Contacts of the helix formed by residues 195 - 204 (chain A) in PDB entry 6YBO
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 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A PRO* 3.5 12.0 - - - +
184A PRO* 5.4 0.4 - - + -
193A LEU 3.3 0.5 + - - +
194A PRO* 1.3 87.2 - - + +
196A VAL* 1.3 64.8 + - - +
197A GLY* 3.1 12.0 + - - -
198A HIS* 2.8 33.7 + - + +
199A ALA* 3.1 18.5 + - - +
221A GLU* 3.5 17.5 - - - +
224A ALA* 4.7 11.2 - - + -
226A LEU* 3.9 23.4 - - + +
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Residues in contact with VAL 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A PRO* 3.6 11.9 - - + +
195A THR* 1.3 74.6 - - - +
197A GLY* 1.3 65.4 + - - +
199A ALA* 3.3 2.5 + - - +
200A LEU* 2.9 43.8 + - + +
214A VAL* 4.7 5.2 - - + -
216A PRO* 3.6 31.4 - - + -
221A GLU* 3.2 30.2 + - + +
231A GLY* 3.9 28.7 - - - +
232A ILE* 5.4 0.2 - - + -
234A GLN* 5.6 1.3 - - + -
235A ALA* 4.5 7.4 - - + -
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Residues in contact with GLY 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A THR* 3.1 8.5 + - - -
196A VAL* 1.3 82.8 - - - +
198A HIS* 1.3 61.9 + - - +
200A LEU* 3.3 9.7 + - - +
201A ALA* 3.0 24.1 + - - +
234A GLN* 5.5 9.2 - - - -
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Residues in contact with HIS 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LEU* 3.8 13.8 - - + +
194A PRO* 3.6 35.7 - - + +
195A THR* 2.8 38.2 + - + +
197A GLY* 1.3 75.1 - - - +
199A ALA* 1.3 58.8 + - - +
201A ALA* 3.4 6.9 + - - +
202A PHE* 3.0 28.6 + - - +
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Residues in contact with ALA 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ILE* 4.1 23.3 - - + -
182A PRO* 4.1 9.2 - - + -
193A LEU* 4.5 12.5 - - + +
195A THR 3.1 12.3 + - - +
196A VAL 3.8 7.2 - - - +
198A HIS* 1.3 76.0 - - - +
200A LEU* 1.3 64.5 + - - +
202A PHE* 3.3 7.2 + - - +
203A ILE* 3.1 29.4 + - - +
214A VAL* 3.8 17.0 - - + -
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Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A VAL* 2.9 39.8 + - + +
197A GLY* 3.7 5.8 - - - +
199A ALA* 1.3 76.5 - - - +
201A ALA* 1.3 63.0 + - - +
203A ILE* 3.4 16.4 + - + +
204A GLU* 3.5 18.0 + - - +
214A VAL* 3.9 16.8 - - + -
234A GLN* 4.2 26.2 - - + +
235A ALA* 4.1 14.4 - - - -
238A ALA* 4.5 9.4 - - + -
240A LYS* 3.6 37.5 - - + -
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Residues in contact with ALA 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A GLY 3.0 15.4 + - - +
198A HIS* 3.7 7.9 - - - +
199A ALA 3.2 0.2 - - - -
200A LEU* 1.3 76.7 - - - +
202A PHE* 1.3 63.3 + - - +
204A GLU* 3.3 20.7 + - - +
205A ARG* 4.0 9.2 + - - +
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Residues in contact with PHE 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A LEU* 4.0 28.3 - - + -
158A MET* 3.5 28.7 - - + -
159A LYS* 3.6 33.0 - - + -
162A PHE* 3.9 18.4 - + - -
180A ILE* 4.0 17.0 - - + -
193A LEU* 3.7 23.6 - - + -
198A HIS 3.0 17.5 + - - +
199A ALA 3.6 3.1 - - - +
201A ALA* 1.3 77.8 - - - +
203A ILE* 1.3 64.5 + - - +
205A ARG* 3.0 25.2 + - + +
206A LEU* 3.7 16.9 + - + +
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Residues in contact with ILE 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ILE* 4.0 16.4 - - + -
199A ALA 3.1 19.0 + - - +
200A LEU* 3.7 11.4 - - + +
201A ALA 3.3 0.2 - - - -
202A PHE* 1.3 75.0 - - - +
204A GLU* 1.3 63.6 + - - +
206A LEU* 3.1 27.0 + - + +
209A PRO* 3.5 23.1 - - + +
212A TYR* 3.7 29.2 - - + +
213A GLY* 3.4 39.0 - - - +
214A VAL* 4.2 10.8 - - + -
240A LYS* 4.0 13.2 - - + +
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Residues in contact with GLU 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A LEU 3.5 15.3 - - - +
201A ALA* 3.3 11.4 + - - +
202A PHE 3.1 1.2 - - - -
203A ILE* 1.3 77.1 - - - +
205A ARG* 1.3 74.5 + - - +
206A LEU 3.5 1.8 - - - +
209A PRO* 4.3 19.1 - - - +
238A ALA* 6.0 1.7 - - - +
240A LYS* 4.0 22.3 - - - +
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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