Contacts of the helix formed by residues 148 - 164 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131D PRO* 3.7 8.1 - - + -
132D ALA* 3.6 41.0 - - + +
135D ALA* 3.9 12.8 - - - +
147D THR* 1.3 70.0 - - - +
149D GLU* 1.3 71.1 + - - +
151D LEU* 2.8 5.4 + - - +
152D LYS* 2.5 63.8 + - - +
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Residues in contact with GLU 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D THR* 3.4 20.4 - - - +
148D THR* 1.3 97.6 + - - +
150D SER* 1.3 63.4 + - - +
152D LYS* 3.6 18.4 + - + +
153D ALA* 2.9 24.6 + - - +
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Residues in contact with SER 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D THR* 4.1 9.2 - - - +
147D THR* 2.8 37.9 + - - -
149D GLU* 1.3 78.3 - - - +
151D LEU* 1.3 62.5 + - - +
153D ALA* 3.3 8.4 + - - +
154D VAL* 3.2 25.6 + - - +
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Residues in contact with LEU 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D PRO* 3.7 11.9 - - + +
134D ALA* 3.5 20.9 - - + +
135D ALA* 3.4 33.2 - - - +
146D THR* 3.9 16.2 - - + -
147D THR 3.3 9.8 + - - +
148D THR 2.8 8.8 + - - +
150D SER* 1.3 79.7 + - - +
152D LYS* 1.3 64.8 + - - +
153D ALA 3.0 1.3 - - - -
154D VAL* 3.1 13.5 + - - +
155D GLN* 3.2 10.0 + - - +
190D LEU* 3.7 22.2 - - + +
191D ILE* 4.6 10.3 - - + -
194D ALA* 3.6 31.4 - - + -
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Residues in contact with LYS 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D PRO* 3.6 21.9 - - + +
132D ALA* 5.8 0.2 - - - +
148D THR* 2.5 40.9 + - + +
149D GLU* 3.6 19.3 + - + +
151D LEU* 1.3 72.0 - - - +
153D ALA* 1.3 57.4 + - - +
155D GLN* 3.3 15.3 + - - +
156D ALA* 3.1 26.7 + - - +
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Residues in contact with ALA 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D GLU 2.9 18.0 + - - +
150D SER* 3.3 9.4 - - - +
151D LEU 3.0 0.2 - - - -
152D LYS* 1.3 75.5 - - - +
154D VAL* 1.3 62.7 + - + +
156D ALA* 3.2 10.4 + - - +
157D LYS* 3.2 26.4 + - - +
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Residues in contact with VAL 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D SER 3.2 17.5 - - - +
151D LEU* 3.1 7.6 + - - +
153D ALA* 1.3 74.7 - - + +
155D GLN* 1.3 61.4 + - - +
156D ALA 3.1 0.2 - - - -
157D LYS* 3.2 16.7 + - - +
158D VAL* 3.1 26.6 + - + +
190D LEU* 4.2 10.8 - - + -
193D THR* 3.9 27.1 - - + -
194D ALA* 3.8 31.2 - - + +
197D LEU* 3.9 18.2 - - + -
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Residues in contact with GLN 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D ALA* 3.0 27.0 + - - +
127D LEU* 3.4 29.4 + - + +
129D ALA* 2.8 33.1 + - - +
131D PRO* 4.0 20.0 - - - +
151D LEU 3.2 6.5 + - - +
152D LYS* 3.3 13.9 - - - +
154D VAL* 1.3 82.4 - - - +
156D ALA* 1.3 56.4 - - - +
158D VAL* 3.5 3.0 + - - -
159D LYS* 3.0 28.2 + - - +
190D LEU* 4.2 15.2 - - + +
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Residues in contact with ALA 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D LYS 3.1 12.2 + - - +
153D ALA* 3.4 12.3 - - - +
154D VAL 3.1 0.4 - - - -
155D GLN* 1.3 75.9 - - - +
157D LYS* 1.3 59.8 + - - +
159D LYS* 3.7 10.7 - - + +
160D ALA* 2.9 29.6 + - - +
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Residues in contact with LYS 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ASP* 5.7 4.6 + - - +
37C LEU* 4.5 25.5 - - + +
153D ALA* 3.2 13.3 + - - +
154D VAL* 3.2 20.0 + - + +
156D ALA* 1.3 76.5 - - - +
158D VAL* 1.3 63.3 + - + +
160D ALA* 3.3 6.8 + - - +
161D LEU* 2.9 28.9 + - - +
197D LEU* 4.3 32.2 - - + +
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Residues in contact with VAL 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D VAL* 4.3 26.2 - - + +
124D ALA* 5.2 2.2 - - - -
126D ALA* 5.3 4.7 - - + -
127D LEU* 3.8 24.9 - - + -
154D VAL* 3.1 16.7 + - + +
155D GLN* 3.5 6.7 + - - +
157D LYS* 1.3 84.2 - - + +
159D LYS* 1.3 61.5 + - - +
161D LEU* 3.1 9.6 + - + +
162D VAL* 2.9 32.6 + - + +
193D THR* 3.9 26.0 - - + -
197D LEU* 5.9 1.6 - - + -
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Residues in contact with LYS 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D LEU* 4.0 22.2 - - + +
155D GLN 3.0 18.4 + - - +
156D ALA* 3.7 9.6 - - - +
158D VAL* 1.3 75.3 - - - +
160D ALA* 1.3 66.6 + - - +
162D VAL* 3.9 2.4 - - + +
163D GLU* 3.0 37.6 + - + +
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Residues in contact with ALA 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D ALA 2.9 19.9 + - - +
157D LYS* 3.6 7.0 - - - +
159D LYS* 1.3 78.0 - - - +
161D LEU* 1.3 61.0 + - - +
163D GLU* 4.0 9.8 - - - +
164D SER* 3.6 19.2 + - - -
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Residues in contact with LEU 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ARG* 3.3 20.9 - - - +
36C ILE 5.1 0.7 - - - +
37C LEU* 4.1 28.9 - - + +
157D LYS 2.9 16.8 + - - +
158D VAL* 3.6 9.0 - - + +
159D LYS 3.0 0.2 - - - -
160D ALA* 1.3 77.7 - - - +
162D VAL* 1.3 65.8 + - + +
164D SER* 2.7 23.2 + - - -
165D GLY 3.7 2.4 + - - -
166D GLN 3.3 24.4 + - - +
167D LEU* 4.1 27.9 - - + +
170D PHE* 4.1 19.7 - - + -
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Residues in contact with VAL 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D ALA* 6.2 5.6 - - + -
127D LEU* 4.6 14.4 - - + -
158D VAL* 2.9 29.5 + - + +
159D LYS* 3.9 5.8 - - + +
161D LEU* 1.3 76.9 - - + +
163D GLU* 1.3 63.8 + - - +
165D GLY* 3.3 15.4 + - - -
167D LEU* 3.8 22.7 - - + +
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Residues in contact with GLU 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D LYS* 3.0 27.8 + - + +
160D ALA* 4.0 9.7 - - - +
162D VAL* 1.3 80.1 - - + +
164D SER* 1.3 57.5 + - - +
165D GLY 3.3 0.2 - - - -
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Residues in contact with SER 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C LYS* 3.3 24.4 - - - +
5C LYS* 5.4 8.7 - - - -
6C ARG* 3.3 22.0 + - - -
160D ALA 3.6 10.5 + - - -
161D LEU* 2.7 21.5 + - - -
163D GLU* 1.3 76.8 - - - +
165D GLY* 1.3 57.0 + - - +
166D GLN* 3.1 21.7 + - - +
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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