Contacts of the helix formed by residues 239 - 247 (chain E) in PDB entry 5U07
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2E THR* 2.6 32.8 + - + +
4E VAL* 3.6 29.6 - - + -
237E VAL* 3.1 13.1 + - + +
238E ASN* 1.3 71.9 - - - +
240E ASP* 1.3 61.8 + - - +
242E LEU* 3.2 5.6 + - + +
243E VAL* 2.9 28.5 + - + +
252E ALA* 6.0 0.2 - - + -
253E ARG* 4.0 27.6 - - - +
256E VAL* 3.7 31.0 - - + -
288E VAL* 5.4 0.2 - - + -
364E VAL* 6.5 0.2 - - + -
367E ALA* 3.7 24.9 - - + +
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Residues in contact with ASP 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E THR* 4.1 20.8 + - + +
3E PHE* 6.3 0.2 - - - -
238E ASN* 2.5 30.3 - - - +
239E LEU* 1.3 74.7 - - - +
241E ARG* 1.3 64.4 + - - +
243E VAL* 3.2 9.0 + - - +
244E GLU* 3.0 25.5 + - - +
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Residues in contact with ARG 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183E ASP* 3.4 30.4 + - - +
184E GLY 3.1 25.1 + - - -
185E ALA* 3.6 12.0 - - - +
187E GLN* 6.1 1.0 - - - +
238E ASN* 3.4 27.0 + - - +
239E LEU 3.3 0.4 - - - -
240E ASP* 1.3 88.9 + - - +
242E LEU* 1.3 58.1 + - - +
244E GLU* 3.0 32.1 + - + +
245E ASN* 2.9 53.5 + - - +
273F ASN* 4.8 6.7 + - - +
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Residues in contact with LEU 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E ASN* 3.3 33.2 - - + +
169E LEU* 3.7 22.7 - - + -
185E ALA* 3.8 12.8 - - + +
237E VAL* 3.8 12.1 - - + -
238E ASN 3.0 17.5 + - - +
239E LEU* 3.6 5.8 - - + +
241E ARG* 1.3 77.8 - - - +
243E VAL* 1.3 57.5 + - - +
245E ASN* 3.2 2.1 + - + +
246E THR* 2.9 41.1 + - + -
252E ALA* 4.5 13.2 - - + +
255E ALA* 5.0 3.4 - - + -
256E VAL* 3.6 31.6 - - + -
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Residues in contact with VAL 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239E LEU 2.9 22.3 + - - +
240E ASP* 3.6 7.0 - - - +
242E LEU* 1.3 76.6 - - - +
244E GLU* 1.3 57.3 + - - +
246E THR* 3.8 5.4 - - - -
247E GLY* 2.7 43.0 + - - +
249E ALA* 4.2 20.4 - - + +
252E ALA* 3.7 19.7 - - + -
253E ARG* 3.9 15.9 - - - +
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Residues in contact with GLU 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240E ASP 3.0 11.4 + - - +
241E ARG* 3.0 40.2 + - - +
243E VAL* 1.3 78.4 - - - +
245E ASN* 1.3 72.7 + - - +
247E GLY* 3.5 7.6 + - - -
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Residues in contact with ASN 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E ARG* 4.0 22.1 + - - +
168E ASN* 3.4 38.2 + - + +
182E VAL* 3.8 17.6 - - + +
183E ASP* 3.2 25.9 + - - +
185E ALA* 4.5 0.8 - - - +
241E ARG* 2.9 30.2 + - - +
242E LEU* 3.7 7.2 - - - +
244E GLU* 1.3 88.7 - - - +
246E THR* 1.3 63.8 + - - +
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Residues in contact with THR 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E VAL* 6.1 1.6 - - + -
168E ASN* 3.6 35.4 - - + +
242E LEU* 2.9 24.2 + - + +
243E VAL 3.6 0.7 + - - -
245E ASN* 1.3 75.4 - - - +
247E GLY* 1.3 55.9 + - - +
248E ASP* 3.1 23.3 + - - +
251E THR* 3.4 22.6 + - - +
252E ALA* 3.6 15.4 - - - +
255E ALA* 5.2 5.2 - - + -
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Residues in contact with GLY 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243E VAL* 2.7 29.6 + - - +
244E GLU* 3.9 7.6 - - - -
245E ASN 3.2 2.6 - - - -
246E THR* 1.3 71.3 + - - +
248E ASP* 1.3 61.0 + - - -
249E ALA 3.9 0.5 + - - -
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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