Contacts of the helix formed by residues 193 - 201 (chain B) in PDB entry 5U3Y
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 THR 193 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B TYR* 4.6 9.4 - - + -
187B LEU* 4.2 26.0 - - + +
190B PHE 4.3 10.3 - - - +
191B ASN 3.8 1.0 + - - -
192B MET* 1.3 76.5 - - - +
194B LYS* 1.3 60.5 + - - +
195B LYS* 3.6 5.2 + - - +
196B LYS* 3.1 47.9 + - - +
197B ALA* 2.8 29.4 + - - +
296B SER* 5.1 0.4 - - - -
345B ASP* 3.6 16.6 - - - +
503B PEG 4.4 1.8 - - - -
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Residues in contact with LYS 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B TYR* 4.4 1.8 + - - -
193B THR* 1.3 72.5 - - - +
195B LYS* 1.3 57.0 + - - +
197B ALA* 3.7 2.4 - - - +
198B ARG* 2.8 54.2 + - + +
296B SER* 3.7 36.5 - - - +
338B PHE* 5.6 3.6 + - - -
339B ASN* 4.0 26.3 + - - +
342B GLU* 4.3 6.7 - - - +
343B LEU* 2.8 40.5 + - - +
344B ASP* 4.7 2.5 - - - -
345B ASP* 2.8 22.3 + - - +
348B LEU* 4.0 12.0 - - + +
503B PEG 4.7 0.2 + - - -
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Residues in contact with LYS 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B THR* 3.2 5.6 - - - +
194B LYS* 1.3 76.2 - - - +
196B LYS* 1.3 65.7 + - + +
198B ARG* 3.3 4.8 + - - +
199B SER* 3.2 23.0 + - - -
345B ASP* 3.0 17.1 + - - +
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Residues in contact with LYS 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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187B LEU 5.8 1.4 + - - -
190B PHE 4.8 2.0 + - - -
191B ASN* 3.2 29.5 + - - +
192B MET* 3.8 13.2 - - + -
193B THR* 3.1 33.8 + - - +
195B LYS* 1.3 78.9 - - + +
197B ALA* 1.3 62.1 + - - +
199B SER* 2.7 24.9 + - - -
200B ILE* 3.3 14.6 + - + +
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Residues in contact with ALA 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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192B MET* 3.5 16.6 - - - -
193B THR 2.8 20.5 + - - +
194B LYS* 3.7 2.9 - - - +
195B LYS 3.3 0.2 - - - -
196B LYS* 1.3 74.1 - - - +
198B ARG* 1.3 57.3 + - - +
200B ILE* 3.2 4.3 + - - +
201B LEU* 3.0 33.7 + - - +
296B SER 3.3 24.7 - - - +
297B ILE* 3.9 14.8 - - + -
304B LEU* 3.8 10.0 - - + +
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Residues in contact with ARG 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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194B LYS* 2.8 45.7 + - + +
195B LYS* 3.9 4.5 - - - +
197B ALA* 1.3 71.7 - - - +
199B SER* 1.3 63.6 + - - +
201B LEU* 3.5 17.6 + - - +
202B THR* 2.8 35.9 + - + +
295B ALA 3.5 6.1 + - - -
296B SER 3.2 25.5 + - - -
298B VAL 2.3 35.4 + - - -
299B ASN* 4.7 8.5 - - - +
339B ASN* 3.9 12.5 - - - +
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Residues in contact with SER 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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195B LYS* 3.2 11.7 + - - -
196B LYS* 2.7 23.7 + - - -
198B ARG* 1.3 78.8 - - - +
200B ILE* 1.3 60.8 + - - +
202B THR* 3.0 28.5 + - - +
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Residues in contact with ILE 200 (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 MET* 4.2 16.2 - - + -
196B LYS* 3.4 15.9 - - + +
197B ALA 3.2 8.1 + - - +
199B SER* 1.3 82.5 + - - +
201B LEU* 1.3 55.8 + - - +
202B THR 3.0 12.9 + - - +
209B ALA* 5.9 0.3 - - - +
210B PRO* 3.9 28.1 - - + +
304B LEU* 3.7 26.9 - - + -
307B ASN 4.6 2.2 - - - +
308B GLY* 4.1 25.1 - - - +
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Residues in contact with LEU 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 ALA 3.0 20.0 + - - +
198B ARG* 3.5 40.8 + - - +
199B SER 3.4 0.2 - - - -
200B ILE* 1.3 73.8 - - - +
202B THR* 1.3 65.7 + - + +
210B PRO* 5.9 1.3 - - + -
296B SER 4.2 1.8 - - - +
297B ILE 3.9 19.3 - - - +
298B VAL 4.2 3.4 - - - +
299B ASN* 3.8 17.4 + - + +
304B LEU* 3.7 20.6 - - + -
311B PHE* 3.6 37.0 - - + -
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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