Contacts of the strand formed by residues 225 - 230 (chain E) in PDB entry 4KZZ
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 ILE 225 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E LYS* 4.0 16.0 + - - +
157E ASN 5.7 0.5 - - - +
175E PHE* 4.9 7.9 - - + -
181E CYS* 3.0 35.9 - - + -
182E MET 4.1 2.5 - - - -
183E VAL* 5.1 4.3 - - + +
184E THR* 5.1 0.4 - - - -
208E VAL* 2.0 77.8 - - + +
210E VAL* 4.5 6.7 - - + -
220E THR* 3.6 17.9 - - - +
221E ARG 3.9 3.6 - - - +
222E LEU* 3.0 19.4 + - + +
223E SER 4.4 1.2 - - - +
224E ASN* 1.3 77.2 - - - +
226E PHE* 1.3 59.5 + - - +
227E VAL* 4.9 2.5 - - + +
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Residues in contact with PHE 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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86E PHE* 3.6 24.0 - + - -
87E MET* 4.2 5.4 - - + -
123E LEU* 3.3 23.3 - - + -
124E CYS 3.4 1.3 - - - -
125E LYS* 3.0 60.3 - - + -
142E HIS* 4.2 12.3 - + - -
159E THR* 3.5 9.4 - - + -
181E CYS* 3.2 7.6 - - - -
182E MET* 2.7 49.7 + - + +
184E THR* 3.6 13.5 - - + -
225E ILE* 1.3 74.1 - - - +
227E VAL* 1.3 89.5 + - - +
228E ILE* 3.7 12.3 - - + -
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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
----------------------------------------------------------
123E LEU* 5.3 1.2 - - - +
157E ASN 3.7 9.2 + - - +
158E ASP* 4.5 0.2 - - - -
159E THR* 2.2 83.9 + - + +
173E ILE* 4.5 13.7 - - + +
174E LYS 4.6 0.2 - - - +
175E PHE* 4.4 31.6 - - + -
179E ASN* 4.4 11.0 - - + +
180E LEU 3.7 7.9 - - - +
181E CYS* 4.0 15.5 - - - -
195E ILE* 5.2 1.1 - - + -
225E ILE* 5.1 0.9 - - + -
226E PHE* 1.3 84.1 - - - +
228E ILE* 1.3 59.1 + - - +
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Residues in contact with ILE 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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87E MET* 4.2 5.4 - - + -
123E LEU* 4.2 7.1 - - + +
173E ILE* 5.2 1.6 - - - -
180E LEU* 2.9 48.3 + - + +
181E CYS 4.0 14.6 - - - +
182E MET* 3.1 49.4 - - + -
192E ILE* 4.1 2.0 - - + -
226E PHE* 3.7 9.0 - - + +
227E VAL* 1.3 79.1 - - - +
229E GLY* 1.3 59.6 + - - +
234E PRO* 4.7 2.5 - - + -
235E TRP* 2.8 35.5 + - - +
236E ILE* 4.9 7.4 - - + -
238E LEU* 4.1 23.3 - - + -
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Residues in contact with GLY 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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173E ILE* 4.6 9.2 - - - +
179E ASN* 3.8 9.4 - - - +
180E LEU* 2.8 26.7 + - - +
227E VAL* 3.7 2.0 - - - +
228E ILE* 1.3 81.4 - - - +
230E LYS* 1.3 63.4 + - - +
233E LYS 3.7 2.5 - - - -
235E TRP* 2.7 26.0 - - - -
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Residues in contact with LYS 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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172E PHE 5.5 1.6 + - - -
173E ILE* 4.6 21.5 - - + +
179E ASN* 4.6 13.4 + - - +
180E LEU* 4.0 3.1 - - - +
229E GLY* 1.3 76.2 - - - +
231E GLY* 1.3 57.7 + - - +
233E LYS* 2.4 76.6 + - + +
235E TRP* 3.9 11.1 - - - +
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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