Contacts of the helix formed by residues 190 - 199 (chain B) in PDB entry 2G9Y
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 SER 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163B VAL* 4.5 1.8 - - - -
168B CYS 3.7 0.7 - - - -
169B TYR 3.6 1.1 + - - -
170B GLY* 3.2 30.6 - - - -
171B PRO* 3.7 0.7 - - - +
174B THR* 2.8 31.1 + - - +
189B GLY* 1.3 75.4 - - - +
191B ILE* 1.3 60.6 + - - +
192B THR* 4.3 0.5 - - - -
193B GLU* 2.8 37.7 + - - +
194B GLN* 2.9 30.1 + - - +
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Residues in contact with ILE 191 (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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120B LEU* 3.7 18.2 - - + -
151B LEU 4.9 0.9 - - - +
152B GLN* 3.7 26.0 - - - +
157B ALA* 3.6 24.5 - - + -
161B ALA* 3.9 17.8 - - + +
163B VAL* 3.9 17.7 - - + +
166B ARG* 3.3 28.0 - - - +
168B CYS 3.0 29.2 + - - +
169B TYR* 3.8 7.0 - - - +
190B SER* 1.3 75.3 - - - +
192B THR* 1.3 59.7 + - - +
194B GLN* 3.4 1.9 + - - +
195B LEU* 2.9 30.7 + - + +
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Residues in contact with THR 192 (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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152B GLN* 3.3 13.4 - - - +
169B TYR 2.8 22.1 + - - -
190B SER* 3.3 0.9 - - - -
191B ILE* 1.3 76.1 - - - +
193B GLU* 1.3 64.3 + - - +
195B LEU* 3.2 8.6 + - + +
196B LEU* 3.0 24.7 + - + +
210B THR* 3.1 14.0 - - + +
211B PHE* 3.7 40.4 - - + -
225B LEU* 3.3 29.8 - - + -
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Residues in contact with GLU 193 (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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171B PRO* 3.2 25.5 - - - +
183B LEU* 3.5 31.3 + - + +
188B LYS 4.7 1.8 - - - +
189B GLY* 4.3 8.1 - - - -
190B SER* 2.8 36.8 + - - +
191B ILE 3.4 0.6 - - - -
192B THR* 1.3 75.6 - - - +
194B GLN* 1.3 63.7 + - - +
196B LEU* 3.2 12.2 + - - +
197B ASN* 3.1 28.6 + - - +
215B ALA* 4.4 10.3 - - - +
216B THR 5.2 0.5 + - - -
225B LEU* 4.2 19.5 - - + -
228B GLN* 5.0 10.6 + - - +
232B ARG* 4.9 0.3 + - - -
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Residues in contact with GLN 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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160B VAL 3.5 17.5 - - - +
161B ALA* 3.6 4.5 - - - -
162B HIS* 2.7 56.2 + - - +
163B VAL* 3.4 9.5 - - - +
181B ASN* 5.0 1.6 - - - +
188B LYS* 3.5 37.6 - - + +
189B GLY 2.8 21.6 + - - +
190B SER 2.9 14.0 + - - +
191B ILE 3.9 2.7 - - - +
193B GLU* 1.3 72.2 - - - +
195B LEU* 1.3 61.8 + - - +
197B ASN* 3.1 10.7 + - - +
198B ALA* 2.8 24.8 + - - +
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Residues in contact with LEU 195 (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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145B ASN* 5.4 4.0 - - - +
151B LEU* 4.3 28.9 - - + +
152B GLN* 5.9 1.8 - - + +
157B ALA* 6.0 0.2 - - - -
160B VAL* 3.7 30.4 + - + +
191B ILE* 2.9 20.5 + - + +
192B THR* 3.2 11.2 + - + +
194B GLN* 1.3 76.8 - - - +
196B LEU* 1.3 79.3 - - + +
198B ALA* 3.1 13.2 + - - +
199B ARG* 3.2 8.7 + - - -
200B ALA 4.9 1.0 + - - -
203B THR* 4.3 30.1 - - + +
211B PHE* 4.8 13.7 - - + -
234B TYR* 3.9 5.1 + - + +
256B LEU* 4.9 5.2 - - + -
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Residues in contact with LEU 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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192B THR 3.0 18.8 + - - +
193B GLU* 3.2 10.7 + - - +
195B LEU* 1.3 80.8 - - + +
197B ASN* 1.3 61.6 + - - +
199B ARG* 3.4 3.6 + - - +
211B PHE* 4.0 17.3 - - + -
225B LEU* 3.8 31.0 - - + +
228B GLN* 3.9 24.7 - - + +
229B ALA* 4.0 18.2 - - + +
232B ARG* 4.0 17.9 + - - +
234B TYR* 2.6 48.5 + - + -
256B LEU* 4.3 6.1 - - + -
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Residues in contact with ASN 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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137B LYS* 4.6 1.7 + - - -
188B LYS* 4.1 13.5 + - - +
193B GLU* 3.1 23.6 + - - +
194B GLN* 3.1 13.0 + - - +
196B LEU* 1.3 74.4 - - - +
198B ALA* 1.3 66.9 + - - +
199B ARG* 3.0 8.9 + - - +
220B TRP* 5.1 2.1 - - - -
232B ARG* 2.6 38.6 + - - +
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Residues in contact with ALA 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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133B LEU* 5.3 5.8 - - + +
134B GLU* 5.5 7.6 - - + +
137B LYS* 2.8 32.2 + - - +
159B LEU 5.3 0.4 - - - +
160B VAL* 3.4 40.2 - - + +
194B GLN 2.8 9.8 + - - +
195B LEU 3.4 9.2 - - - +
197B ASN* 1.3 75.5 - - - +
199B ARG* 1.3 57.2 + - - +
200B ALA* 3.5 2.5 + - - +
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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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137B LYS* 2.9 22.4 + - - +
195B LEU 3.2 5.7 + - - -
196B LEU 3.8 3.5 + - - +
197B ASN 3.0 9.0 - - - +
198B ALA* 1.3 78.2 - - - +
200B ALA* 1.3 64.1 + - - +
201B ASP 3.9 0.2 + - - -
232B ARG* 2.8 43.6 + - - +
233B GLY* 4.1 1.0 - - - -
234B TYR* 2.9 38.5 - - + +
251B GLN* 2.5 48.9 + - - +
252B GLN* 4.1 8.5 + - - +
254B PRO* 3.4 23.9 - - + +
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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