Contacts of the strand formed by residues 187 - 193 (chain D) in PDB entry 5ON2
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 187 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153D THR* 3.5 29.2 - - + +
154D SER* 3.9 12.5 + - - +
155D ALA* 4.5 3.7 + - - +
185D ARG* 6.3 1.8 - - + -
186D LYS* 1.3 79.5 - - - +
188D ILE* 1.3 61.5 + - - +
189D PRO* 4.0 4.7 - - - +
286D ARG* 5.0 25.2 + - + +
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Residues in contact with ILE 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D THR* 4.3 1.8 - - - -
154D SER* 3.1 25.3 + - - +
156D VAL* 3.6 39.9 - - + -
158D TRP* 4.9 2.7 - - + -
165D VAL* 4.8 7.4 - - + -
186D LYS* 3.5 42.0 + - + +
187D GLU* 1.3 74.5 - - - +
189D PRO* 1.4 84.9 - - + +
190D GLN* 3.6 6.4 + - + +
425D GLN* 3.8 22.7 - - - +
488D ASP* 5.7 0.4 - - - +
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Residues in contact with PRO 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D LYS* 4.2 27.7 - - + +
152D LYS 3.5 9.4 - - - +
153D THR* 4.1 9.2 - - + +
187D GLU 4.0 5.8 - - - +
188D ILE* 1.4 92.9 - - + +
190D GLN* 1.3 64.5 + - - +
488D ASP* 5.4 1.6 - - - +
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Residues in contact with GLN 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D LYS* 3.4 9.2 - - - +
152D LYS 2.8 35.0 + - - +
154D SER* 3.8 22.6 + - - -
155D ALA 5.0 0.4 + - - -
156D VAL* 3.8 12.4 - - - +
188D ILE* 4.1 11.8 + - + +
189D PRO* 1.3 79.9 - - - +
191D TRP* 1.3 63.6 + - - +
192D PHE* 3.4 17.3 - - + -
421D GLY* 6.3 0.4 - - - -
423D SER* 3.2 26.3 + - - +
425D GLN* 3.0 18.5 + - - +
488D ASP* 4.7 1.8 - - - +
74E C 2.8 34.3 + - - +
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Residues in contact with TRP 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D PHE* 4.3 11.4 - + + -
144D TYR* 4.2 22.0 - + - -
149D VAL* 4.1 16.6 - - + -
150D TYR* 3.9 1.3 - - - -
151D LYS* 3.8 52.6 - - + +
190D GLN* 1.3 73.4 - - - +
192D PHE* 1.3 64.9 + - - +
421D GLY* 3.8 0.7 - - - -
422D VAL* 3.1 37.1 + - + +
423D SER* 2.7 29.0 + - - +
432D ILE* 4.1 18.8 - - + -
434D MET* 3.7 30.3 - - + +
442D VAL* 3.7 27.8 - - + -
486D GLU* 3.4 28.0 + - + +
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Residues in contact with PHE 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D VAL* 3.5 5.6 - - - +
150D TYR* 2.9 58.2 + - + +
152D LYS* 3.7 37.2 - - + -
154D SER* 3.6 32.5 - - - -
190D GLN* 3.4 25.1 - - + -
191D TRP* 1.3 79.6 - - - +
193D ILE* 1.3 63.0 + - - +
419D ASP* 3.5 22.9 - - + -
420D TRP 3.3 4.7 - - - +
421D GLY* 3.3 32.1 - - - -
422D VAL* 5.2 0.2 - - - -
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Residues in contact with ILE 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D PHE* 3.9 26.5 - - + -
143D LEU* 4.3 22.2 - - + -
148D LEU* 3.5 11.7 - - + +
149D VAL* 4.3 4.9 - - + -
150D TYR* 4.8 0.4 - - - -
192D PHE* 1.3 75.2 - - - +
194D LYS* 1.3 63.2 + - - +
195D ILE 3.0 8.5 + - - -
419D ASP* 3.7 3.7 - - - +
420D TRP* 2.9 43.5 + - + +
422D VAL* 3.9 9.2 - - + -
494D MET* 3.6 33.2 - - + -
543D PHE* 3.7 29.6 - - + -
544D PHE* 5.5 2.0 - - + -
547D LEU* 4.9 1.6 - - + -
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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
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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