Contacts of the strand formed by residues 223 - 228 (chain E) in PDB entry 2XTJ
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 223 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136E GLY* 3.6 8.9 - - - -
137E PRO* 3.9 31.2 - - + +
216E VAL* 3.6 2.1 - - + +
217E ASN* 3.3 5.2 + - - +
218E HIS* 2.8 34.0 + - - -
221E SER* 2.7 26.4 + - - -
222E ASN* 1.3 77.8 + - - +
224E LYS* 1.3 62.7 + - - +
225E VAL* 4.2 20.9 - - + +
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Residues in contact with LYS 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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216E VAL 3.2 5.6 - - - +
217E ASN* 3.3 35.0 - - + +
222E ASN* 4.1 3.6 + - - -
223E THR* 1.3 74.3 - - - +
225E VAL* 1.3 66.6 + - - +
226E ASP* 5.9 1.6 - - - +
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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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137E PRO 5.5 3.1 - - - +
139E VAL* 3.9 35.7 - - + +
214E CYS 3.4 3.3 - - - +
215E ASN* 3.6 0.7 - - - -
216E VAL* 2.8 41.1 + - + +
223E THR* 4.2 17.7 - - + +
224E LYS* 1.3 80.9 - - - +
226E ASP* 1.3 74.8 + - - +
227E LYS* 4.2 8.3 - - + +
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Residues in contact with ASP 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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174E SER* 5.8 0.2 - - - -
213E ILE* 3.7 12.1 - - + -
214E CYS 3.6 2.5 - - - -
215E ASN* 2.4 42.9 + - - +
224E LYS* 5.9 1.0 - - - +
225E VAL* 1.3 76.9 - - - +
227E LYS* 1.3 58.9 + - - +
228E LYS 4.1 1.4 + - - -
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Residues in contact with LYS 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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122C GLU* 3.2 36.6 + - - +
139E VAL* 3.6 47.6 + - + +
140E PHE* 5.5 0.2 - - - -
141E PRO* 3.8 17.0 - - - +
158E CYS* 4.7 1.1 - - - -
212E TYR 3.7 0.5 - - - +
213E ILE* 3.3 5.9 - - - +
214E CYS* 3.0 38.7 + - - -
225E VAL* 3.9 7.4 - - + -
226E ASP* 1.3 73.4 - - - +
228E LYS* 1.3 73.1 + - - +
229E VAL* 3.8 10.4 + - + +
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Residues in contact with LYS 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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141E PRO* 4.8 2.3 - - - +
211E THR* 3.9 34.7 + - + +
212E TYR 3.5 10.8 - - - +
213E ILE* 4.3 9.0 - - + +
226E ASP 4.1 2.4 + - - -
227E LYS* 1.3 91.7 - - - +
229E VAL* 1.3 64.7 + - - +
230E GLU* 3.3 43.5 + - + +
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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