Contacts of the helix formed by residues 151 - 163 (chain B) in PDB entry 2FGY
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 151 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152B ASP* 1.3 68.8 + - - +
153B SER* 3.2 17.1 + - - -
154B ALA* 3.8 6.4 + - - +
155B SER* 3.5 19.4 + - - -
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Residues in contact with ASP 152 (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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151B ASP* 1.3 77.3 - - - +
153B SER* 1.3 54.8 + - - +
155B SER* 3.1 9.1 + - - -
156B ALA* 2.7 39.6 + - - +
189B PRO* 3.5 30.2 - - + +
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Residues in contact with SER 153 (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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151B ASP 3.9 15.6 + - - +
152B ASP* 1.3 77.1 - - - +
154B ALA* 1.3 63.2 + - - +
156B ALA* 3.3 5.4 + - - +
157B ILE* 3.2 35.3 + - - +
190B LEU 5.0 6.1 + - - -
191B THR* 4.0 9.1 - - - +
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Residues in contact with ALA 154 (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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151B ASP* 3.8 7.0 + - - +
152B ASP 3.5 0.6 - - - -
153B SER* 1.3 81.6 + - - +
155B SER* 1.3 60.1 + - - +
157B ILE* 3.7 10.1 + - - +
158B GLY* 3.0 24.7 + - - -
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Residues in contact with SER 155 (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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151B ASP 3.5 12.9 + - - -
152B ASP* 3.4 13.7 - - - -
154B ALA* 1.3 77.5 - - - +
156B ALA* 1.3 59.4 + - - +
158B GLY* 3.4 1.8 + - - -
159B PHE* 3.0 27.4 + - - +
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Residues in contact with ALA 156 (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 ASP* 2.7 18.7 + - - +
153B SER 3.5 5.4 - - - +
154B ALA 3.3 0.2 - - - -
155B SER* 1.3 74.9 - - - +
157B ILE* 1.3 63.7 + - - +
159B PHE* 3.4 8.9 + - - +
160B PHE* 3.2 29.7 + - + -
189B PRO* 3.3 35.0 - - + -
191B THR* 3.6 13.2 - - + -
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Residues in contact with ILE 157 (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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153B SER* 3.2 25.5 + - - +
154B ALA* 3.7 7.6 + - - +
156B ALA* 1.3 73.6 - - - +
158B GLY* 1.3 60.3 + - - +
160B PHE* 3.2 13.6 + - + +
161B LEU* 3.0 43.1 + - + +
166B HIS 5.6 1.3 - - - +
191B THR* 4.0 22.7 - - - +
192B ALA* 5.1 3.8 - - + +
193B PHE* 3.9 27.6 - - + -
226B PRO* 3.8 28.9 - - + -
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Residues in contact with GLY 158 (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 ALA 3.0 18.5 + - - -
155B SER* 3.4 3.3 + - - -
156B ALA 3.3 0.4 - - - -
157B ILE* 1.3 77.2 - - - +
159B PHE* 1.3 55.6 + - - +
161B LEU* 3.7 9.8 - - - +
162B ASP* 2.9 39.8 + - - +
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Residues in contact with PHE 159 (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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155B SER 3.0 13.5 + - - +
156B ALA* 3.6 9.9 - - - +
157B ILE 3.3 0.2 - - - -
158B GLY* 1.3 72.6 - - - +
160B PHE* 1.3 77.7 + + - +
162B ASP* 3.5 5.0 + - - +
163B CYS* 3.2 48.4 + - - -
188B LEU* 5.9 4.0 - - + -
366B ARG* 3.7 38.4 - - + +
367B PHE* 3.9 17.0 - + - -
370B GLN* 3.6 41.5 - - + -
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Residues in contact with PHE 160 (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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156B ALA* 3.2 17.4 + - + -
157B ILE* 3.2 18.1 + - + +
159B PHE* 1.3 80.8 - + - +
161B LEU* 1.3 62.4 - - + +
163B CYS* 3.1 14.5 + - - +
164B GLY 3.1 0.7 + - - -
165B PHE* 2.9 38.5 + - + +
166B HIS 5.5 0.7 - - - -
167B ALA* 5.2 2.0 - - - -
168B VAL* 3.7 35.9 - - + -
188B LEU* 4.4 19.5 - - + -
189B PRO* 5.0 7.2 - - + -
191B THR* 4.0 14.1 - - + -
193B PHE* 4.4 10.3 - - + -
194B THR* 3.1 32.1 - - + -
367B PHE* 4.0 20.4 - + - -
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Residues in contact with LEU 161 (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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157B ILE* 3.0 32.2 + - + +
158B GLY* 3.7 8.7 - - - +
160B PHE* 1.3 78.8 - - - +
162B ASP* 1.3 56.9 + - - +
164B GLY* 2.7 27.7 + - - -
165B PHE 3.4 16.6 - - - +
166B HIS* 4.0 9.6 - - - -
226B PRO* 3.8 25.1 - - + +
227B ASN* 3.7 34.3 - - + +
233B THR* 4.1 7.7 - - + +
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Residues in contact with ASP 162 (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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158B GLY* 2.9 24.3 + - - +
159B PHE* 3.7 7.0 + - - +
160B PHE 3.3 0.2 - - - -
161B LEU* 1.3 77.7 - - - +
163B CYS* 1.3 57.9 + - - +
164B GLY* 3.2 0.9 + - - -
363B GLY* 4.6 4.3 - - - -
366B ARG* 3.3 32.9 + - - +
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Residues in contact with CYS 163 (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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159B PHE* 3.2 51.0 + - - +
160B PHE 3.1 11.0 + - - +
162B ASP* 1.3 75.2 - - - +
164B GLY* 1.3 58.5 + - - +
165B PHE* 3.7 22.6 - - + -
361B SER* 4.8 1.7 + - - -
363B GLY* 3.2 45.7 - - - +
364B MET 3.6 1.9 + - - -
366B ARG* 4.0 11.4 - - - -
367B PHE* 3.9 10.1 - - + -
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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