Contacts of the strand formed by residues 218 - 226 (chain E) in PDB entry 5U0A
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 SER 218 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205E THR* 4.7 5.7 - - - -
206E ALA 3.8 7.2 - - - -
207E VAL* 4.1 4.9 - - - +
208E ASP 4.1 2.9 - - - +
216E HIS* 3.6 1.0 - - - +
217E GLY* 1.3 76.1 - - - +
219E GLY* 1.3 59.8 + - - +
220E HIS 4.4 0.2 + - - -
221E MET* 4.4 7.8 - - - +
63I ARG* 5.1 0.3 + - - -
38K G 3.8 26.4 - - - +
39K U 5.0 0.2 - - - -
23M G 3.2 8.6 + - - +
24M A 2.5 62.2 + - - +
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Residues in contact with GLY 219 (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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206E ALA 2.6 15.1 + - - -
208E ASP* 3.5 20.8 - - - +
218E SER* 1.3 73.6 - - - +
220E HIS* 1.3 61.0 + - - +
63I ARG* 2.8 37.7 + - - -
116I LEU* 4.6 12.3 - - - -
24M A 4.0 1.3 - - - +
25M C 3.9 4.7 - - - +
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Residues in contact with HIS 220 (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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204E PHE* 4.5 4.9 - + - -
205E THR* 3.0 10.7 - - - -
206E ALA* 2.9 37.3 + - + +
218E SER* 3.5 1.7 + - - -
219E GLY* 1.3 79.9 + - - +
221E MET* 1.3 74.1 + - - +
222E ASN* 2.4 31.1 + - - -
116I LEU* 4.2 11.9 - - + +
37K U 4.2 8.5 - - - -
25M C 3.2 34.3 + - - -
26M A 3.1 57.6 + + - -
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Residues in contact with MET 221 (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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203E PHE* 3.4 28.0 - - + -
204E PHE 3.5 5.4 - - - -
205E THR* 3.6 11.7 - - + -
218E SER* 4.4 1.8 - - - +
220E HIS* 1.3 90.0 + - - +
222E ASN* 1.3 81.0 + - - +
21I ASP* 4.6 1.6 - - - +
39K U 4.5 4.7 - - + +
24M A 3.4 57.2 - - + +
25M C 3.5 56.0 + - + +
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Residues in contact with ASN 222 (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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203E PHE* 3.6 6.7 - - - -
204E PHE* 2.7 61.3 + - + +
220E HIS* 2.4 30.4 + - - -
221E MET* 1.3 88.1 + - - +
223E ALA* 1.3 57.3 + - - +
224E GLY 4.0 0.7 - - - -
32L ARG* 4.3 9.1 - - - +
33L ARG* 4.0 21.0 - - - +
25M C 4.9 0.4 + - - -
26M A 2.7 33.2 + - - +
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Residues in contact with ALA 223 (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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201E VAL* 3.6 22.9 - - + -
202E ASP 3.5 5.8 - - - +
203E PHE* 4.2 7.6 - - + +
204E PHE* 4.7 1.1 - - - -
222E ASN* 1.3 75.9 - - - +
224E GLY* 1.3 59.3 + - - +
225E GLN* 3.0 14.7 + - - +
33L ARG* 3.7 27.4 - - - +
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Residues in contact with GLY 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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201E VAL* 4.7 0.4 - - - -
202E ASP* 2.9 43.5 + - - +
204E PHE* 4.0 16.0 - - - -
222E ASN 4.0 1.2 - - - -
223E ALA* 1.3 71.5 - - - +
225E GLN* 1.3 63.7 + - - -
226E PHE* 3.8 15.4 + - - -
271E LYS* 5.7 1.6 - - - -
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Residues in contact with GLN 225 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16E ASN* 2.4 32.1 + - - +
22E LEU* 4.3 8.7 + - - +
23E GLY* 3.7 12.4 + - - +
24E SER* 3.5 37.8 - - - +
25E PRO* 3.6 4.1 - - + +
199E VAL* 3.6 18.6 - - + -
200E GLU 3.4 7.6 - - - +
201E VAL* 4.1 16.7 - - + +
223E ALA 3.0 19.0 + - - +
224E GLY* 1.3 71.3 - - - -
226E PHE* 1.3 59.3 + - - +
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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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14E TYR* 3.1 40.8 + + + -
16E ASN* 2.9 39.9 - - + +
25E PRO* 4.7 2.5 - - - -
199E VAL* 4.3 0.5 - - - +
200E GLU* 2.8 37.4 + - - +
202E ASP* 5.2 7.0 - - + -
224E GLY* 3.8 17.1 + - - -
225E GLN* 1.3 79.6 - - - +
227E SER* 1.3 63.6 + - - +
271E LYS* 2.4 48.7 - - + -
274E ALA* 5.1 4.5 - - + -
275E THR* 3.8 22.0 - - + -
41I GLN* 6.1 0.2 - - - -
190I HIS* 3.9 11.0 - + - -
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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