Contacts of the helix formed by residues 237 - 242 (chain C) in PDB entry 5E5R
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 VAL 237 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C PHE 3.5 13.9 - - - +
108C ASP* 3.5 28.0 - - + +
109C ASN 4.1 2.2 - - - -
110C GLU* 4.0 26.7 - - + +
213C ALA 5.7 0.8 + - - -
236C PHE* 1.3 82.1 - - - +
238C LEU* 1.3 64.1 + - - +
239C ARG* 4.1 4.9 - - + +
240C ASP* 2.9 47.0 + - - +
241C LEU* 3.6 6.1 + - - +
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Residues in contact with LEU 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C PHE* 3.5 34.9 + - + +
109C ASN 4.5 2.6 + - - -
128C LEU* 4.8 9.0 - - + -
132C TYR* 3.6 52.2 - - + +
145C ALA* 5.1 2.2 - - + -
148C VAL* 4.6 11.9 - - + -
174C MET* 5.6 0.2 - - + -
176C ILE* 4.2 20.6 - - + -
236C PHE* 4.0 16.5 + - + -
237C VAL* 1.3 71.8 - - - +
239C ARG* 1.3 62.8 + - - +
241C LEU* 3.0 40.1 + - + +
242C LEU* 3.5 6.8 + - - +
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Residues in contact with ARG 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C LEU* 4.1 19.7 - - - +
107C PHE* 2.8 34.3 + - + +
108C ASP* 4.2 18.2 - - - +
237C VAL* 3.2 6.0 + - + -
238C LEU* 1.3 72.2 - - - +
240C ASP* 1.3 62.8 + - - +
242C LEU* 2.9 30.4 + - - +
243C PRO 2.8 20.4 + - - -
244C ALA* 3.1 25.9 + - - +
245C SER* 5.0 0.2 - - - +
246C LEU* 3.7 27.5 - - - +
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Residues in contact with ASP 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C ASN* 4.9 2.1 + - - -
213C ALA* 3.5 36.6 - - + +
237C VAL* 2.9 37.7 + - - +
239C ARG* 1.3 82.2 - - - +
241C LEU* 1.3 59.8 + - + +
242C LEU 3.1 7.6 + - - +
274C VAL* 4.5 9.2 - - - +
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Residues in contact with LEU 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ILE* 5.5 4.0 - - + -
148C VAL* 5.8 1.8 - - + -
174C MET* 3.1 42.7 - - + +
202C ILE* 3.8 2.1 - - - +
204C PHE* 4.3 2.6 - - + -
213C ALA 3.9 15.9 - - - +
214C LEU* 3.6 31.4 - - + -
217C ILE* 4.3 20.2 - - + -
236C PHE* 4.0 19.5 - - + -
237C VAL 4.0 8.3 - - - +
238C LEU* 3.0 31.1 + - + +
240C ASP* 1.3 78.2 - - - +
242C LEU* 1.3 59.0 + - + +
274C VAL* 3.6 14.9 - - - +
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Residues in contact with LEU 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C LEU* 3.9 20.9 - - + -
107C PHE* 3.8 24.9 - - + -
174C MET* 4.2 1.6 - - + -
176C ILE* 3.9 17.3 - - + -
200C MET* 4.4 11.0 - - - -
202C ILE* 3.6 29.6 - - + -
238C LEU 3.8 12.3 - - - +
239C ARG* 2.9 27.2 + - - +
240C ASP* 3.7 6.9 - - - +
241C LEU* 1.3 85.6 - - - +
243C PRO* 1.3 74.7 - - + +
246C LEU* 4.4 6.3 - - + -
270C PHE* 4.6 8.7 - - + -
274C VAL* 3.5 5.6 - - - +
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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