Contacts of the helix formed by residues 148 - 164 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131L PRO* 3.7 8.1 - - + -
132L ALA* 3.6 41.5 - - + +
135L ALA* 3.9 14.3 - - - +
147L THR* 1.3 70.6 - - - +
149L GLU* 1.3 69.3 + - - +
151L LEU* 2.8 5.6 + - - +
152L LYS* 2.5 63.0 + - - +
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Residues in contact with GLU 149 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147L THR* 3.4 20.3 - - - +
148L THR* 1.3 98.6 + - - +
150L SER* 1.3 63.2 + - - +
152L LYS* 3.6 18.6 + - + +
153L ALA* 2.9 24.4 + - - +
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Residues in contact with SER 150 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146L THR* 4.1 8.5 - - - +
147L THR* 2.8 38.3 + - - -
149L GLU* 1.3 77.6 - - - +
151L LEU* 1.3 63.7 + - - +
153L ALA* 3.3 8.5 + - - +
154L VAL* 3.2 25.2 + - - +
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Residues in contact with LEU 151 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131L PRO* 3.7 11.9 - - + +
134L ALA* 3.5 20.9 - - + +
135L ALA* 3.4 33.0 - - - +
146L THR* 3.9 17.0 - - + -
147L THR 3.3 10.3 + - - +
148L THR 2.8 8.1 + - - +
150L SER* 1.3 79.6 + - - +
152L LYS* 1.3 65.7 + - - +
153L ALA 3.0 1.8 - - - -
154L VAL* 3.1 14.6 + - + +
155L GLN* 3.2 9.7 + - - +
190L LEU* 3.7 21.2 - - + +
191L ILE* 4.6 9.6 - - + -
194L ALA* 3.6 30.7 - - + -
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Residues in contact with LYS 152 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131L PRO* 3.6 21.2 - - + +
132L ALA* 5.8 0.4 - - - +
148L THR* 2.5 41.9 + - + +
149L GLU* 3.6 19.5 + - + +
151L LEU* 1.3 71.2 - - - +
153L ALA* 1.3 56.7 + - - +
155L GLN* 3.3 16.4 + - - +
156L ALA* 3.1 26.2 + - - +
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Residues in contact with ALA 153 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149L GLU 2.9 17.8 + - - +
150L SER* 3.3 9.2 - - - +
151L LEU 3.0 0.2 - - - -
152L LYS* 1.3 75.7 - - - +
154L VAL* 1.3 63.9 + - + +
156L ALA* 3.2 10.2 + - - +
157L LYS* 3.2 25.4 + - - +
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Residues in contact with VAL 154 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150L SER 3.2 16.8 - - - +
151L LEU* 3.1 8.4 + - - +
153L ALA* 1.3 74.0 - - + +
155L GLN* 1.3 62.1 + - - +
157L LYS* 3.2 16.3 + - - +
158L VAL* 3.1 26.8 + - + +
190L LEU* 4.2 11.2 - - + -
193L THR* 3.9 27.6 - - + -
194L ALA* 3.8 29.8 - - + +
197L LEU* 3.9 18.4 - - + -
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Residues in contact with GLN 155 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126L ALA* 3.0 27.1 + - - +
127L LEU* 3.4 29.6 + - + +
129L ALA* 2.8 33.1 + - - +
131L PRO* 4.0 19.7 - - - +
151L LEU 3.2 7.1 + - - +
152L LYS* 3.3 14.9 - - - +
153L ALA 3.2 0.2 - - - -
154L VAL* 1.3 82.3 - - - +
156L ALA* 1.3 57.3 - - - +
158L VAL* 3.5 3.2 + - - +
159L LYS* 3.0 27.8 + - - +
190L LEU* 4.2 13.4 - - + +
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Residues in contact with ALA 156 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152L LYS 3.1 13.3 + - - +
153L ALA* 3.4 12.3 - - - +
154L VAL 3.1 0.2 - - - -
155L GLN* 1.3 74.5 - - - +
157L LYS* 1.3 60.7 + - - +
159L LYS* 3.7 10.7 - - + +
160L ALA* 2.9 30.0 + - - +
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Residues in contact with LYS 157 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153L ALA* 3.2 13.9 + - - +
154L VAL* 3.2 20.7 + - + +
156L ALA* 1.3 76.6 - - - +
158L VAL* 1.3 64.2 + - + +
160L ALA* 3.3 6.6 + - - +
161L LEU* 2.9 29.1 + - - +
197L LEU* 4.3 30.1 - - + +
33S ASP* 5.7 4.8 + - - +
37S LEU* 4.5 25.7 - - + +
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Residues in contact with VAL 158 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123L VAL* 4.3 25.1 - - + +
124L ALA* 5.2 2.2 - - - -
126L ALA* 5.3 4.7 - - + -
127L LEU* 3.8 24.7 - - + -
154L VAL* 3.1 17.4 + - + +
155L GLN* 3.8 6.7 - - - +
157L LYS* 1.3 83.8 - - + +
159L LYS* 1.3 61.5 + - - +
161L LEU* 3.1 9.0 + - + +
162L VAL* 2.9 31.8 + - + +
193L THR* 3.9 26.2 - - + -
197L LEU* 5.9 1.8 - - + -
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Residues in contact with LYS 159 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127L LEU* 4.0 21.5 - - + +
155L GLN 3.0 18.4 + - - +
156L ALA* 3.7 10.1 - - - +
157L LYS 3.2 0.2 - - - -
158L VAL* 1.3 76.2 - - - +
160L ALA* 1.3 66.4 + - - +
162L VAL* 3.9 2.4 - - + +
163L GLU* 3.0 38.3 + - + +
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Residues in contact with ALA 160 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156L ALA 2.9 20.0 + - - +
157L LYS* 3.6 7.6 - - - +
158L VAL 3.3 0.2 - - - -
159L LYS* 1.3 77.6 - - - +
161L LEU* 1.3 62.3 + - - +
163L GLU* 4.0 9.7 - - - +
164L SER* 3.6 18.4 + - - -
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Residues in contact with LEU 161 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157L LYS 2.9 17.4 + - - +
158L VAL* 3.1 10.1 + - + +
159L LYS 3.0 0.2 - - - -
160L ALA* 1.3 78.0 - - - +
162L VAL* 1.3 66.1 + - + +
164L SER* 2.7 23.6 + - - -
165L GLY 3.7 2.1 + - - -
166L GLN 3.3 23.3 + - - +
167L LEU* 4.1 28.2 - - + +
170L PHE* 4.1 20.4 - - + -
6S ARG* 3.3 20.9 - - - +
36S ILE 5.1 0.7 - - - +
37S LEU* 4.1 30.1 - - + +
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Residues in contact with VAL 162 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124L ALA* 6.2 5.4 - - + -
127L LEU* 4.6 15.0 - - + -
158L VAL* 2.9 28.5 + - + +
159L LYS* 3.9 5.6 - - + +
161L LEU* 1.3 78.3 - - + +
163L GLU* 1.3 64.1 - - - +
165L GLY* 3.3 15.1 + - - -
167L LEU* 3.8 23.9 - - + +
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Residues in contact with GLU 163 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159L LYS* 3.0 27.5 + - + +
160L ALA* 4.0 9.5 - - - +
162L VAL* 1.3 81.7 - - + +
164L SER* 1.3 56.7 + - - +
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Residues in contact with SER 164 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160L ALA 3.6 9.9 + - - -
161L LEU* 2.7 21.1 + - - -
162L VAL 3.2 0.4 - - - -
163L GLU* 1.3 77.8 - - - +
165L GLY* 1.3 57.8 + - - +
166L GLN* 3.1 20.6 + - - +
4S LYS* 3.3 24.1 - - - +
5S LYS* 5.4 9.2 - - - -
6S ARG* 3.3 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