Contacts of the helix formed by residues 188 - 193 (chain E) in PDB entry 3P05
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 188 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184E ALA* 2.9 19.4 + - - +
187E GLU* 1.3 81.2 - - - +
189E LEU* 1.3 77.2 + - + +
190E LEU 3.2 2.5 + - - -
191E VAL* 3.6 2.1 + - - +
192E GLN* 2.9 46.9 + - + +
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Residues in contact with LEU 189 (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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150E ILE* 3.9 30.5 - - + +
151E LEU* 3.6 34.1 - - + -
164E TYR* 3.5 0.3 + - - -
168E PHE* 3.6 9.9 - - + -
185E ALA* 2.9 23.8 + - + +
188E THR* 1.3 86.6 - - + +
190E LEU* 1.3 61.3 + - - +
192E GLN* 3.8 10.8 - - + +
193E ASN* 2.7 62.5 + - - +
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Residues in contact with LEU 190 (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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161E PHE* 4.9 3.4 - - + -
164E TYR* 2.8 39.1 + - + -
165E VAL* 4.4 13.7 - - + -
168E PHE* 3.7 41.1 - - + -
169E TYR* 4.2 20.2 - - + +
185E ALA 3.0 6.1 + - - -
186E THR* 3.4 22.2 - - + +
188E THR 3.2 0.8 - - - -
189E LEU* 1.3 78.4 - - - +
191E VAL* 1.3 63.0 + - + +
194E ALA* 3.5 5.7 + - - +
202E LEU* 5.7 0.2 - - - -
211E LEU* 4.4 17.0 - - + -
214E MET* 4.0 24.0 - - + -
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Residues in contact with VAL 191 (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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186E THR 4.4 2.6 + - - +
187E GLU 5.1 8.1 - - - +
188E THR 3.6 4.5 + - - +
190E LEU* 1.3 73.5 - - + +
192E GLN* 1.3 69.1 + - - +
194E ALA* 3.0 18.0 + - - +
199E LYS* 3.7 12.8 - - + +
202E LEU* 4.0 32.5 - - + +
203E LYS* 4.4 28.3 - - + +
214E MET* 3.9 26.2 - - + -
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Residues in contact with GLN 192 (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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188E THR* 2.9 39.6 + - + +
189E LEU* 3.7 10.8 - - + +
191E VAL* 1.3 77.7 - - - +
193E ASN* 1.3 74.8 + - - +
194E ALA 3.6 1.0 + - - +
199E LYS* 3.0 38.7 + - - +
203E LYS* 6.4 0.2 - - - +
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Residues in contact with ASN 193 (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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150E ILE 4.4 1.8 + - - -
151E LEU 4.1 12.1 + - - -
153E ILE 3.5 20.1 + - - +
154E ARG* 3.3 29.9 + - + +
155E GLN 3.0 22.9 + - - +
164E TYR* 3.4 11.7 - - - +
168E PHE* 5.2 0.8 - - - -
189E LEU* 2.7 53.3 + - - +
192E GLN* 1.3 85.6 + - - +
194E ALA* 1.3 63.2 + - - +
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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