Contacts of the helix formed by residues 177 - 188 (chain B) in PDB entry 3GYQ
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 GLY 177 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148B VAL* 4.3 1.8 - - - -
176B SER* 1.3 90.3 + - - +
178B ARG* 1.3 66.6 + - - -
179B GLU* 3.4 4.9 - - - -
180B GLU* 3.4 18.5 + - - -
181B ALA* 3.1 11.4 + - - +
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Residues in contact with ARG 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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122B ASP* 2.8 26.2 + - - -
148B VAL* 3.8 18.0 - - + +
149B ASP* 4.1 20.2 + - - +
177B GLY* 1.3 72.6 - - - +
179B GLU* 1.3 74.5 + - + +
181B ALA* 3.3 2.5 + - - +
182B ILE* 3.1 36.1 + - + +
225B SER* 3.6 22.6 - - - -
227B LEU* 4.4 19.2 - - - +
228B PHE* 3.5 36.0 - - + -
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Residues in contact with GLU 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 GLY* 4.5 1.9 - - - -
178B ARG* 1.3 87.9 + - + +
180B GLU* 1.3 59.1 + - + +
182B ILE* 3.4 9.1 + - + +
183B ALA* 3.0 30.0 + - - +
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Residues in contact with GLU 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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108B PHE* 3.8 14.4 - - + -
175B LEU 5.4 0.2 - - - +
176B SER* 3.5 14.2 + - - +
177B GLY* 3.4 20.8 + - - +
178B ARG 3.3 0.6 - - - -
179B GLU* 1.3 77.6 - - + +
181B ALA* 1.3 63.8 + - - +
183B ALA* 3.3 7.3 + - - +
184B PHE* 3.0 24.3 + - - +
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Residues in contact with ALA 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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108B PHE* 4.0 9.0 - - - -
120B VAL* 5.2 1.6 - - + -
146B ILE* 4.0 23.1 - - + -
148B VAL* 4.1 11.2 - - + -
176B SER* 3.4 9.1 + - - +
177B GLY 3.1 17.3 + - - +
178B ARG 3.6 4.5 - - - +
180B GLU* 1.3 76.1 - - - +
182B ILE* 1.3 61.7 + - - +
184B PHE* 3.3 2.9 + - - +
185B ILE* 3.0 35.2 + - + +
228B PHE* 5.1 6.1 - - + -
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Residues in contact with ILE 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 ARG* 3.1 28.8 + - + +
179B GLU* 3.7 8.1 - - - +
181B ALA* 1.3 75.7 - - - +
183B ALA* 1.3 58.0 + - - +
185B ILE* 3.8 7.8 - - - +
186B ARG* 2.9 40.8 + - + +
192B LEU* 5.5 1.1 - - + -
227B LEU* 4.2 17.3 - - + +
228B PHE* 3.6 35.2 - - + -
230B GLU* 6.2 0.7 - - + -
231B ALA* 3.6 26.9 - - + +
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Residues in contact with ALA 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 GLU 3.0 18.1 + - - +
180B GLU* 3.6 7.4 - - - +
181B ALA 3.3 0.2 - - - -
182B ILE* 1.3 77.8 - - - +
184B PHE* 1.3 56.9 + - - +
186B ARG* 3.3 28.5 + - - +
187B ASP* 3.0 38.2 + - - +
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Residues in contact with PHE 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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108B PHE* 3.5 67.1 - + + -
111B ILE* 4.4 10.5 - - + -
112B ALA* 4.1 24.5 - - + -
146B ILE* 4.0 18.2 - - + -
180B GLU 3.0 16.5 + - - +
181B ALA 3.3 3.1 + - - +
183B ALA* 1.3 77.0 - - - +
185B ILE* 1.3 66.2 + - + +
187B ASP* 3.8 2.2 - - - +
188B SER* 3.0 44.3 + - - -
190B MET* 3.8 20.4 - - + -
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Residues in contact with ILE 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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118B VAL* 6.0 0.2 - - + -
120B VAL* 3.9 32.1 - - + -
146B ILE* 4.8 5.6 - - + -
181B ALA* 3.0 26.1 + - + +
182B ILE* 3.8 6.5 - - - +
184B PHE* 1.3 81.7 - - + +
186B ARG* 1.3 64.6 + - - +
188B SER* 3.5 5.7 + - - -
190B MET* 3.5 50.1 + - + +
192B LEU* 4.1 29.2 - - + -
214B ALA* 3.9 22.4 - - + -
228B PHE* 5.4 3.6 - - + -
231B ALA* 6.3 1.3 - - + -
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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 ILE* 2.9 30.6 + - + +
183B ALA* 3.3 35.9 - - - +
185B ILE* 1.3 80.1 - - - +
187B ASP* 1.3 93.3 + - - +
188B SER 3.3 1.2 + - - -
189B GLY* 3.5 9.4 + - - -
190B MET 5.1 2.2 - - - +
231B ALA* 5.9 4.0 - - + +
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Residues in contact with ASP 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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183B ALA* 3.0 18.3 + - - +
184B PHE* 3.8 2.2 - - - +
186B ARG* 1.3 113.3 + - - +
188B SER* 1.3 59.2 + - - +
189B GLY 3.3 1.2 + - - -
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Residues in contact with SER 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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112B ALA* 4.8 8.1 - - - +
184B PHE* 3.0 38.2 + - - -
185B ILE 3.9 4.7 - - - -
186B ARG 3.2 0.8 - - - -
187B ASP* 1.3 79.0 - - - +
189B GLY* 1.3 60.4 + - - +
190B MET* 3.3 23.3 + - - +
212B ARG* 5.3 3.6 + - - -
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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