242I LEU* 2.9 25.1 + - + +
243I VAL 3.9 0.7 + - - -
245I ASN* 1.3 74.6 - - - +
247I GLY* 1.3 58.9 + - - +
248I ASP* 3.1 20.8 + - - +
251I THR* 3.2 26.0 + - - +
252I ALA* 3.7 11.2 - - - +
255I ALA* 5.3 3.4 - - + -
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Residues in contact with GLY 247 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243I VAL* 2.9 28.1 + - - +
244I GLU 4.2 6.1 - - - -
245I ASN 3.2 3.0 - - - -
246I THR* 1.3 75.8 + - - +
248I ASP* 1.3 59.2 + - - +
249I ALA 3.9 0.7 + - - -
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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