Contacts of the helix formed by residues 151 - 164 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A ASP* 1.3 67.8 - - - +
153A SER* 3.3 17.7 - - - -
154A ALA* 3.8 6.2 + - - +
155A SER* 3.5 18.2 + - - -
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Residues in contact with ASP 152 (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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151A ASP* 1.3 77.2 - - - +
153A SER* 1.3 59.6 + - - +
155A SER* 3.2 6.7 + - - -
156A ALA* 2.7 39.7 + - - +
189A PRO* 3.5 30.8 - - + +
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Residues in contact with SER 153 (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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151A ASP 3.9 15.0 - - - -
152A ASP* 1.3 76.4 - - - +
154A ALA* 1.3 69.5 + - - +
156A ALA* 3.4 5.4 + - - +
157A ILE* 3.2 35.2 + - - +
189A PRO* 5.9 0.2 - - - +
190A LEU 5.0 6.8 + - - -
191A THR* 4.0 9.2 - - - +
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Residues in contact with ALA 154 (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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151A ASP* 3.8 7.9 + - - +
152A ASP 3.4 0.4 - - - -
153A SER* 1.3 81.3 + - - +
155A SER* 1.3 58.4 + - - +
157A ILE* 3.9 10.3 - - - +
158A GLY* 2.9 25.2 + - - -
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Residues in contact with SER 155 (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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151A ASP 3.5 14.0 + - - -
152A ASP* 3.5 12.3 - - - -
154A ALA* 1.3 77.6 - - - +
156A ALA* 1.3 57.0 + - - +
158A GLY* 3.4 2.2 + - - -
159A PHE* 2.9 27.5 + - - +
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Residues in contact with ALA 156 (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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152A ASP* 2.7 19.3 + - - +
153A SER 3.5 4.9 - - - +
155A SER* 1.3 75.1 - - - +
157A ILE* 1.3 63.4 + - - +
159A PHE* 3.4 8.2 + - - +
160A PHE* 3.2 30.3 + - + -
189A PRO* 3.1 36.3 - - + -
191A THR* 3.6 12.3 - - + -
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Residues in contact with ILE 157 (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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153A SER* 3.2 25.8 + - - +
154A ALA* 3.6 7.8 + - - +
156A ALA* 1.3 71.9 - - - +
158A GLY* 1.3 66.3 + - - +
160A PHE* 3.2 13.2 + - + +
161A LEU* 3.0 32.9 + - + +
166A HIS 5.8 1.1 - - - +
191A THR* 3.9 23.6 - - - +
192A ALA* 5.1 3.8 - - + +
193A PHE* 4.0 26.2 - - + -
226A PRO* 3.9 27.8 - - + -
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Residues in contact with GLY 158 (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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154A ALA 2.9 18.8 + - - -
155A SER* 3.7 2.7 - - - -
156A ALA 3.3 0.2 - - - -
157A ILE* 1.3 75.6 - - - +
159A PHE* 1.3 55.5 + - - +
161A LEU* 3.5 11.0 + - - +
162A ASP* 3.0 38.7 + - - +
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Residues in contact with PHE 159 (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 SER 2.9 17.2 + - - +
156A ALA* 3.7 7.2 - - - +
157A ILE 3.2 0.2 - - - -
158A GLY* 1.3 73.9 - - - +
160A PHE* 1.3 77.2 + + - +
162A ASP* 3.5 5.5 + - - +
163A CYS* 3.2 48.7 + - - -
188A LEU* 5.9 4.0 - - + -
366A ARG* 3.7 35.2 - - + -
367A PHE* 3.9 21.1 - + - -
370A GLN* 3.7 41.3 - - + -
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Residues in contact with PHE 160 (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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156A ALA* 3.2 17.4 + - + -
157A ILE* 3.2 16.8 + - + +
159A PHE* 1.3 81.9 - + - +
161A LEU* 1.3 63.0 + - + +
163A CYS* 3.0 9.3 + - - +
164A GLY 3.0 6.1 + - - -
165A PHE* 2.9 41.6 + - + +
166A HIS* 5.5 1.6 - - - -
167A ALA* 5.2 1.8 - - - -
168A VAL* 3.7 34.1 - - + -
188A LEU* 4.5 17.9 - - + -
189A PRO* 5.0 6.3 - - + -
191A THR* 3.9 14.1 - - + -
193A PHE* 4.4 9.6 - - + -
194A THR* 3.1 32.5 - - + -
367A PHE* 4.1 20.9 - + - -
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Residues in contact with LEU 161 (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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157A ILE* 3.0 30.7 + - + +
158A GLY* 3.6 9.4 - - - +
160A PHE* 1.3 78.9 - - - +
162A ASP* 1.3 59.8 + - - +
164A GLY* 2.8 22.5 + - - -
165A PHE 3.5 15.0 - - - +
166A HIS* 4.1 10.1 - - + -
226A PRO* 3.8 24.9 - - + +
227A ASN* 3.6 34.5 - - + +
233A THR* 4.1 8.6 - - + +
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Residues in contact with ASP 162 (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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158A GLY* 3.0 21.7 + - - +
159A PHE* 3.7 6.9 - - - +
161A LEU* 1.3 76.9 - - - +
163A CYS* 1.3 60.5 + - - +
164A GLY* 3.3 0.7 + - - -
363A GLY* 4.5 4.7 - - - -
366A ARG* 3.3 32.2 + - - +
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Residues in contact with CYS 163 (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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159A PHE* 3.2 49.6 + - - +
160A PHE 3.0 9.8 + - - +
162A ASP* 1.3 75.3 - - - +
164A GLY* 1.3 58.8 + - - +
165A PHE* 3.6 23.0 - - + -
361A SER* 4.8 1.9 + - - -
363A GLY* 3.1 45.5 - - - +
364A MET 3.7 1.9 + - - -
366A ARG* 4.0 10.8 - - - +
367A PHE* 3.7 12.3 - - + -
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Residues in contact with GLY 164 (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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161A LEU 2.8 13.0 + - - -
162A ASP 3.3 1.4 - - - -
163A CYS* 1.3 78.8 - - - +
165A PHE* 1.3 68.9 + - - +
232A PRO 4.2 5.7 - - - +
233A THR* 3.2 15.7 - - - -
234A ARG* 2.9 22.3 + - - +
289A ASP* 4.3 2.6 - - - +
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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