Contacts of the strand formed by residues 213 - 218 (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 ILE 213 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E SER 3.8 0.2 - - - +
172E TRP* 3.4 8.7 - - - -
173E ASN* 2.8 47.0 + - - +
211E THR* 4.0 20.4 - - + -
212E TYR* 1.3 76.4 - - - +
214E CYS* 1.3 62.8 + - - +
215E ASN* 3.8 11.9 + - - +
226E ASP* 3.7 20.4 - - + -
227E LYS 3.3 23.1 - - - +
228E LYS* 4.3 12.3 - - + +
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Residues in contact with CYS 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139E VAL* 3.9 14.6 - - - -
158E CYS* 2.0 50.7 - - + -
170E VAL* 4.3 7.2 - - + -
171E SER 3.3 5.4 - - - +
172E TRP* 3.6 23.8 - - + -
213E ILE* 1.3 72.1 - - - +
215E ASN* 1.3 60.5 + - - +
216E VAL* 4.1 7.0 - - - -
225E VAL 3.4 5.2 - - - +
226E ASP* 3.6 0.3 - - - -
227E LYS* 3.0 30.1 + - - -
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Residues in contact with ASN 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169E THR 3.6 1.7 - - - +
170E VAL* 3.3 6.4 - - - -
171E SER* 2.6 58.8 + - - +
173E ASN 3.6 1.4 + - - -
174E SER* 2.9 43.3 + - - +
213E ILE* 3.8 14.5 + - - +
214E CYS* 1.3 70.5 - - - +
216E VAL* 1.3 61.7 + - - +
226E ASP* 2.4 37.1 + - - +
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Residues in contact with VAL 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E PRO* 4.2 10.5 - - + -
139E VAL* 3.9 30.3 - - + -
160E VAL* 3.9 15.9 - - + -
168E VAL* 4.0 18.8 - - + -
169E THR 3.6 2.0 - - - -
170E VAL* 3.7 19.7 - - + -
214E CYS* 4.1 19.1 - - - -
215E ASN* 1.3 74.8 - - - +
217E ASN* 1.3 64.6 + - - +
218E HIS 4.2 0.7 - - - +
223E THR* 3.6 2.0 - - + +
224E LYS* 3.2 6.8 - - - +
225E VAL* 2.8 42.5 + - + +
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Residues in contact with ASN 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168E VAL* 3.2 9.3 - - - +
169E THR* 2.9 51.5 + - - +
215E ASN 4.1 0.8 + - - -
216E VAL* 1.3 75.2 - - - +
218E HIS* 1.3 63.7 + - - +
219E LYS* 3.6 45.4 + - - +
222E ASN* 5.6 0.5 - - - -
223E THR 3.3 3.0 + - - +
224E LYS* 3.3 32.2 - - + +
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Residues in contact with HIS 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E LYS 3.2 23.4 + - - -
136E GLY* 4.0 0.6 - - - -
137E PRO* 3.8 23.1 - - + -
163E TYR* 3.5 16.0 - + - -
164E PHE 3.2 14.4 - - - -
165E PRO 2.6 24.6 + - - -
167E PRO 3.3 20.2 - - - -
168E VAL* 4.6 3.4 - - + -
216E VAL* 4.2 0.8 - - - +
217E ASN* 1.3 74.5 - - - +
219E LYS* 1.3 65.6 + - - +
220E PRO* 3.7 19.1 - - + +
221E SER* 2.7 39.2 + - - +
222E ASN 3.1 9.4 + - - -
223E THR 2.8 16.6 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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