Contacts of the helix formed by residues 199 - 206 (chain B) in PDB entry 5SY1
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 GLN 199 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B HIS* 4.0 25.3 + - - -
89B LEU* 3.8 24.9 - - + +
195B PHE* 3.3 41.4 + - + +
196B LEU* 3.5 5.6 + - + +
197B SER 3.4 1.0 + - - -
198B PHE* 1.3 83.2 - - - +
200B TYR* 1.3 61.1 + - + +
201B PRO 3.5 0.7 - - - -
202B LEU* 3.6 13.8 - - - +
203B LEU* 2.7 59.2 + - + +
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Residues in contact with TYR 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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89B LEU* 3.7 42.8 - - + +
138B LEU* 2.2 47.7 + - + -
139B LEU* 4.3 0.5 - - - +
141B CYS* 4.6 7.4 - - + +
142B GLY 5.3 0.2 - - - -
150B TYR* 3.8 29.7 - + + +
153B GLY* 3.2 37.0 - - - -
154B SER* 3.4 19.8 + - - +
157B SER* 4.3 3.4 - - - -
196B LEU* 3.4 28.2 + - + +
199B GLN* 1.3 83.9 - - + +
201B PRO* 1.3 61.7 - - + +
203B LEU* 5.8 0.4 - - + -
204B LEU* 3.0 27.0 + - - +
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Residues in contact with PRO 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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154B SER* 3.4 23.6 - - - +
157B SER* 5.2 0.4 - - - +
158B TRP* 4.3 18.8 - - + +
196B LEU 4.2 1.1 - - - +
197B SER* 3.3 27.6 - - - +
199B GLN 4.1 0.2 - - - +
200B TYR* 1.3 88.9 - - + +
202B LEU* 1.3 58.6 + - - +
204B LEU* 3.7 8.6 - - + +
205B PHE* 3.0 28.2 + - - +
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Residues in contact with LEU 202 (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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198B PHE 3.3 27.8 - - - +
199B GLN* 3.2 18.9 + - - +
201B PRO* 1.3 80.7 - - - +
203B LEU* 1.3 61.0 + - - +
205B PHE* 3.5 14.3 + - + +
206B LYS* 3.4 29.2 + - + +
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Residues in contact with LEU 203 (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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86B HIS* 6.3 2.5 - - + +
89B LEU* 5.2 11.2 - - + -
145B HIS* 4.6 10.8 - - + +
150B TYR* 3.3 45.3 - - + +
199B GLN* 2.7 38.1 + - + +
200B TYR* 5.8 0.4 - - + -
202B LEU* 1.3 71.4 - - - +
204B LEU* 1.3 64.3 + - - +
206B LYS* 3.4 42.6 + - + +
207B GLY* 3.7 4.5 + - - -
211B THR* 5.0 4.6 + - - +
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Residues in contact with LEU 204 (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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146B ASN 5.4 0.2 - - - -
147B LYS* 4.6 17.3 - - + -
150B TYR* 3.7 31.3 - - + +
151B VAL* 3.8 30.7 - - + +
154B SER* 5.1 4.0 - - - +
200B TYR 3.0 18.6 + - - +
201B PRO* 3.7 7.6 - - + +
202B LEU 3.3 0.2 - - - -
203B LEU* 1.3 77.2 - - - +
205B PHE* 1.3 57.7 + - - +
207B GLY* 3.0 21.2 + - - -
208B LEU 4.4 0.3 + - - -
212B GLU* 5.8 0.9 - - - +
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Residues in contact with PHE 205 (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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201B PRO 3.0 17.5 + - - +
202B LEU* 3.7 15.5 - - + +
203B LEU 3.3 0.4 - - - -
204B LEU* 1.3 76.3 - - - +
206B LYS* 1.3 63.7 + - + +
207B GLY 3.3 0.3 + - - -
208B LEU* 3.5 35.3 + - + +
209B GLN* 5.8 0.3 - - - +
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Residues in contact with LYS 206 (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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199B GLN* 6.3 0.4 - - - +
202B LEU* 3.4 20.5 + - + +
203B LEU* 3.7 34.5 - - + +
204B LEU 3.2 0.8 - - - -
205B PHE* 1.3 76.0 - - + +
207B GLY* 1.3 59.6 + - - +
208B LEU 3.1 6.7 + - - -
209B GLN* 3.3 17.1 + - + +
211B THR* 2.9 30.7 + - + +
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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