Contacts of the strand formed by residues 225 - 228 (chain E) in PDB entry 4PEI
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 TYR 225 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175E ASP 3.1 14.1 + - - +
176E ILE* 3.3 17.3 - - + +
177E SER 2.8 30.5 + - - -
223E PRO* 3.7 5.1 - - - +
224E LYS* 1.3 89.8 - - + +
226E TRP* 1.3 55.6 + - - +
227E ILE* 4.2 12.3 - - + -
242E THR* 4.2 3.4 - - - -
243E HIS* 3.2 44.2 - + + +
245E ILE* 4.1 16.2 - - + -
259E LEU* 4.1 21.6 - - + +
261E LEU* 3.9 32.3 - - + +
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Residues in contact with TRP 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E VAL* 4.5 3.6 - - + -
177E SER* 3.2 39.0 - - - -
179E SER* 2.8 29.0 + - - +
183E PRO* 3.4 19.6 - - + +
214E ASN* 3.6 37.7 - - + -
217E ILE* 3.7 22.7 - - + -
218E LEU* 3.4 35.9 - - + -
221E LEU* 5.8 0.7 - - + -
223E PRO* 3.6 14.6 - - + -
225E TYR* 1.3 72.3 - - - +
227E ILE* 1.3 63.3 + - - +
228E SER* 3.4 13.9 - - - -
242E THR* 3.8 13.8 - - + +
243E HIS 2.9 7.3 + - - +
244E PHE* 3.4 9.4 - + + -
245E ILE 2.7 32.2 + - - +
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Residues in contact with ILE 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E ILE* 3.7 37.5 - - + -
41E ILE* 5.1 2.0 - - + -
43E THR* 3.5 16.1 - - + +
176E ILE* 4.2 21.3 - - + -
177E SER 3.0 6.5 + - - -
178E LEU* 3.5 15.6 - - + -
179E SER 3.0 24.6 + - - +
225E TYR* 4.4 7.0 - - + -
226E TRP* 1.3 78.6 - - - +
228E SER* 1.3 66.2 + - - +
245E ILE* 3.2 16.6 - - + +
247E LEU* 4.0 24.5 - - + -
259E LEU* 4.0 16.6 - - + -
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Residues in contact with SER 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E THR* 3.7 6.8 + - - -
179E SER* 2.5 29.2 + - - -
180E HIS 3.7 4.9 - - - -
181E ASP 3.6 3.3 + - - -
182E TRP* 3.6 27.1 - - - -
183E PRO* 3.7 0.9 - - - +
226E TRP* 3.4 13.3 + - - -
227E ILE* 1.3 70.5 - - - +
229E GLY* 1.3 58.6 + - - +
230E HIS 4.1 0.4 - - - -
244E PHE* 3.5 12.7 - - - -
245E ILE 2.9 6.7 + - - -
246E ALA* 3.4 3.7 - - - +
247E LEU* 3.1 26.0 + - - +
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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