Contacts of the helix formed by residues 243 - 248 (chain B) in PDB entry 3EWS
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 GLU 243 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60B SER* 3.6 27.0 + - - -
64B LYS* 3.2 25.1 - - - -
144B LYS* 5.8 7.2 - - - +
145B THR* 6.0 0.2 - - - +
170B PRO* 3.5 5.7 - - + +
174B LEU* 3.8 22.3 - - - +
178B THR* 4.9 0.5 + - - -
242B ASP* 1.3 102.2 + - - +
244B ALA* 1.3 61.2 + - - +
245B ASP* 3.3 11.7 - - - +
246B VAL* 3.0 27.9 - - + +
247B MET* 3.4 5.5 + - - +
273B PHE* 3.4 13.6 + - - +
274B SER* 4.6 2.0 - - - +
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Residues in contact with ALA 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B LEU* 3.6 24.9 - - + -
242B ASP 3.5 0.6 + - - -
243B GLU* 1.3 68.9 - - - +
245B ASP* 1.3 63.1 + - - +
246B VAL 3.0 7.3 + - - -
247B MET* 3.1 10.8 + - - +
248B ILE* 3.2 21.6 + - - +
272B LEU* 4.1 20.2 - - + -
273B PHE 3.1 17.5 + - - +
274B SER* 4.5 3.4 - - - -
281B VAL* 4.7 6.7 - - + -
284B PHE* 4.4 12.3 - - + -
285B ALA* 6.0 0.2 - - + -
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Residues in contact with ASP 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ARG* 3.9 18.6 + - - -
243B GLU* 3.3 22.0 - - - +
244B ALA* 1.3 73.1 - - - +
246B VAL* 1.3 63.4 + - - +
248B ILE* 3.5 23.3 - - - +
274B SER* 3.1 21.3 + - - +
275B ALA* 3.3 24.0 + - - +
276B THR* 3.5 25.0 + - + -
278B GLU* 6.0 0.2 - - - +
281B VAL* 4.2 7.4 - - + +
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Residues in contact with VAL 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ARG* 3.9 17.3 - - + +
57B ALA* 3.6 41.7 - - + +
60B SER* 4.6 6.3 - - - +
170B PRO* 3.3 22.9 - - + +
174B LEU* 4.8 1.1 - - + -
243B GLU* 3.0 40.2 - - + +
245B ASP* 1.3 81.2 + - - +
247B MET* 1.3 62.6 + - - +
248B ILE 3.2 2.9 + - - -
249B ALA* 3.7 16.2 + - + +
250B THR 5.1 0.3 + - - -
253B HIS* 5.6 0.7 + - - -
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Residues in contact with MET 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B LEU* 3.8 8.1 - - - +
169B SER 3.5 4.3 - - - -
170B PRO* 3.2 33.7 - - + -
218B PRO* 3.7 25.4 - - - -
241B LEU* 3.7 21.1 - - + -
242B ASP 3.2 26.2 - - - +
243B GLU 3.4 5.9 + - - +
244B ALA* 3.1 9.0 + - - +
246B VAL* 1.3 77.6 - - - +
248B ILE* 1.3 61.8 + - + +
249B ALA 3.3 1.5 + - - -
250B THR 3.7 2.9 - - - +
253B HIS* 3.1 48.5 + - + +
254B GLN* 4.4 2.5 + - - +
257B SER* 4.0 9.6 - - - +
284B PHE* 5.8 4.2 - - + -
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Residues in contact with ILE 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ARG* 6.0 0.7 - - - +
244B ALA 3.2 18.1 + - - +
245B ASP* 3.5 16.8 - - - +
247B MET* 1.3 78.2 - - - +
249B ALA* 1.3 60.5 + - - +
250B THR 3.0 10.4 + - - -
251B GLN 4.5 0.5 + - - -
254B GLN* 3.4 37.7 + - + +
278B GLU* 5.5 2.7 - - - +
280B SER* 4.0 20.0 - - - +
281B VAL* 3.5 33.4 - - + +
284B PHE* 3.8 32.5 - - + -
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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