Contacts of the helix formed by residues 221 - 231 (chain E) in PDB entry 1PF7
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 221 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84E ARG* 3.4 15.3 + - - +
113E VAL* 3.4 31.3 - - + +
114E THR 4.2 1.0 + - - -
115E ASN* 2.7 34.9 + - - +
132E ILE* 4.0 10.8 - - + -
166E TYR* 4.3 4.5 - - - +
192E TYR* 4.0 5.6 - - + -
220E SER* 1.3 74.6 - - - +
222E VAL* 1.3 68.9 + - - +
223E PRO 3.3 1.1 - - - -
224E GLU* 3.0 21.3 + - - +
225E VAL* 2.9 30.6 + - + +
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Residues in contact with VAL 222 (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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135E HIS* 3.6 47.1 - - + +
136E ILE 4.4 1.1 - - - +
137E ASN* 3.4 40.8 - - + +
166E TYR* 4.6 0.4 - - - +
192E TYR* 3.7 12.1 - - + -
194E MET* 3.5 28.7 - - + +
220E SER 2.6 9.1 + - - -
221E THR* 1.3 71.8 - - - +
223E PRO* 1.4 66.7 - - + +
225E VAL* 3.4 3.1 + - - +
226E ILE* 3.0 29.5 + - + +
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Residues in contact with PRO 223 (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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93E LEU* 3.6 33.4 - - + -
96E VAL* 4.3 8.1 - - + -
97E THR* 3.3 18.4 - - + -
137E ASN* 5.6 1.3 - - - +
146E PRO* 3.9 15.5 - - + -
194E MET* 3.6 29.6 - - + -
220E SER* 3.8 6.5 - - - +
221E THR 3.6 4.3 - - - +
222E VAL* 1.4 90.3 - - + +
224E GLU* 1.3 63.6 + - - +
226E ILE* 3.2 2.8 + - + +
227E VAL* 3.1 26.3 + - - +
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Residues in contact with GLU 224 (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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30E ILE* 3.9 21.8 - - + +
81E MET* 5.3 1.6 - - - +
84E ARG* 3.0 36.8 + - - +
85E PHE 4.0 7.7 + - - +
96E VAL* 4.3 19.1 - - - +
97E THR* 3.7 13.0 - - + -
99E PRO* 5.8 0.9 - - + -
100E VAL* 3.9 18.3 - - + +
111E LEU* 4.5 1.6 - - + -
113E VAL* 4.6 6.5 - - + -
220E SER* 4.0 1.4 - - - -
221E THR* 3.0 35.5 + - - +
223E PRO* 1.3 78.6 - - - +
225E VAL* 1.3 64.9 + - - +
227E VAL* 3.3 2.9 + - - +
228E ALA* 2.8 24.9 + - - +
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Residues in contact with VAL 225 (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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111E LEU* 4.6 0.4 - - - -
113E VAL* 4.1 6.7 - - + -
135E HIS* 4.1 5.2 - - + -
165E ALA* 4.0 21.1 - - + -
166E TYR* 3.5 40.8 - - + +
221E THR* 2.9 31.5 + - + +
222E VAL* 3.6 7.0 - - - +
224E GLU* 1.3 74.1 - - - +
226E ILE* 1.3 66.0 + - - +
228E ALA* 2.9 8.8 + - - +
229E ARG* 2.8 25.1 + - + +
235E VAL* 3.9 21.8 - - + -
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Residues in contact with ILE 226 (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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135E HIS* 4.2 16.2 - - + +
137E ASN* 3.1 32.3 - - + +
145E ASN* 4.0 14.4 - - - +
146E PRO* 3.7 19.5 - - + -
147E LEU* 3.5 25.8 - - + -
162E MET* 3.5 28.2 - - + +
222E VAL* 3.0 19.8 + - + +
223E PRO 3.4 6.7 - - - +
225E VAL* 1.3 75.4 - - - +
227E VAL* 1.3 58.6 + - - +
230E HIS* 3.0 25.1 + - - +
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Residues in contact with VAL 227 (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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97E THR* 3.4 29.4 - - - +
100E VAL* 3.4 29.6 - - + -
101E ARG* 4.1 17.9 - - + +
146E PRO* 3.4 22.7 - - + +
147E LEU* 4.2 12.6 - - + -
223E PRO 3.1 15.0 + - - +
224E GLU 3.9 2.0 - - - +
226E ILE* 1.3 73.3 - - - +
228E ALA* 1.3 67.5 - - - +
230E HIS* 3.3 8.4 + - - +
231E CYS* 3.0 25.8 + - - +
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Residues in contact with ALA 228 (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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100E VAL* 3.5 15.3 - - + -
111E LEU* 3.6 16.4 - - + -
224E GLU 2.8 14.0 + - - +
225E VAL 2.9 7.8 + - - +
227E VAL* 1.3 76.3 - - - +
229E ARG* 1.3 57.7 + - - +
231E CYS* 2.9 24.0 + - - +
232E GLY 3.0 6.4 + - - -
233E LEU* 3.0 19.3 + - + +
235E VAL* 3.4 22.0 - - + -
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Residues in contact with ARG 229 (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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160E PRO* 5.2 2.4 - - - +
161E ALA 4.9 5.5 + - - +
162E MET* 3.8 17.3 - - + -
164E ASP* 4.4 22.2 + - - -
165E ALA* 3.2 48.6 + - + +
225E VAL* 2.8 18.8 + - + +
226E ILE 3.8 4.0 - - - +
228E ALA* 1.3 74.7 - - - +
230E HIS* 1.3 65.7 + - - +
232E GLY* 2.9 23.1 + - - +
233E LEU 2.7 30.1 + - - -
234E ARG* 4.3 5.5 - - - +
235E VAL* 3.7 14.1 - - + +
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Residues in contact with HIS 230 (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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2E GLU* 4.2 5.1 + - - -
101E ARG* 2.9 30.5 + - - -
147E LEU* 3.8 18.6 - - + -
151E ASN* 2.8 15.2 + - - -
152E ASP 4.0 2.5 - - - -
155E PHE* 2.8 26.3 - - + +
156E GLY* 3.2 30.6 - - - -
157E ASP 2.7 38.8 + - - -
160E PRO* 3.7 25.5 - - + +
162E MET* 4.4 0.4 - - - +
226E ILE 3.0 18.7 + - - +
227E VAL 3.5 5.4 - - - +
228E ALA 3.3 0.4 - - - -
229E ARG* 1.3 76.0 - - - +
231E CYS* 1.3 54.8 + - - +
232E GLY* 3.4 0.5 + - - -
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Residues in contact with CYS 231 (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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100E VAL* 4.7 2.0 - - - -
101E ARG* 4.2 26.0 - - - -
104E HIS* 3.5 57.7 + - + +
155E PHE* 3.4 16.4 - - - +
227E VAL 3.0 15.1 + - - +
228E ALA* 2.9 14.1 - - - +
230E HIS* 1.3 77.1 - - - +
232E GLY* 1.3 58.5 + - - +
233E LEU* 3.6 8.9 + - + +
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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