Contacts of the strand formed by residues 187 - 193 (chain u) in PDB entry 5GJQ
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 PHE 187 (chain u).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23u ALA* 4.7 0.4 - - + -
24u ALA 3.6 12.6 - - - +
25u ASP* 3.7 7.6 - - - +
26u MET* 4.0 5.6 - - - -
169u VAL* 5.1 0.7 - - + -
170u GLU* 5.2 8.3 - - + -
173u MET* 3.7 35.0 - - + -
184u TYR 5.1 0.7 - - - +
185u ASN 3.4 10.3 - - - +
186u ARG* 1.3 77.9 - - - +
188u GLN* 1.3 73.5 - - - +
189u ILE* 3.7 28.3 - - + -
201u GLY 3.9 0.9 - - - +
202u PRO* 3.7 4.5 - - - +
203u LEU* 2.9 65.0 + - + +
204u SER 3.9 7.9 - - - -
205u THR* 3.6 30.3 - - + -
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Residues in contact with GLN 188 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22u ILE 3.9 0.2 - - - +
23u ALA* 3.3 5.7 - - - +
24u ALA 3.0 35.6 + - - +
26u MET* 3.4 36.0 - - + +
40u SER* 2.7 35.3 + - - -
41u ARG 4.1 3.8 + - - -
42u ILE* 4.0 16.8 + - + +
187u PHE* 1.3 75.9 - - - +
189u ILE* 1.3 64.6 - - - +
190u ALA 4.3 0.2 - - - -
199u ILE* 4.0 22.5 - - + +
200u GLU 3.9 12.7 + - - +
201u GLY* 5.0 6.4 - - - -
202u PRO* 5.5 1.4 - - - +
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Residues in contact with ILE 189 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21u VAL* 3.5 24.2 - - + -
22u ILE 3.4 2.7 - - - -
23u ALA* 4.1 11.2 - - + -
166u ARG* 4.0 43.5 - - + +
169u VAL* 3.9 15.9 - - + -
170u GLU* 5.5 2.0 - - + +
187u PHE* 3.7 27.5 + - + -
188u GLN* 1.3 78.9 - - - +
190u ALA* 1.3 62.7 + - - +
191u THR* 4.0 10.3 - - - +
198u GLU 3.9 0.5 - - - +
199u ILE* 3.6 3.4 - - - -
200u GLU* 2.9 37.6 + - + +
203u LEU* 4.1 8.6 - - + +
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Residues in contact with ALA 190 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21u VAL* 3.4 2.6 - - - +
22u ILE 2.8 34.7 + - - +
42u ILE* 3.9 22.4 - - + +
50u MET* 3.3 25.7 - - - +
188u GLN 4.3 0.2 - - - -
189u ILE* 1.3 72.6 - - - +
191u THR* 1.3 63.0 + - - +
197u VAL* 4.8 0.9 - - + -
198u GLU 3.2 9.0 - - - +
199u ILE* 4.0 17.7 - - + -
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Residues in contact with THR 191 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16u PHE* 3.7 27.4 - - + -
20u VAL 3.3 11.0 - - - +
21u VAL* 4.3 4.8 - - + +
50u MET* 4.3 1.1 - - - -
162u GLN* 3.8 19.7 + - + +
166u ARG* 6.1 0.2 - - - -
189u ILE* 4.0 13.3 - - - +
190u ALA* 1.3 79.3 + - - +
192u VAL* 1.3 65.3 + - - +
193u THR* 4.1 6.9 + - + +
196u GLY 3.4 1.6 - - - +
197u VAL* 3.3 4.4 - - - +
198u GLU* 2.9 39.8 + - - +
200u GLU* 4.1 12.2 + - - -
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Residues in contact with VAL 192 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16u PHE* 4.3 0.3 - - - -
19u GLY* 2.9 6.6 - - - -
20u VAL* 2.9 51.1 + - + +
47u ASN 4.3 2.5 - - - +
48u SER* 4.1 18.8 - - - +
49u THR* 4.2 5.8 - - - +
50u MET* 3.6 14.8 - - + -
113u GLY 4.2 0.2 - - - +
114u GLY* 4.0 16.8 - - - +
115u TYR* 4.2 10.1 - - + +
191u THR* 1.3 73.7 - - - +
193u THR* 1.3 61.9 + - - +
196u GLY 3.3 3.1 - - - +
197u VAL* 3.3 35.0 - - + -
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Residues in contact with THR 193 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16u PHE* 4.2 9.6 - - + -
18u GLY 3.6 16.2 - - - +
47u ASN 4.9 2.8 - - - +
48u SER* 6.0 0.3 - - - -
115u TYR* 3.7 14.9 - - - +
162u GLN* 3.9 30.3 - - - +
191u THR* 4.1 4.0 + - + -
192u VAL* 1.3 80.9 - - - +
194u GLU* 1.3 67.6 + - - +
195u LYS* 3.2 22.8 + - - +
196u GLY* 3.0 18.0 + - - +
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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