Contacts of the strand formed by residues 200 - 207 (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 GLU 200 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14E TYR* 3.1 33.6 + - + +
198E THR* 3.3 10.9 + - - +
199E VAL* 1.3 71.6 - - - +
201E VAL* 1.3 71.8 + - - +
225E GLN* 3.4 1.8 - - - -
226E PHE 2.8 45.2 + - - +
227E SER* 5.0 2.5 - - - -
27I THR* 3.5 25.9 + - - +
28I VAL* 5.1 0.9 - - - -
29I VAL* 4.0 22.8 + - - +
37I ARG* 5.1 1.3 + - - +
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Residues in contact with VAL 201 (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* 4.4 2.0 + - - -
199E VAL* 3.8 14.5 + - + +
200E GLU* 1.3 85.9 + - - +
202E ASP* 1.3 62.8 + - - +
203E PHE* 3.9 3.7 + - + +
223E ALA* 3.6 34.3 - - + +
224E GLY 4.5 2.0 - - - +
225E GLN* 4.1 15.9 - - + +
37I ARG* 4.8 1.0 + - - -
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Residues in contact with ASP 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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14E TYR* 3.9 9.4 - - + +
200E GLU 3.8 1.0 + - - -
201E VAL* 1.3 69.9 - - - +
203E PHE* 1.3 59.5 + - - +
204E PHE* 3.4 12.6 + - - +
223E ALA* 4.4 1.3 - - - -
224E GLY* 2.9 43.9 + - - +
226E PHE* 5.2 5.7 - - + -
26I LYS* 3.2 21.1 + - - +
37I ARG* 2.7 43.4 + - - +
39I SER* 5.1 0.2 - - - -
41I GLN* 3.6 20.0 + - - +
190I HIS* 5.1 4.6 - - - -
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Residues in contact with PHE 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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201E VAL* 3.9 5.3 + - + +
202E ASP* 1.3 71.6 + - - +
204E PHE* 1.3 58.2 + - - +
205E THR* 3.6 23.8 - - + -
221E MET* 3.4 35.0 - - + -
222E ASN 3.6 17.5 - - - -
223E ALA* 4.2 7.0 - - + +
20I ASP* 4.6 5.7 - - + +
21I ASP* 3.1 56.8 - - + +
26I LYS* 3.5 23.5 + - - +
39K U 4.1 19.8 + + - +
33L ARG* 4.7 15.0 - - - -
25M C 5.9 0.2 - - - -
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Residues in contact with PHE 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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202E ASP* 3.4 15.0 + - - +
203E PHE* 1.3 74.9 - - - +
205E THR* 1.3 70.9 + - - +
206E ALA 4.8 0.2 - - - -
220E HIS* 4.5 7.2 - + - -
222E ASN* 2.7 69.5 + - + +
223E ALA 4.7 0.2 - - - -
224E GLY* 4.0 22.7 - - - -
41I GLN* 3.8 7.9 - - - +
37K U 3.4 67.8 - + - +
39K U 3.7 15.0 - - - +
26M A 4.5 1.3 - - - -
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Residues in contact with THR 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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203E PHE* 3.6 21.5 - - + -
204E PHE* 1.3 85.6 - - - +
206E ALA* 1.3 60.6 + - - +
207E VAL 3.8 0.3 + - - -
218E SER* 4.7 5.6 - - - +
220E HIS 3.0 9.4 - - - -
221E MET* 3.6 26.5 - - + -
37K U 3.8 1.4 + - - +
38K G 3.2 39.2 + - - +
39K U 2.5 42.7 + - + +
24M A 5.4 0.4 - - + -
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Residues in contact with ALA 206 (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 3.2 - - - -
205E THR* 1.3 72.0 - - - +
207E VAL* 1.3 54.5 + - - +
218E SER* 3.5 1.8 - - - -
219E GLY* 2.6 31.6 + - - -
220E HIS* 2.9 26.2 + - + +
61I ARG* 5.0 4.5 - - - -
116I LEU* 4.8 12.3 - - + -
37K U 3.3 38.1 - - + +
38K G 3.6 6.5 - - - +
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Residues in contact with VAL 207 (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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205E THR 3.8 1.0 + - - -
206E ALA* 1.3 72.6 - - - +
208E ASP* 1.3 76.5 + - - +
209E ASP* 3.8 10.1 + - - +
216E HIS 5.0 3.1 - - - +
217E GLY 4.2 5.6 - - - +
218E SER* 4.1 4.5 - - - +
219E GLY* 3.9 2.9 - - - +
45I ARG* 3.6 31.9 - - - +
61I ARG* 4.0 16.6 - - - +
116I LEU* 5.3 1.6 - - - +
38K G 3.0 59.8 + - + +
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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