Contacts of the helix formed by residues 227 - 236 (chain C) in PDB entry 5U07
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 THR 227 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33C ARG* 3.1 31.9 + - + +
51C SER 3.8 6.3 - - - -
52C HIS* 3.8 17.8 + - - +
53C GLU 5.0 0.4 - - - -
54C LEU 3.1 20.6 - - - +
55C SER* 3.3 12.1 - - - -
224C LEU* 5.2 1.7 - - - +
225C GLY 4.4 1.1 - - - -
226C ARG* 1.3 68.7 + - - +
228C LEU* 1.3 65.5 + - - +
229C PHE* 3.8 5.4 + - - +
230C GLU* 2.3 60.8 + - - +
231C SER* 3.3 12.3 + - - -
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Residues in contact with LEU 228 (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 VAL* 3.6 23.1 - - + +
48C LEU* 6.0 0.2 - - - -
51C SER* 3.0 26.7 - - - +
54C LEU* 3.0 45.1 - - + +
55C SER 3.0 12.9 + - - +
56C ASP* 4.4 12.6 - - - +
57C VAL* 3.5 34.8 - - + -
69C TRP* 4.8 6.3 - - + -
72C LEU* 5.5 2.9 - - + -
224C LEU* 5.8 0.7 - - - -
227C THR* 1.3 76.7 - - - +
229C PHE* 1.3 57.6 + - - +
231C SER* 2.5 22.5 + - - +
232C LEU* 2.8 29.1 + - + +
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Residues in contact with PHE 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C SER* 2.9 41.0 + - - +
52C HIS* 4.1 4.7 - - + +
101C ILE 4.7 2.0 - - - -
102C LEU* 5.8 1.8 - - + -
104C LYS* 4.0 2.9 - - - -
105C GLY* 3.2 30.3 - - - -
106C ARG* 3.3 26.9 - - - -
107C LEU* 3.4 37.9 - - + -
227C THR* 3.1 2.8 + - - +
228C LEU* 1.3 83.8 - - - +
230C GLU* 1.3 88.2 + - + +
232C LEU* 3.0 22.3 - - + +
233C ILE* 3.0 32.1 + - + +
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Residues in contact with GLU 230 (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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102C LEU* 4.8 7.2 - - + -
225C GLY* 3.9 13.5 - - - -
226C ARG* 2.5 20.2 + - - +
227C THR* 2.3 57.1 + - - +
229C PHE* 1.3 89.3 - - + +
231C SER* 1.3 56.3 + - - +
233C ILE* 3.3 7.7 + - - +
234C LEU* 2.9 41.5 + - + +
368C VAL* 4.4 18.8 - - + -
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Residues in contact with SER 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C TRP* 4.1 7.1 - - - -
223C PRO 3.9 6.0 - - - +
224C LEU* 3.7 32.2 - - - +
225C GLY 3.7 11.7 - - - +
227C THR 3.5 9.8 + - - -
228C LEU* 2.5 31.5 + - - +
229C PHE 3.1 0.2 - - - -
230C GLU* 1.3 80.7 - - - +
232C LEU* 1.3 58.9 + - - +
234C LEU* 3.1 7.4 + - - +
235C ASN* 2.9 33.9 + - - +
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Residues in contact with LEU 232 (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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48C LEU* 4.3 20.4 - - + -
51C SER* 4.6 9.2 - - - -
69C TRP* 4.8 6.3 - - + -
72C LEU* 5.0 23.3 - - + +
73C ALA* 4.4 1.9 - - - +
76C THR* 3.6 32.3 + - + +
107C LEU* 6.0 1.6 - - + -
228C LEU* 2.8 26.2 + - + +
229C PHE* 3.0 24.9 - - + +
231C SER* 1.3 79.2 + - - +
233C ILE* 1.3 76.6 + - + +
235C ASN* 3.1 29.5 + - + +
236C ILE* 3.5 11.6 + - - +
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Residues in contact with ILE 233 (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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76C THR* 5.9 0.7 - - - -
98C ARG* 2.5 37.8 + - - +
101C ILE* 4.0 26.7 - - + +
102C LEU* 3.8 23.8 - - + -
107C LEU* 4.2 4.9 - - + -
229C PHE* 3.0 53.0 + - + +
230C GLU* 3.7 8.1 - - - +
232C LEU* 1.3 90.5 - - + +
234C LEU* 1.3 57.2 + - - +
236C ILE* 3.2 24.3 + - + +
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Residues in contact with LEU 234 (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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98C ARG* 3.2 26.0 - - - +
102C LEU* 3.7 31.9 - - + -
223C PRO* 4.1 18.5 - - + +
224C LEU 6.0 2.5 - - - +
230C GLU* 2.9 35.2 + - + +
231C SER* 3.7 5.8 - - - +
233C ILE* 1.3 75.5 - - - +
235C ASN* 1.3 61.4 + - - +
236C ILE 3.2 1.1 + - - +
354C ILE* 3.5 8.5 - - - +
358C CYS* 3.1 41.3 - - + +
365C PRO* 5.2 4.5 - - + -
368C VAL* 4.9 13.0 - - + -
369C LEU* 5.1 9.9 - - + -
372C LEU* 5.2 10.8 - - + -
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Residues in contact with ASN 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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69C TRP* 3.3 36.3 + - - +
73C ALA* 3.8 15.0 - - + +
222C HIS* 3.3 32.2 + - - +
223C PRO* 3.6 14.8 + - - +
224C LEU* 6.3 0.2 - - - +
231C SER* 2.9 19.6 + - - -
232C LEU* 3.2 17.1 - - - +
233C ILE 3.1 0.6 - - - -
234C LEU* 1.3 76.9 - - - +
236C ILE* 1.3 62.0 + - - +
237C PRO* 3.2 4.9 - - - +
312C TYR* 2.9 23.1 + - - +
354C ILE* 3.4 10.7 - - - +
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Residues in contact with ILE 236 (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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73C ALA* 3.5 15.7 - - - +
76C THR* 3.5 21.8 - - - +
77C ALA* 3.6 32.8 - - + +
80C THR* 4.8 4.3 - - - +
81C GLY 5.7 0.2 - - - +
94C TRP* 4.1 21.8 + - + -
98C ARG* 4.2 12.4 + - - +
232C LEU 3.6 12.6 - - - +
233C ILE* 3.2 25.4 + - + +
234C LEU 4.0 6.1 - - - +
235C ASN* 1.3 75.1 - - - +
237C PRO* 1.3 79.3 - - + +
238C TYR 3.8 0.7 + - - -
239C PRO* 5.2 0.9 - - + -
267C LEU* 5.7 1.1 - - + -
354C ILE* 4.7 1.8 - - - +
357C ASN* 5.6 1.2 + - - -
358C CYS* 4.9 2.8 - - - -
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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