Contacts of the helix formed by residues 193 - 201 (chain B) in PDB entry 5AM8
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 ASP 193 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B ASN* 3.5 11.2 - - - +
186B TYR* 4.7 2.9 - - - -
187B LYS* 4.5 4.3 - - - +
191B PHE* 3.2 10.1 - - - +
192B THR* 1.3 91.0 + - - +
194B THR* 1.3 64.6 + - - +
195B GLY* 2.7 30.5 + - - -
196B ALA* 3.0 21.4 + - - +
197B TYR 3.3 7.4 + - - -
199B ARG* 4.7 5.6 + - - -
447B TRP 4.9 1.0 - - - +
450B PHE* 3.4 29.4 - - - +
451B SER* 3.4 22.4 - - - -
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Residues in contact with THR 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B PHE* 5.8 0.2 - - + -
182B SER* 2.6 41.4 + - - +
183B ASN* 2.9 18.5 + - - +
186B TYR* 3.8 16.3 - - + +
193B ASP* 1.3 70.3 - - - +
195B GLY* 1.3 56.6 + - - +
197B TYR* 3.0 9.1 + - - +
198B TRP* 2.9 51.6 + - + +
450B PHE* 3.5 22.6 - - + -
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Residues in contact with GLY 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ASP* 2.7 16.0 + - - -
194B THR* 1.3 74.2 - - - +
196B ALA* 1.3 55.0 + - - -
198B TRP* 3.3 5.9 + - - +
199B ARG* 2.9 48.6 + - - +
447B TRP* 4.0 15.2 + - - -
450B PHE* 3.7 15.2 - - - -
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Residues in contact with ALA 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B PHE* 3.9 10.1 - - + -
192B THR* 3.6 28.0 - - + +
193B ASP* 3.0 15.9 + - - +
195B GLY* 1.3 71.7 - - - +
197B TYR* 1.3 67.0 + - - +
199B ARG* 3.4 23.0 + - - +
200B SER* 3.0 22.9 + - - -
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Residues in contact with TYR 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B THR* 4.0 22.1 - - + +
186B TYR* 3.2 50.6 + + + -
191B PHE* 3.5 43.2 - + + -
193B ASP 3.3 4.1 + - - +
194B THR 3.0 10.4 + - - +
196B ALA* 1.3 79.1 - - - +
198B TRP* 1.3 76.6 + + - +
200B SER* 2.6 25.3 + - - -
201B TRP* 3.5 40.4 + + - -
381B ARG* 5.9 0.7 + - - -
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Residues in contact with TRP 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B PHE* 5.4 3.4 - + - -
186B TYR* 5.4 2.0 + - - -
194B THR* 2.9 30.7 + - + +
195B GLY 3.6 7.4 - - - +
197B TYR* 1.3 92.0 - + - +
199B ARG* 1.3 62.7 + - - +
201B TRP* 3.3 53.8 + + + +
202B TYR* 4.2 5.1 - - - -
443B ASP* 4.2 8.5 - - - -
446B ARG* 3.5 45.5 - - + -
447B TRP* 4.7 13.7 - + - +
450B PHE* 3.7 28.7 - + - -
495B VAL* 4.5 14.6 - - + -
496B THR 4.7 0.7 - - - -
497B PRO* 3.8 33.4 - - + -
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Residues in contact with ARG 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B THR* 5.2 1.2 + - - -
193B ASP* 4.7 6.5 + - - -
195B GLY* 2.9 32.3 + - - +
196B ALA* 3.5 27.4 - - - +
197B TYR 3.3 0.4 - - - -
198B TRP* 1.3 76.3 - - - +
200B SER* 1.3 60.6 + - - +
202B TYR* 3.0 28.6 + - - +
203B ASN 4.2 1.2 + - - -
204B SER 5.5 1.4 + - - +
207B PHE* 4.1 16.5 - - + +
208B GLU* 3.2 35.7 + - - -
447B TRP* 3.3 65.6 + - + +
499B ILE* 6.3 0.7 - - - -
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Residues in contact with SER 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B PHE* 3.8 17.9 - - - -
196B ALA 3.0 14.3 + - - -
197B TYR* 2.6 32.3 + - - -
199B ARG* 1.3 74.9 - - - +
201B TRP* 1.3 60.6 + - - +
202B TYR 3.0 0.7 - - - -
203B ASN* 3.0 24.4 + - - +
204B SER 6.1 0.2 - - - +
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Residues in contact with TRP 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B TYR* 3.5 52.5 + + - -
198B TRP* 3.3 39.9 - + + +
200B SER* 1.3 81.9 + - - +
202B TYR* 1.3 63.3 + + + +
203B ASN* 3.4 3.5 + - - +
383B ALA 4.9 1.9 - - - +
384B ASN* 4.0 15.4 - - - +
385B PRO* 3.9 29.5 - - + +
497B PRO* 3.6 21.1 - - + -
500B ARG* 3.5 23.3 - - - -
552B TRP* 4.8 1.7 - - - -
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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