Contacts of the helix formed by residues 243 - 248 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A SER* 3.3 23.0 + - - -
64A LYS* 3.1 31.9 - - - +
144A LYS* 6.0 1.6 - - - -
145A THR* 5.3 0.2 + - - -
170A PRO* 3.6 24.2 - - + -
174A LEU* 4.2 9.7 - - + +
242A ASP* 1.3 97.0 + - - +
244A ALA* 1.3 55.7 + - - +
245A ASP* 3.1 13.0 - - - +
246A VAL* 2.7 33.4 + - + +
247A MET 3.0 8.5 + - - -
273A PHE 3.5 8.0 + - - -
274A SER* 5.1 0.7 - - - +
275A ALA* 5.9 1.6 - - - +
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Residues in contact with ALA 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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241A LEU* 3.8 20.9 - - + -
242A ASP 3.2 1.6 + - - -
243A GLU* 1.3 74.3 - - - +
245A ASP* 1.3 63.4 + - - +
246A VAL 3.0 1.2 + - - -
247A MET* 3.1 11.7 + - - +
248A ILE* 3.2 19.4 + - - +
272A LEU* 3.8 25.6 - - + -
273A PHE 3.0 19.7 + - - +
274A SER* 3.8 6.7 - - - +
281A VAL* 4.1 10.5 - - + -
284A PHE* 4.7 5.3 - - + -
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Residues in contact with ASP 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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56A ARG* 3.7 35.3 + - - +
243A GLU* 3.6 17.5 - - - +
244A ALA* 1.3 76.7 - - - +
246A VAL* 1.3 69.0 + - - +
248A ILE* 3.4 19.2 - - - +
249A ALA* 4.9 0.9 + - - +
274A SER* 3.4 13.6 + - - +
275A ALA* 3.2 35.6 + - - +
276A THR* 3.7 21.9 + - - +
281A VAL* 4.3 7.9 - - + -
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Residues in contact with VAL 246 (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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56A ARG* 4.2 16.2 - - + +
57A ALA* 3.9 30.7 - - + +
60A SER* 4.1 22.9 - - - +
170A PRO* 3.7 21.7 - - + +
174A LEU* 4.6 2.2 - - + -
243A GLU* 2.7 31.9 + - + +
245A ASP* 1.3 89.5 - - - +
247A MET* 1.3 58.2 + - - +
248A ILE 3.3 0.7 - - - -
249A ALA* 3.1 25.8 - - + +
253A HIS* 5.4 1.0 + - - -
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Residues in contact with MET 247 (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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168A LEU* 3.6 12.6 - - - +
169A SER 3.4 5.2 - - - +
170A PRO* 3.2 33.2 - - + -
218A PRO* 3.5 31.0 - - - -
241A LEU* 4.4 11.4 - - + -
242A ASP 3.1 24.7 - - - +
243A GLU 3.0 5.7 + - - +
244A ALA* 3.1 9.4 + - - +
246A VAL* 1.3 74.4 - - - +
248A ILE* 1.3 61.1 + - - +
249A ALA 3.0 6.5 + - - -
250A THR 3.5 4.2 + - - +
253A HIS* 3.2 47.5 + - + +
254A GLN* 4.3 2.4 + - - -
257A SER* 3.9 12.1 - - - +
284A PHE* 5.4 5.4 - - + -
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Residues in contact with ILE 248 (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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56A ARG* 4.8 8.3 - - - +
244A ALA 3.2 12.0 + - - +
245A ASP 3.4 20.6 - - - +
247A MET* 1.3 76.4 - - - +
249A ALA* 1.3 65.2 + - - +
250A THR 3.2 3.9 + - - -
251A GLN* 4.3 0.5 + - - +
254A GLN* 3.2 32.9 + - + +
278A GLU* 5.0 1.3 - - - +
280A SER* 3.6 24.9 - - - +
281A VAL* 3.5 31.6 - - + +
284A PHE* 3.8 36.6 - - + -
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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