Contacts of the strand formed by residues 201 - 205 (chain E) in PDB entry 5IJ7
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 LEU 201 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175E HIS* 4.3 0.2 - - - -
193E LEU* 4.1 11.7 - - + -
194E SER 3.3 7.9 - - - +
195E VAL* 3.4 31.2 - - + -
200E ALA* 1.3 78.5 - - - +
202E ARG* 1.3 67.6 + - - +
214E ILE* 3.5 1.9 - - - +
215E PHE* 2.8 60.1 + - + +
221E HIS* 4.0 10.5 - - + -
225E VAL* 4.0 14.6 - - + -
228E ALA* 3.8 7.0 - - + -
237E ILE* 4.8 3.1 - - + -
239E SER* 3.7 35.0 - - - +
249E TRP* 4.1 10.3 - - + +
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Residues in contact with ARG 202 (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 GLY* 3.0 35.1 + - - -
175E HIS* 3.6 23.8 + - + +
176E GLY 5.2 0.4 - - - +
192E LEU 3.4 1.9 - - - +
193E LEU* 3.2 8.1 - - - -
194E SER* 2.8 48.5 + - - +
198E ASP* 4.8 4.2 + - - -
200E ALA* 5.4 1.2 - - + +
201E LEU* 1.3 79.3 - - - +
203E LEU* 1.3 59.4 + - - +
204E TRP* 3.5 26.6 - - - +
211E LEU* 3.6 29.0 - - + +
213E ALA 3.6 4.9 - - - +
214E ILE* 4.2 19.0 - - + +
569S ASP 4.7 1.6 + - - -
570S THR* 2.9 37.7 + - - +
571S CYS* 4.5 2.2 - - - +
572S LEU* 4.6 0.8 - - - +
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Residues in contact with LEU 203 (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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191E LEU* 4.0 20.6 - - + -
192E LEU 3.4 8.5 - - - +
193E LEU* 4.6 4.9 - - + +
202E ARG* 1.3 72.1 - - - +
204E TRP* 1.3 56.3 + - - +
211E LEU* 3.4 4.7 - - - +
212E VAL* 2.8 45.6 + - + -
213E ALA 3.0 13.8 + - - +
215E PHE* 3.8 20.5 - - + -
230E TYR* 3.2 30.7 - - + +
237E ILE* 5.3 1.1 - - + -
251E ILE* 4.8 8.1 - - + -
256E MET* 3.6 29.6 - - + -
260E ILE* 4.5 13.7 - - + -
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Residues in contact with TRP 204 (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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158E ILE* 3.3 22.3 - - + +
172E TYR* 3.9 41.5 - + + -
173E VAL 4.1 5.8 - - - -
174E GLY* 4.6 0.2 - - - -
175E HIS* 4.6 8.3 - - - -
190E ASN 3.4 2.1 - - - +
191E LEU* 3.4 6.8 - - - +
192E LEU* 2.8 45.0 + - + +
194E SER* 2.9 27.5 + - - -
202E ARG* 3.5 44.5 - - + +
203E LEU* 1.3 72.6 - - - +
205E ASN* 1.4 59.9 + - - +
206E ILE* 3.7 20.0 - - + -
209E ASP 5.6 1.3 - - - -
210E THR 3.4 10.8 - - - +
211E LEU* 3.9 24.2 - - + -
212E VAL* 4.2 3.8 - - - -
572S LEU* 4.0 23.3 - - + -
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Residues in contact with ASN 205 (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 TYR* 4.5 0.7 + - - -
190E ASN* 3.4 4.7 - - - +
191E LEU* 4.1 9.0 - - + +
204E TRP* 1.4 70.6 - - - +
206E ILE* 1.3 58.8 + - - +
207E GLN* 3.0 22.5 + - - +
208E THR* 3.1 16.6 + - - -
209E ASP* 3.0 23.7 + - - -
210E THR* 2.8 30.7 + - - +
212E VAL* 3.9 6.2 - - + +
263E SER* 2.8 24.9 + - - +
264E TYR* 3.5 35.7 - - - -
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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