Contacts of the helix formed by residues 177 - 188 (chain B) in PDB entry 2YG9
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 177 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157B TRP* 2.9 36.2 + - + +
174B SER* 3.0 20.8 + - - +
176B GLY* 1.3 74.9 - - - +
178B LEU* 1.3 68.0 + - - +
179B ALA* 3.1 8.9 + - - +
180B LEU* 2.9 35.2 + - + +
181B ARG* 3.0 25.6 + - - +
212B TRP* 3.1 31.6 + - - -
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Residues in contact with LEU 178 (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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176B GLY 3.3 6.3 + - - +
177B ASP* 1.3 73.4 + - - +
179B ALA* 1.3 54.0 + - - +
181B ARG* 3.3 7.5 + - + -
182B GLN* 2.8 72.3 + - + +
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Residues in contact with ALA 179 (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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177B ASP* 3.1 10.2 + - - +
178B LEU* 1.3 76.2 - - - +
180B LEU* 1.3 66.5 + - - +
182B GLN* 3.4 11.7 + - - +
183B GLY* 3.0 21.7 + - - -
211B LEU* 5.5 1.8 - - - +
212B TRP* 3.9 18.6 - - + +
215B SER* 5.6 9.9 - - - +
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Residues in contact with LEU 180 (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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164B LEU* 6.1 0.2 - - + -
173B PHE* 3.7 18.4 - - + -
174B SER* 3.6 26.9 - - - +
177B ASP* 2.9 24.6 + - + +
179B ALA* 1.3 74.8 - - - +
181B ARG* 1.3 58.4 + - - +
183B GLY* 3.3 1.6 + - - -
184B VAL* 3.0 34.3 + - - +
208B SER* 3.4 46.9 - - - +
211B LEU* 3.7 22.0 - - + +
212B TRP* 3.5 31.0 - - + +
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Residues in contact with ARG 181 (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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173B PHE* 4.2 13.2 - - + -
174B SER 4.8 0.9 - - - +
175B SER* 2.9 51.7 + - - +
176B GLY 5.1 0.2 - - - -
177B ASP 3.0 17.5 + - - +
178B LEU* 3.8 10.8 - - + +
180B LEU* 1.3 75.5 - - - +
182B GLN* 1.3 57.0 + - - +
184B VAL* 3.6 4.2 + - - +
185B GLU* 3.1 28.2 + - - +
193B TRP* 3.3 50.4 - - - +
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Residues in contact with GLN 182 (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 LEU* 2.8 59.4 + - + +
179B ALA* 3.8 11.3 - - - +
180B LEU 3.3 0.2 - - - -
181B ARG* 1.3 71.6 - - - +
183B GLY* 1.3 57.3 - - - +
185B GLU* 3.5 6.1 + - - +
186B ARG* 2.9 32.7 + - - +
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Residues in contact with GLY 183 (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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179B ALA 3.0 15.8 + - - -
180B LEU* 3.8 1.8 - - - -
181B ARG 3.3 0.2 - - - -
182B GLN* 1.3 75.6 - - - +
184B VAL* 1.3 58.2 + - - +
186B ARG* 4.2 5.2 - - - -
187B LEU* 2.9 43.6 + - - +
211B LEU* 4.5 12.1 - - - -
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Residues in contact with VAL 184 (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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173B PHE* 4.1 15.3 - - + -
180B LEU 3.0 20.5 + - - +
181B ARG* 4.0 6.3 - - - +
183B GLY* 1.3 73.4 - - - +
185B GLU* 1.3 58.9 + - - +
188B TYR* 2.8 48.8 + - + +
191B GLU 5.6 2.0 - - - +
193B TRP* 3.9 28.9 - - + -
196B VAL* 4.2 11.4 - - + -
197B THR* 4.2 2.5 - - + -
200B TRP* 4.0 15.9 - - + -
211B LEU* 3.7 19.5 - - + -
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Residues in contact with GLU 185 (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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181B ARG 3.1 18.6 + - - +
182B GLN* 3.7 7.0 - - - +
184B VAL* 1.3 76.5 - - - +
186B ARG* 1.3 62.7 + - - +
188B TYR 4.6 3.4 - - - +
189B PRO* 3.3 31.4 - - - +
190B GLY* 3.6 21.3 + - - -
191B GLU 5.2 4.2 - - - +
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Residues in contact with ARG 186 (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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182B GLN 2.9 19.0 + - - +
183B GLY* 3.6 7.4 - - - +
185B GLU* 1.3 79.6 - - - +
187B LEU* 1.3 70.4 + - + +
189B PRO* 3.5 10.4 - - - +
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Residues in contact with LEU 187 (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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41B VAL* 3.9 26.8 - - + +
45B VAL* 4.4 7.4 - - + -
183B GLY* 2.9 25.7 + - - +
186B ARG* 1.3 86.6 - - + +
188B TYR* 1.3 73.8 + - + +
189B PRO* 3.4 6.1 - - - +
191B GLU* 5.0 0.2 - - - +
211B LEU* 3.8 23.6 - - + -
214B ASN* 4.1 24.7 - - + +
225B LEU* 4.1 32.3 - - + +
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Residues in contact with TYR 188 (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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39B ASP* 2.6 32.7 + - - -
41B VAL* 3.3 33.4 - - + +
42B LEU* 3.8 5.0 - - - +
184B VAL* 2.8 31.5 + - + +
185B GLU* 4.1 2.4 - - - +
187B LEU* 1.3 97.9 - - + +
189B PRO* 1.3 68.0 - - - +
190B GLY 3.2 0.5 + - - -
191B GLU* 3.2 44.4 + - - +
196B VAL* 3.8 40.4 - - + -
200B TRP* 3.3 19.3 - + - -
211B LEU* 5.2 1.8 - - + -
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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