Contacts of the helix formed by residues 162 - 174 (chain B) in PDB entry 2FG8
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 GLU 162 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158B LEU 4.5 1.7 - - - +
160B GLY* 2.9 4.2 - - - -
161B PRO* 1.3 81.3 - - + +
163B ALA* 1.3 58.3 + - - +
164B GLY 3.1 3.1 - - - -
165B LEU* 2.9 46.3 + - + +
166B GLY* 3.1 9.9 + - - -
158D LEU 6.1 0.2 - - - -
159D GLY 4.6 8.2 - - - +
161D PRO* 4.0 14.6 - - - +
162D GLU* 3.0 45.3 + - + +
162G GLU* 3.1 34.8 - - + +
165G LEU* 5.2 1.8 - - + +
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Residues in contact with ALA 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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95B LYS* 5.7 8.5 - - + +
158B LEU 3.8 5.5 - - - +
159B GLY 2.9 24.9 - - - +
160B GLY* 3.4 3.7 - - - -
161B PRO* 3.0 5.9 - - + +
162B GLU* 1.3 78.0 - - - +
164B GLY* 1.3 58.2 + - - +
166B GLY* 3.2 0.7 + - - -
167B GLU* 2.9 30.7 + - - +
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Residues in contact with GLY 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LYS* 5.8 6.1 - - - +
161B PRO 4.6 2.2 + - - -
162B GLU* 3.1 1.6 - - - +
163B ALA* 1.3 79.9 - - - +
165B LEU* 1.3 61.3 + - - +
167B GLU* 3.6 6.7 + - - -
168B TYR* 3.3 14.4 + - - +
157D ARG* 3.2 42.4 - - - +
158D LEU* 4.7 0.2 - - - +
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Residues in contact with LEU 165 (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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162B GLU* 2.9 34.9 + - + +
164B GLY* 1.3 77.8 - - - +
166B GLY* 1.3 59.0 + - - +
168B TYR* 3.4 2.6 + - - +
169B LEU* 3.0 35.5 + - + +
157D ARG 4.0 3.0 + - - -
158D LEU* 3.6 26.0 - - + -
162D GLU* 5.4 4.3 - - + +
165D LEU* 4.6 18.4 - - + -
166D GLY* 5.1 2.7 - - - -
169D LEU* 3.3 31.2 - - + -
165G LEU* 3.5 28.0 - - + -
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Residues in contact with GLY 166 (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 LEU* 5.4 0.7 - - - -
158B LEU* 3.7 35.7 - - - +
162B GLU 3.1 11.2 + - - -
163B ALA 3.2 3.5 + - - -
165B LEU* 1.3 76.0 - - - +
167B GLU* 1.3 59.2 + - - +
169B LEU* 3.7 5.1 - - - +
170B PHE* 2.8 32.4 + - - +
165G LEU* 4.6 4.9 - - - +
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Residues in contact with GLU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.7 19.8 - - + +
95B LYS* 3.3 25.8 - - - +
96B THR* 2.7 54.3 + - + +
97B PRO* 4.7 5.4 - - + -
155B LEU* 4.7 5.6 - - + +
163B ALA 2.9 16.5 + - - +
164B GLY* 3.8 7.3 - - - +
165B LEU 3.3 0.2 - - - -
166B GLY* 1.3 74.0 - - - +
168B TYR* 1.3 57.6 + - - +
170B PHE* 3.4 6.7 + - - +
171B GLU* 3.1 28.4 + - - +
157D ARG* 3.6 18.8 + - - +
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Residues in contact with TYR 168 (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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48B LEU* 4.5 9.0 - - + -
164B GLY 3.3 11.0 + - - +
165B LEU 3.7 5.6 - - - +
166B GLY 3.2 0.6 - - - -
167B GLU* 1.3 80.2 - - - +
169B LEU* 1.3 64.8 + - + +
171B GLU* 3.3 7.0 + - - +
172B ARG* 2.9 54.0 + - + +
154D ASN* 3.6 24.5 - - + -
157D ARG* 4.2 6.0 - - - +
158D LEU* 3.9 31.2 - - + -
169D LEU* 4.2 20.2 - - + -
170D PHE* 3.4 21.7 - + - -
173D LEU* 3.4 12.7 - - + +
174D THR* 2.8 44.3 + - - -
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Residues in contact with LEU 169 (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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165B LEU* 3.0 35.8 + - + +
166B GLY* 3.3 5.1 + - - +
168B TYR* 1.3 79.6 - - + +
170B PHE* 1.3 60.3 + - - +
172B ARG* 3.8 2.4 - - - +
173B LEU* 2.8 37.1 + - + +
169D LEU* 3.8 23.1 - - + -
173D LEU* 3.7 28.3 - - + -
165G LEU* 3.6 29.6 - - + -
168G TYR* 3.3 17.7 + - + -
169G LEU* 3.8 20.2 - - + -
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Residues in contact with PHE 170 (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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96B THR* 4.4 6.7 - - + -
100B MET* 4.9 2.0 - - + -
151B HIS* 3.5 39.3 - + + -
154B ASN* 4.2 21.3 - - + -
155B LEU* 3.6 35.7 - - + -
158B LEU* 4.6 4.9 - - + -
166B GLY 2.8 17.3 + - - +
167B GLU 3.6 4.9 - - - +
168B TYR 3.2 0.2 - - - -
169B LEU* 1.3 78.3 - - - +
171B GLU* 1.3 58.3 + - + +
174B THR* 3.0 45.6 + - + -
175B LEU* 3.1 36.1 + - + -
168G TYR* 3.3 24.2 - + + +
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Residues in contact with GLU 171 (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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48B LEU* 3.7 28.9 - - + +
49B GLU 3.9 4.8 + - - -
50B GLY* 2.8 36.7 + - - +
51B VAL* 3.9 7.6 - - + +
96B THR* 6.0 1.3 - - - +
167B GLU 3.1 16.6 + - - +
168B TYR* 3.7 6.8 - - - +
170B PHE* 1.3 77.5 - - + +
172B ARG* 1.3 102.8 + - - +
175B LEU* 4.0 14.3 - - + +
176B LYS* 3.4 21.5 + - - -
177B HIS* 3.9 3.1 + - - -
154D ASN* 5.4 0.9 - - - +
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Residues in contact with ARG 172 (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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49B GLU* 4.4 13.5 + - - +
168B TYR* 2.9 43.5 + - + +
169B LEU* 3.8 2.5 - - - +
171B GLU* 1.3 114.2 + - - +
173B LEU* 1.3 78.0 + - + +
176B LYS* 3.7 15.2 - - - +
177B HIS* 3.3 37.3 + - - -
173D LEU* 3.0 42.8 + - + -
174D THR* 4.0 16.9 + - - +
176D LYS* 4.0 5.5 - - - +
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Residues in contact with LEU 173 (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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169B LEU* 2.8 30.4 + - + +
172B ARG* 1.3 91.4 - - + +
174B THR* 1.3 57.4 + - - +
176B LYS* 2.8 21.1 - - - +
173D LEU* 3.7 19.7 - - + -
168G TYR* 3.6 10.5 - - + +
169G LEU* 4.0 21.5 - - + -
172G ARG* 3.0 24.2 + - + -
173G LEU* 3.8 31.4 - - + -
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Residues in contact with THR 174 (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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147B LYS* 5.7 2.7 + - - +
151B HIS* 3.7 20.4 - - + +
154B ASN* 5.7 0.5 - - - -
170B PHE* 3.0 36.9 + - + -
172B ARG 3.6 0.2 - - - -
173B LEU* 1.3 77.5 - - - +
175B LEU* 1.3 67.7 + - - +
176B LYS* 3.3 18.7 + - - +
168G TYR* 2.8 30.0 + - - -
172G ARG* 3.4 18.9 + - - +
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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