Contacts of the helix formed by residues 148 - 164 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131H PRO* 3.7 8.5 - - + -
132H ALA* 3.6 41.2 - - + +
135H ALA* 3.9 13.0 - - - +
147H THR* 1.3 71.0 - - - +
149H GLU* 1.3 70.9 + - - +
151H LEU* 2.8 6.0 + - - +
152H LYS* 2.5 63.1 + - - +
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Residues in contact with GLU 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147H THR* 3.4 20.7 - - - +
148H THR* 1.3 99.2 + - - +
150H SER* 1.3 62.6 + - - +
152H LYS* 3.6 17.3 + - + +
153H ALA* 2.9 24.6 + - - +
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Residues in contact with SER 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146H THR* 4.1 8.3 - - - +
147H THR* 2.8 38.3 + - - -
149H GLU* 1.3 78.3 - - - +
151H LEU* 1.3 63.4 + - - +
153H ALA* 3.3 8.0 + - - +
154H VAL* 3.2 25.7 + - - +
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Residues in contact with LEU 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H PRO* 3.7 12.8 - - + +
134H ALA* 3.5 21.3 - - + +
135H ALA* 3.4 33.0 - - - +
138H ALA* 6.3 0.2 - - + -
146H THR* 3.9 16.6 - - + -
147H THR 3.3 10.1 + - - +
148H THR 2.8 7.9 + - - +
150H SER* 1.3 80.6 + - - +
152H LYS* 1.3 65.5 + - - +
153H ALA 3.0 1.8 - - - -
154H VAL* 3.1 14.6 + - + +
155H GLN* 3.2 9.0 + - - +
190H LEU* 3.7 22.0 - - + +
191H ILE* 4.6 9.4 - - + -
194H ALA* 3.6 30.3 - - + -
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Residues in contact with LYS 152 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131H PRO* 3.6 22.8 - - + +
132H ALA* 5.8 0.2 - - - +
148H THR* 2.5 43.0 + - + +
149H GLU* 3.6 19.1 + - + +
151H LEU* 1.3 71.4 - - - +
153H ALA* 1.3 55.7 + - - +
155H GLN* 3.3 15.8 + - - +
156H ALA* 3.1 27.0 + - - +
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Residues in contact with ALA 153 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149H GLU 2.9 17.3 + - - +
150H SER* 3.3 9.2 - - - +
151H LEU 3.0 0.2 - - - -
152H LYS* 1.3 76.1 - - - +
154H VAL* 1.3 62.9 + - - +
156H ALA* 3.2 9.8 + - - +
157H LYS* 3.2 26.3 + - - +
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Residues in contact with VAL 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150H SER 3.2 17.3 - - - +
151H LEU* 3.1 6.9 + - - +
153H ALA* 1.3 73.7 - - + +
155H GLN* 1.3 61.5 + - - +
157H LYS* 3.2 16.4 + - - +
158H VAL* 3.1 27.1 + - + +
190H LEU* 4.2 11.9 - - + -
193H THR* 3.9 27.8 - - + -
194H ALA* 3.8 30.1 - - + +
197H LEU* 3.9 17.9 - - + -
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Residues in contact with GLN 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H ALA* 3.0 27.1 + - - +
127H LEU* 3.4 29.9 + - + +
129H ALA* 2.8 33.5 + - - +
131H PRO* 4.0 19.2 - - - +
151H LEU 3.2 7.3 + - - +
152H LYS* 3.3 14.1 - - - +
153H ALA 3.2 0.2 - - - -
154H VAL* 1.3 81.6 - - - +
156H ALA* 1.3 56.0 - - - +
158H VAL* 3.5 3.4 + - - -
159H LYS* 3.0 27.4 + - - +
190H LEU* 4.2 14.8 - - + +
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Residues in contact with ALA 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152H LYS 3.1 12.0 + - - +
153H ALA* 3.4 13.0 - - - +
154H VAL 3.1 0.4 - - - -
155H GLN* 1.3 74.8 - - - +
157H LYS* 1.3 61.1 + - - +
159H LYS* 3.7 10.9 - - - +
160H ALA* 2.9 30.1 + - - +
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Residues in contact with LYS 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G ASP* 5.7 5.2 + - - +
37G LEU* 4.5 24.8 - - + +
153H ALA* 3.2 13.2 + - - +
154H VAL* 3.3 20.1 - - + +
156H ALA* 1.3 76.9 - - - +
158H VAL* 1.3 63.5 + - + +
160H ALA* 3.3 6.4 + - - +
161H LEU* 2.9 28.9 + - - +
197H LEU* 4.3 30.4 - - + +
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Residues in contact with VAL 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123H VAL* 4.3 25.1 - - + +
124H ALA* 5.2 2.7 - - - -
126H ALA* 5.3 4.5 - - + -
127H LEU* 3.8 24.7 - - + -
154H VAL* 3.1 16.5 + - + +
155H GLN* 3.8 6.7 - - - +
157H LYS* 1.3 83.8 - - + +
159H LYS* 1.3 61.9 + - - +
161H LEU* 3.1 9.4 + - + +
162H VAL* 2.9 31.8 + - + +
193H THR* 3.9 26.7 - - + -
197H LEU* 5.9 1.1 - - + -
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Residues in contact with LYS 159 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H LEU* 4.0 22.2 - - + +
155H GLN 3.0 18.2 + - - +
156H ALA* 3.7 10.3 - - + +
157H LYS 3.2 0.2 - - - -
158H VAL* 1.3 74.9 - - - +
160H ALA* 1.3 65.4 + - - +
162H VAL* 3.9 2.5 - - + +
163H GLU* 3.0 38.9 + - + +
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Residues in contact with ALA 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156H ALA 2.9 20.3 + - - +
157H LYS* 3.6 7.6 - - - +
159H LYS* 1.3 78.5 - - - +
161H LEU* 1.3 62.0 + - - +
163H GLU* 3.9 10.1 + - - +
164H SER* 3.6 18.4 + - - -
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Residues in contact with LEU 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G ARG* 3.3 21.1 - - - +
36G ILE 5.1 0.7 - - - +
37G LEU* 4.1 29.6 - - + +
157H LYS 2.9 17.7 + - - +
158H VAL* 3.6 9.9 - - + +
159H LYS 3.0 0.4 - - - -
160H ALA* 1.3 77.1 - - - +
162H VAL* 1.3 65.2 + - + +
164H SER* 2.7 23.7 + - - -
165H GLY 3.7 1.9 + - - -
166H GLN 3.3 24.1 + - - +
167H LEU* 4.1 28.5 - - + +
170H PHE* 4.1 19.5 - - + -
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Residues in contact with VAL 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H ALA* 6.2 4.9 - - + -
127H LEU* 4.6 15.3 - - + -
158H VAL* 2.9 27.8 + - + +
159H LYS* 3.9 5.8 - - + +
161H LEU* 1.3 78.5 - - + +
163H GLU* 1.3 65.0 + - + +
165H GLY* 3.3 15.8 + - - -
167H LEU* 3.8 23.7 - - + +
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Residues in contact with GLU 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159H LYS* 3.0 27.8 + - + +
160H ALA* 4.0 9.7 - - - +
162H VAL* 1.3 79.8 - - + +
164H SER* 1.3 56.2 + - - +
165H GLY 3.3 0.2 - - - -
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Residues in contact with SER 164 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G LYS* 3.3 24.3 - - - +
5G LYS* 5.4 9.2 - - - -
6G ARG* 3.3 21.7 + - - -
160H ALA 3.6 10.0 + - - -
161H LEU* 2.7 21.2 + - - -
162H VAL 3.2 0.4 - - - -
163H GLU* 1.3 77.0 - - - +
165H GLY* 1.3 57.4 + - - +
166H GLN* 3.1 21.1 + - - +
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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