Contacts of the helix formed by residues 239 - 245 (chain C) in PDB entry 4U7D
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 GLY 239 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236C LYS 4.1 1.7 + - - -
237C ALA 3.2 2.8 + - - -
238C LEU* 1.3 76.6 - - - +
240C ILE* 1.3 60.7 + - - +
241C LEU 3.2 1.5 + - - -
242C LYS 3.8 2.1 + - - -
243C ARG* 3.2 31.0 + - - +
268C ILE 2.9 29.1 + - - -
269C LEU* 3.7 8.0 - - - +
270C CYS* 3.6 15.7 - - - +
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Residues in contact with ILE 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C ILE* 3.8 25.4 - - + +
201C MET* 4.3 13.9 - - + -
237C ALA 3.2 17.4 + - - +
238C LEU 2.9 1.4 + - - -
239C GLY* 1.3 76.0 - - - +
241C LEU* 1.3 67.0 + - + +
242C LYS 3.5 0.2 - - - -
243C ARG* 3.0 42.5 - - + +
244C GLN* 2.8 56.8 + - + +
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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
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135C LEU* 4.7 10.5 - - + -
137C ILE* 4.5 20.2 - - + -
194C ILE* 4.2 25.6 - - + -
201C MET* 4.9 3.4 - - - -
204C LEU* 5.0 0.7 - - + -
213C PHE* 5.8 0.2 - - + -
216C ILE* 4.2 24.5 - - + -
218C VAL* 5.2 4.0 - - + -
238C LEU* 3.0 39.6 + - + +
240C ILE* 1.3 82.5 - - + +
242C LYS* 1.3 54.1 + - - +
245C PHE* 2.7 65.2 + - + +
250C LEU* 5.3 5.6 - - + -
269C LEU* 5.6 0.4 - - + -
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Residues in contact with LYS 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C GLU* 3.1 37.3 + - - +
216C ILE* 5.0 2.7 - - + -
238C LEU 4.6 0.4 + - - -
239C GLY 3.8 2.8 + - - +
241C LEU* 1.3 76.0 - - - +
243C ARG* 1.3 66.0 + - - +
245C PHE 3.9 7.0 - - - +
246C PRO* 2.8 51.9 + - - +
248C ALA 3.4 17.2 + - - +
250C LEU* 4.2 25.4 - - + -
269C LEU 3.9 13.9 + - - +
270C CYS 4.1 11.9 - - - +
271C ILE* 4.2 15.5 - - + +
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Residues in contact with ARG 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C ALA* 4.5 4.2 + - - +
239C GLY* 3.2 16.7 + - - +
240C ILE* 3.0 58.9 + - + +
241C LEU 3.1 0.8 - - - -
242C LYS* 1.3 81.7 - - - +
244C GLN* 1.3 66.4 + - - +
246C PRO* 3.9 6.9 - - - +
270C CYS* 3.9 22.1 - - + -
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Residues in contact with GLN 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C MET* 4.7 7.2 - - + -
205C GLU* 3.9 19.2 + - - -
208C TYR* 4.5 5.7 - - - -
240C ILE* 2.8 46.5 + - + +
243C ARG* 1.3 78.4 + - - +
245C PHE* 1.3 83.3 + - + +
246C PRO* 3.2 10.5 - - - +
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Residues in contact with PHE 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C MET* 4.2 18.4 - - + -
204C LEU* 4.0 22.4 - - + -
205C GLU* 4.0 28.5 - - + -
208C TYR* 3.8 38.6 - + + -
213C PHE* 3.9 18.4 - + - -
216C ILE* 4.8 2.1 - - + +
241C LEU* 2.7 54.2 + - + +
242C LYS* 4.0 5.5 - - - +
244C GLN* 1.3 95.0 - - + +
246C PRO* 1.3 63.8 - - - +
247C ASN 3.2 3.1 - - - -
248C ALA* 3.2 26.0 + - + +
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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