Contacts of the helix formed by residues 230 - 243 (chain E) in PDB entry 1PPF
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 PRO 230 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101E ASN 6.3 0.2 - - - +
179E SER 3.2 24.7 - - - +
180E ASN 4.6 1.1 - - - -
181E VAL* 3.7 28.9 - - + +
210E HIS 3.7 0.7 - - - +
228E PHE 3.8 2.9 - - - +
229E ALA* 1.4 80.8 - - + +
231E VAL* 1.3 66.2 + - - +
232E ALA* 3.2 4.3 - - + +
233E GLN* 2.9 46.3 + - + +
234E PHE* 3.3 23.6 - - + -
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Residues in contact with VAL 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E MET* 4.1 8.7 - - + -
103E ILE* 5.2 2.0 - - - -
123E LEU* 3.8 21.3 - - + -
124E PRO* 4.1 6.3 - - + -
209E ILE 3.4 22.9 - - - +
210E HIS 3.0 20.6 + - - +
211E GLY 3.8 4.5 - - - +
212E ILE* 3.7 33.9 - - + -
229E ALA 3.3 0.6 + - - +
230E PRO* 1.3 71.4 - - - +
232E ALA* 1.4 53.2 + - - +
233E GLN 3.0 0.2 - - - -
234E PHE* 2.7 34.4 + - - +
235E VAL* 3.4 9.9 + - + +
238E ILE* 4.3 13.9 - - + +
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Residues in contact with ALA 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* 3.9 15.1 - - + +
125E ALA 3.9 6.5 - - - +
126E GLN* 3.3 8.3 + - - -
127E GLY* 2.6 27.2 + - - +
128E ARG* 3.2 37.0 - - + +
210E HIS* 4.5 7.6 + - - +
230E PRO* 3.1 3.6 + - + -
231E VAL* 1.4 77.2 - - - +
233E GLN* 1.4 58.1 + - + +
234E PHE 3.1 1.1 + - - -
235E VAL* 3.9 10.8 + - - -
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Residues in contact with GLN 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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126E GLN* 3.1 21.4 + - - +
127E GLY* 4.6 5.8 - - - +
129E ARG* 6.1 1.2 - - - +
178E ARG 3.2 24.3 + - - -
179E SER* 3.9 10.9 - - - +
230E PRO* 2.9 42.3 + - + +
232E ALA* 1.4 79.1 - - + +
234E PHE* 1.3 74.1 + - + +
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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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92E ASN* 3.9 19.3 - - - -
101E ASN* 3.6 47.6 - - + -
102E ASP 5.4 0.2 - - - -
103E ILE* 3.9 42.0 - - + -
126E GLN* 3.7 0.4 - - - -
229E ALA* 5.2 3.4 - - + -
230E PRO* 3.3 48.2 - - + -
231E VAL* 2.7 9.0 + - - +
233E GLN* 1.3 93.1 - - + +
235E VAL* 1.3 62.7 + - - +
236E ASN 3.4 2.7 - - - -
237E TRP* 3.0 14.3 + + + +
238E ILE* 2.7 30.4 + - + +
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Residues in contact with VAL 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E LEU* 4.8 7.9 - - + -
124E PRO* 3.3 28.7 - - + +
125E ALA* 4.3 2.5 - - - -
126E GLN* 2.9 27.1 + - + +
231E VAL* 3.5 22.7 - - + +
232E ALA* 4.0 10.5 - - - -
234E PHE* 1.3 79.0 - - - +
236E ASN* 1.3 51.4 + - - +
238E ILE* 3.0 15.0 + - + +
239E ASP* 2.7 51.9 + - - +
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Residues in contact with ASN 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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126E GLN* 2.8 43.5 + - - +
235E VAL* 1.3 70.2 - - - +
237E TRP* 1.3 62.3 + - - +
239E ASP* 3.5 9.0 + - - +
240E SER* 3.1 22.7 + - - -
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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 PHE* 3.7 20.7 - - + +
90E GLU 3.6 27.4 + - - -
92E ASN* 3.6 37.3 - - + +
103E ILE* 3.8 30.5 - - + -
105E ILE* 3.4 32.5 - - + -
234E PHE* 3.0 23.4 + + + +
236E ASN* 1.3 76.8 - - - +
238E ILE* 1.3 74.5 + - + +
240E SER* 2.7 30.5 + - - -
241E ILE* 3.5 22.3 + - + +
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Residues in contact with ILE 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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47E ILE* 4.4 10.8 - - + -
53E MET* 4.2 21.5 - - - -
103E ILE* 4.3 3.1 - - + -
105E ILE* 4.4 8.1 - - + -
123E LEU* 4.2 16.8 - - + -
231E VAL* 4.3 13.5 - - + -
234E PHE* 2.7 35.6 + - + +
235E VAL* 3.3 14.1 - - + +
237E TRP* 1.3 87.7 - - + +
239E ASP* 1.3 62.7 + - - +
241E ILE* 2.9 25.7 + - - +
242E ILE* 3.0 34.9 + - + +
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Residues in contact with ASP 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* 6.1 0.3 - - - +
235E VAL* 2.7 36.3 + - - +
236E ASN* 3.8 10.0 - - - +
237E TRP 3.3 0.2 - - - -
238E ILE* 1.3 78.3 - - - +
240E SER* 1.3 62.6 + - - +
241E ILE 3.1 1.2 + - - -
242E ILE* 4.2 14.5 - - - +
243E GLN* 3.1 40.2 + - - +
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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 ASN 3.1 14.0 + - - -
237E TRP* 2.7 25.2 + - - -
239E ASP* 1.3 76.3 - - - +
241E ILE* 1.3 62.4 + - - +
243E GLN* 5.0 1.0 + - - +
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Residues in contact with ILE 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 PHE* 3.4 41.2 - - + -
89E PHE* 3.7 49.1 - - + -
105E ILE* 3.8 16.8 - - + -
237E TRP* 3.7 36.3 - - + +
238E ILE* 2.9 8.0 + - - +
240E SER* 1.3 84.0 - - - +
242E ILE* 1.3 68.5 + - + +
243E GLN* 3.3 7.4 + - - +
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Residues in contact with ILE 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 ILE* 3.8 36.8 - - + +
48E ALA* 4.3 11.7 - - + +
51E PHE* 3.8 36.1 - - + -
105E ILE* 5.1 0.7 - - + -
123E LEU* 4.9 6.3 - - + -
238E ILE* 3.0 38.5 + - + +
239E ASP* 3.3 11.0 + - - +
241E ILE* 1.3 85.0 - - + +
243E GLN* 1.3 64.8 + - - +
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Residues in contact with GLN 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 ASP* 3.1 32.7 + - - +
240E SER 5.5 0.9 - - - +
241E ILE 3.3 3.9 - - - +
242E ILE* 1.3 81.8 - - - +
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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