Contacts of the helix formed by residues 148 - 164 (chain F) in PDB entry 2FRV
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 THR 148 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131F PRO* 3.7 8.3 - - + -
132F ALA* 3.6 41.7 - - + +
135F ALA* 3.9 13.7 - - - +
147F THR* 1.3 69.9 - - - +
149F GLU* 1.3 69.8 + - - +
151F LEU* 2.8 5.8 + - - +
152F LYS* 2.5 62.7 + - - +
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Residues in contact with GLU 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F THR* 3.4 20.7 - - - +
148F THR* 1.3 97.4 + - - +
150F SER* 1.3 63.0 + - - +
152F LYS* 3.6 18.6 + - + +
153F ALA* 2.9 24.8 + - - +
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Residues in contact with SER 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146F THR* 4.1 8.3 - - - +
147F THR* 2.8 38.6 + - - -
149F GLU* 1.3 77.0 - - - +
151F LEU* 1.3 63.2 + - - +
153F ALA* 3.3 7.8 + - - +
154F VAL* 3.2 25.7 + - - +
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Residues in contact with LEU 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131F PRO* 3.7 11.7 - - + +
134F ALA* 3.5 20.9 - - + +
135F ALA* 3.4 34.1 - - - +
146F THR* 3.9 15.9 - - + -
147F THR 3.3 10.7 + - - +
148F THR 2.8 8.6 + - - +
150F SER* 1.3 79.8 + - - +
152F LYS* 1.3 65.6 + - - +
153F ALA 3.0 1.6 - - - -
154F VAL* 3.1 15.0 + - + +
155F GLN* 3.2 9.0 + - - +
190F LEU* 3.7 22.7 - - + +
191F ILE* 4.6 9.2 - - + -
194F ALA* 3.6 31.0 - - + -
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Residues in contact with LYS 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131F PRO* 3.6 21.0 - - + +
132F ALA* 5.8 0.4 - - - +
148F THR* 2.5 41.3 + - + +
149F GLU* 3.6 19.3 + - + +
151F LEU* 1.3 71.9 - - - +
153F ALA* 1.3 56.5 + - - +
155F GLN* 3.3 15.4 + - - +
156F ALA* 3.1 26.9 + - - +
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Residues in contact with ALA 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F GLU 2.9 17.1 + - - +
150F SER* 3.3 9.4 - - - +
151F LEU 3.0 0.2 - - - -
152F LYS* 1.3 76.1 - - - +
154F VAL* 1.3 63.8 + - + +
156F ALA* 3.2 9.5 + - - +
157F LYS* 3.2 26.2 + - - +
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Residues in contact with VAL 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F SER 3.2 16.8 - - - +
151F LEU* 3.1 8.0 + - - +
153F ALA* 1.3 73.8 - - + +
155F GLN* 1.3 61.2 + - - +
157F LYS* 3.2 16.2 + - - +
158F VAL* 3.1 26.8 + - + +
190F LEU* 4.2 11.4 - - + -
193F THR* 3.9 27.8 - - + -
194F ALA* 3.8 30.1 - - + +
197F LEU* 3.9 18.2 - - + -
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Residues in contact with GLN 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F ALA* 3.0 27.1 + - - +
127F LEU* 3.4 30.7 + - + +
129F ALA* 2.8 32.5 + - - +
131F PRO* 4.0 19.6 - - - +
151F LEU 3.2 7.5 + - - +
152F LYS* 3.3 14.2 - - - +
154F VAL* 1.3 82.2 - - - +
156F ALA* 1.3 55.4 + - - +
158F VAL* 3.5 3.4 + - - -
159F LYS* 3.0 27.5 + - - +
190F LEU* 4.2 13.9 - - + +
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Residues in contact with ALA 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152F LYS 3.1 12.2 + - - +
153F ALA* 3.4 12.6 - - - +
154F VAL 3.1 0.4 - - - -
155F GLN* 1.3 76.1 - - - +
157F LYS* 1.3 61.1 + - - +
159F LYS* 3.7 10.9 - - + +
160F ALA* 2.9 30.0 + - - +
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Residues in contact with LYS 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E ASP* 5.7 5.1 + - - +
37E LEU* 4.5 25.2 - - + +
153F ALA* 3.2 13.1 + - - +
154F VAL* 3.3 19.8 - - + +
156F ALA* 1.3 77.4 - - - +
158F VAL* 1.3 62.1 + - + +
160F ALA* 3.3 6.2 + - - +
161F LEU* 2.9 28.8 + - - +
197F LEU* 4.3 31.4 - - + +
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Residues in contact with VAL 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F VAL* 4.3 25.1 - - + +
124F ALA* 5.2 2.2 - - - -
126F ALA* 5.3 4.5 - - + -
127F LEU* 3.8 24.5 - - + -
154F VAL* 3.1 17.8 + - + +
155F GLN* 3.8 6.3 - - - +
157F LYS* 1.3 83.7 - - + +
159F LYS* 1.3 61.1 + - - +
161F LEU* 3.1 9.2 + - + +
162F VAL* 2.9 31.6 + - + +
190F LEU* 6.4 0.2 - - + -
193F THR* 3.9 26.2 - - + -
197F LEU* 5.9 1.3 - - + -
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Residues in contact with LYS 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127F LEU* 4.0 22.6 - - + +
155F GLN 3.0 18.0 + - - +
156F ALA* 3.7 10.1 - - + +
158F VAL* 1.3 75.5 - - - +
160F ALA* 1.3 66.1 + - - +
162F VAL* 3.9 2.8 - - + +
163F GLU* 3.0 37.6 + - + +
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Residues in contact with ALA 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156F ALA 2.9 21.1 + - - +
157F LYS* 3.6 6.3 - - - +
159F LYS* 1.3 77.9 - - - +
161F LEU* 1.3 62.0 + - - +
163F GLU* 4.0 10.2 - - - +
164F SER* 3.6 18.4 + - - -
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Residues in contact with LEU 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E ARG* 3.3 21.8 - - - +
36E ILE 5.1 0.7 - - - +
37E LEU* 4.1 29.2 - - + +
157F LYS 2.9 16.8 + - - +
158F VAL* 3.6 9.9 - - + +
159F LYS 3.0 0.2 - - - -
160F ALA* 1.3 77.8 - - - +
162F VAL* 1.3 65.4 + - + +
164F SER* 2.7 24.0 + - - -
165F GLY 3.7 2.1 + - - -
166F GLN 3.3 23.8 + - - +
167F LEU* 4.1 28.6 - - + +
170F PHE* 4.1 19.7 - - + -
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Residues in contact with VAL 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F ALA* 6.2 5.2 - - + -
127F LEU* 4.6 14.8 - - + -
158F VAL* 2.9 28.7 + - + +
159F LYS* 3.9 5.6 - - + +
161F LEU* 1.3 77.3 - - + +
163F GLU* 1.3 62.6 + - + +
165F GLY* 3.3 15.9 + - - -
167F LEU* 3.8 23.9 - - + +
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Residues in contact with GLU 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159F LYS* 3.0 28.3 + - + +
160F ALA* 4.0 9.3 - - - +
162F VAL* 1.3 80.8 - - + +
164F SER* 1.3 56.1 + - - +
165F GLY 3.3 0.4 - - - -
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Residues in contact with SER 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E LYS* 3.3 24.3 - - - +
5E LYS* 5.4 9.6 - - - +
6E ARG* 3.3 20.6 + - - -
160F ALA 3.6 9.9 + - - -
161F LEU* 2.7 21.0 + - - -
162F VAL 3.2 0.4 - - - -
163F GLU* 1.3 77.1 - - - +
165F GLY* 1.3 57.3 + - - +
166F GLN* 3.1 21.0 + - - +
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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