Contacts of the helix formed by residues 231 - 243 (chain E) in PDB entry 2STA
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 231 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53E VAL* 5.7 0.2 - - + -
103E ILE* 4.1 8.7 - - + -
123E LEU* 4.4 7.0 - - + -
124E PRO* 3.7 14.1 - - + -
209E LEU* 3.5 32.8 - - + +
210E GLN 3.1 21.9 + - - +
211E GLY* 3.9 3.6 - - - +
212E VAL* 3.8 28.5 - - + -
229E ALA 4.0 1.6 - - - +
230E LYS* 1.3 70.0 - - - +
232E CYS* 1.3 56.4 + - - +
234E PHE* 2.8 31.4 + - - +
235E ASN* 3.8 4.9 + - - -
238E LEU* 4.0 20.4 - - + -
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Residues in contact with CYS 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E PRO* 3.7 17.8 - - + +
127E SER* 4.0 7.9 - - - +
128E CYS* 2.0 64.3 - - - +
210E GLN* 4.2 7.6 + - - +
230E LYS* 3.6 22.7 - - - -
231E VAL* 1.3 77.6 - - - +
233E ILE* 1.3 61.1 + - - +
235E ASN* 3.4 18.5 + - - +
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Residues in contact with ILE 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E ASN* 5.0 1.3 - - - +
128E CYS* 4.6 4.0 - - - -
178E ASN* 3.7 20.6 - - + +
179E ALA* 3.6 31.4 - - + +
230E LYS* 3.4 34.9 + - + +
231E VAL 3.0 0.2 + - - -
232E CYS* 1.3 80.9 - - - +
234E PHE* 1.3 79.0 + - + +
235E ASN 3.6 0.9 - - - -
236E ASP* 5.3 2.3 + - - +
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Residues in contact with PHE 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E HIS* 3.5 38.4 - + - -
101E ASN* 3.5 34.3 - - - -
103E ILE* 4.0 25.4 - - + -
179E ALA* 3.8 17.9 - - + -
229E ALA* 5.0 2.5 - - + -
230E LYS 3.2 32.3 - - - -
231E VAL* 2.8 12.0 + - - +
233E ILE* 1.3 94.5 - - + +
235E ASN* 1.3 64.3 + - - +
236E ASP 3.2 2.9 - - - -
237E TRP* 3.2 9.6 + - + +
238E LEU* 2.9 36.8 + - + +
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Residues in contact with ASN 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E LEU* 3.8 24.3 - - - +
124E PRO* 3.2 32.3 + - - +
125E THR 5.4 1.8 - - - -
231E VAL 3.8 1.9 + - - -
232E CYS* 3.4 30.9 + - - +
233E ILE 3.6 2.2 - - - -
234E PHE* 1.3 77.6 - - - +
236E ASP* 1.3 57.3 + - - +
238E LEU* 4.4 7.9 - - - -
239E THR* 2.7 39.8 + - + +
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Residues in contact with ASP 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233E ILE 5.3 2.4 + - - +
234E PHE 3.2 0.8 - - - -
235E ASN* 1.3 77.6 - - - +
237E TRP* 1.3 62.4 + - - +
239E THR* 3.6 4.5 + - - -
240E SER* 2.9 41.2 + - - -
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Residues in contact with TRP 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E ILE* 3.5 35.0 - - + -
90E ARG 3.7 16.6 - - - -
91E HIS* 3.6 36.6 - + + +
92E PRO* 3.4 25.7 - - + +
103E ILE* 4.4 11.9 - - + -
104E MET* 4.5 1.6 - - - -
105E LEU* 3.9 20.6 - - + -
234E PHE* 3.2 10.2 + - + +
236E ASP* 1.3 79.5 - - - +
238E LEU* 1.3 91.6 + - + +
240E SER* 4.8 2.9 - - - -
241E THR* 2.8 54.4 + - + +
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Residues in contact with LEU 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E VAL* 4.2 12.6 - - + -
103E ILE* 4.3 13.9 - - + -
104E MET 5.3 0.2 - - - +
105E LEU* 3.9 21.9 - - + +
123E LEU* 4.1 27.4 - - + -
231E VAL* 4.0 26.5 - - + -
234E PHE* 2.9 30.6 + - + +
235E ASN* 4.0 4.9 - - - +
237E TRP* 1.3 102.3 - - + +
239E THR* 1.3 58.8 + - - +
241E THR* 3.9 0.3 - - - -
242E MET* 2.9 38.5 + - + +
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Residues in contact with THR 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E LEU* 4.1 21.8 - - + -
235E ASN* 2.7 29.4 + - + +
236E ASP* 3.6 5.0 + - - -
238E LEU* 1.3 76.6 - - - +
240E SER* 1.3 64.2 + - - +
242E MET* 3.6 15.8 + - + +
243E ALA* 3.8 12.1 + - - +
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Residues in contact with SER 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E ASP* 2.9 31.7 + - - -
237E TRP* 4.1 3.4 - - - -
239E THR* 1.3 76.5 + - - +
241E THR* 1.3 63.0 + - - +
243E ALA* 3.1 8.7 + - - +
244E SER* 2.8 25.3 + - - -
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Residues in contact with THR 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E TRP* 3.9 10.1 - - + -
87E ARG* 4.2 4.4 + - - +
89E ILE* 4.0 34.5 - - + -
105E LEU* 3.8 22.7 - - + -
237E TRP* 2.8 40.0 + - + -
240E SER* 1.3 77.9 - - - +
242E MET* 1.3 56.0 + - - +
243E ALA 2.9 5.9 + - - -
244E SER* 3.1 23.3 + - - +
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Residues in contact with MET 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E VAL* 3.8 13.7 - - + -
48E ASN* 3.4 27.8 - - - +
51E TRP* 3.4 52.1 + - + +
53E VAL* 6.1 0.2 - - + -
105E LEU* 3.9 14.6 - - + -
123E LEU* 3.9 28.3 - - + -
238E LEU* 2.9 28.8 + - + +
239E THR* 3.6 11.2 + - + +
240E SER 3.3 0.6 - - - -
241E THR* 1.3 73.2 - - - +
243E ALA* 1.3 58.4 + - - +
245E TYR 4.9 1.3 - - - +
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Residues in contact with ALA 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239E THR 3.8 8.4 + - - +
240E SER* 3.1 8.5 + - - +
241E THR 3.0 0.4 - - - -
242E MET* 1.3 77.3 - - - +
244E SER* 1.3 63.6 + - - +
245E TYR* 3.4 6.4 + - - +
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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