Contacts of the helix formed by residues 234 - 245 (chain C) in PDB entry 1C9T
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 TYR 234 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C HIS* 3.9 28.5 - + - -
101C ASN* 2.9 35.2 + - - -
103C ILE* 3.7 32.3 - - + -
179C ASN* 2.9 43.7 + - + +
229C THR* 3.7 17.0 - - + -
230C LYS 3.2 28.5 - - - -
231C VAL 3.0 6.4 + - - +
233C ASN* 1.3 86.1 - - + +
235C VAL* 1.3 63.7 + - - +
236C SER 3.2 2.7 - - - -
237C TRP* 3.1 14.1 + - + +
238C ILE* 2.9 25.3 + - + +
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Residues in contact with VAL 235 (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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123C LEU* 4.2 13.2 - - + -
124C PRO* 3.5 35.2 - - + +
125C THR* 5.6 1.6 - - - -
231C VAL* 3.3 11.3 + - + +
232C CYS* 3.2 24.7 - - - +
233C ASN 3.6 1.6 - - - -
234C TYR* 1.3 76.7 - - - +
236C SER* 1.3 63.2 + - - +
238C ILE* 3.4 9.4 + - - +
239C LYS* 2.9 50.8 + - + +
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Residues in contact with SER 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C ASN 5.0 3.8 + - - -
234C TYR 3.2 0.4 - - - -
235C VAL* 1.3 78.9 - - - +
237C TRP* 1.3 54.5 + - - +
239C LYS* 3.1 10.0 + - - +
240C GLN* 2.8 36.5 + - - +
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Residues in contact with TRP 237 (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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89C ILE* 3.7 31.4 - - + +
90C VAL 4.1 0.7 - - - -
91C HIS* 3.8 40.6 - + + +
92C PRO* 3.9 15.6 - - + +
103C ILE* 3.7 31.6 - - + -
105C LEU* 3.6 33.2 - - + -
234C TYR* 3.1 17.0 + - + +
236C SER* 1.3 77.1 - - - +
238C ILE* 1.3 82.5 + - + +
240C GLN* 3.8 6.1 - - + +
241C THR* 2.8 48.4 + - - +
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Residues in contact with ILE 238 (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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47C ILE* 3.9 15.7 - - + -
53C VAL* 4.7 3.6 - - + -
103C ILE* 4.3 13.2 - - + -
105C LEU* 3.8 18.4 - - + -
123C LEU* 3.7 36.8 - - + -
231C VAL* 4.3 13.5 - - + -
234C TYR* 2.9 28.8 + - + +
235C VAL* 3.5 7.6 - - - +
237C TRP* 1.3 90.3 - - + +
239C LYS* 1.3 62.0 + - - +
241C THR* 3.2 1.7 + - - -
242C ILE* 3.1 44.6 + - + +
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Residues in contact with LYS 239 (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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123C LEU* 4.7 13.5 - - + -
125C THR* 6.1 2.6 - - - +
235C VAL* 2.9 40.3 + - + +
236C SER* 3.1 6.9 + - - +
238C ILE* 1.3 75.5 - - - +
240C GLN* 1.3 63.3 + - - +
242C ILE* 3.6 9.7 + - + +
243C ALA* 3.2 23.0 + - - +
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Residues in contact with GLN 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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236C SER 2.8 19.1 + - - +
237C TRP* 3.9 6.5 - - + +
239C LYS* 1.3 70.7 - - - +
241C THR* 1.3 61.1 + - - +
243C ALA* 3.2 11.7 + - - +
244C SER* 2.8 53.7 + - - +
76F VAL* 5.5 14.0 - - + +
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Residues in contact with THR 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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51C TRP* 4.5 2.7 - - + -
89C ILE* 3.7 28.9 - - + -
105C LEU* 3.7 18.8 - - + -
237C TRP* 2.8 41.1 + - - -
238C ILE 3.6 3.1 - - - -
240C GLN* 1.3 74.8 - - - +
242C ILE* 1.3 58.2 + - - +
244C SER* 3.3 2.3 + - - -
245C ASN* 2.8 54.9 + - - +
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Residues in contact with ILE 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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47C ILE* 4.5 9.6 - - + -
48C ASN* 4.5 14.4 - - - +
51C TRP* 3.6 52.6 + - + +
105C LEU* 4.5 4.0 - - + -
123C LEU* 5.5 1.3 - - + -
238C ILE* 3.1 39.7 + - + +
239C LYS* 3.8 7.6 - - + +
241C THR* 1.3 77.1 - - - +
243C ALA* 1.3 61.9 + - - +
244C SER 3.3 0.9 + - - -
245C ASN* 3.6 14.9 + - - +
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Residues in contact with ALA 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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239C LYS 3.2 13.6 + - - +
240C GLN* 3.2 13.7 + - - +
242C ILE* 1.3 80.2 - - - +
244C SER* 1.3 59.8 + - - +
245C ASN* 4.7 1.6 - - - +
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Residues in contact with SER 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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240C GLN* 2.8 37.7 + - - +
241C THR* 3.9 3.4 - - - -
243C ALA* 1.3 77.9 - - - +
245C ASN* 1.3 70.0 + - - +
80F GLU* 5.1 14.9 - - - +
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Residues in contact with ASN 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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51C TRP* 3.6 17.8 - - + -
87C LYS* 3.9 16.1 + - + +
89C ILE* 3.5 12.6 - - + +
107C LYS* 2.7 40.7 + - + +
241C THR* 2.8 47.1 + - - +
242C ILE 3.6 11.3 + - - +
243C ALA 4.7 1.7 - - - +
244C SER* 1.3 91.6 - - - +
80F GLU 5.6 1.0 - - - +
82F PHE* 3.7 39.1 + - - +
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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