Contacts of the helix formed by residues 137 - 150 (chain B) in PDB entry 3F22
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 GLN 137 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138B ASP* 1.3 79.5 + - - +
139B GLN 2.8 5.1 + - - -
140B GLU* 3.0 36.1 + - - +
141B GLN* 2.6 37.1 + - - +
182B LYS* 5.6 3.8 - - - +
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Residues in contact with ASP 138 (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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137B GLN* 1.3 84.4 + - - +
139B GLN* 1.3 68.0 + - + +
141B GLN* 4.1 2.7 + - - +
142B ARG* 2.7 41.5 + - - +
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Residues in contact with GLN 139 (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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137B GLN 2.8 4.2 + - - -
138B ASP* 1.3 86.4 - - + +
140B GLU* 1.3 55.9 + - - +
142B ARG* 3.0 29.0 + - - +
143B ILE* 2.7 43.3 + - + +
165B LEU* 5.2 2.6 - - - +
167B THR* 3.5 33.8 + - + +
171B GLU* 5.1 10.3 - - + +
172B ILE* 4.9 4.7 - - + +
174B ARG* 6.2 0.7 - - - +
175B VAL* 3.9 24.2 - - + -
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Residues in contact with GLU 140 (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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137B GLN* 3.0 41.9 + - - +
139B GLN* 1.3 79.1 - - - +
141B GLN* 1.3 76.4 + - - +
143B ILE* 3.2 3.3 + - - +
144B LEU* 3.1 26.8 + - - +
175B VAL* 3.6 26.7 - - + +
178B SER* 4.5 7.3 + - - -
179B LEU* 3.5 25.8 - - + +
182B LYS* 3.3 25.5 + - - -
184B LYS* 5.4 0.7 - - - +
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Residues in contact with GLN 141 (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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137B GLN* 2.6 47.8 + - - +
138B ASP* 4.5 2.5 - - - +
140B GLU* 1.3 86.7 + - - +
142B ARG* 1.3 54.1 + - + +
144B LEU* 3.1 14.2 + - - +
145B LYS* 2.8 40.0 + - - +
184B LYS* 5.7 5.1 - - - +
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Residues in contact with ARG 142 (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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138B ASP* 2.7 29.8 + - - +
139B GLN* 3.0 35.1 + - - +
141B GLN* 1.3 80.1 - - + +
143B ILE* 1.3 61.9 + - + +
145B LYS* 3.4 10.5 + - + +
146B PHE* 3.1 22.0 + - - +
165B LEU* 3.0 50.4 + - + +
166B GLY 5.2 0.4 + - - -
167B THR* 3.7 11.3 + - - -
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Residues in contact with ILE 143 (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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139B GLN* 2.7 21.7 + - + +
140B GLU 3.7 4.3 - - - +
142B ARG* 1.3 70.4 - - + +
144B LEU* 1.3 61.2 + - - +
146B PHE* 3.2 5.2 + - - +
147B LEU* 3.0 39.6 + - + +
161B LEU* 3.9 9.4 - - + -
165B LEU* 3.9 21.5 - - + -
172B ILE* 3.9 27.1 - - + +
175B VAL* 3.3 36.3 - - + -
176B LEU* 3.6 26.2 - - + -
179B LEU* 4.5 8.3 - - + -
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Residues in contact with LEU 144 (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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140B GLU 3.1 13.9 + - - +
141B GLN* 3.1 14.2 + - + +
143B ILE* 1.3 75.2 - - - +
145B LYS* 1.3 60.7 + - - +
147B LEU* 3.2 1.7 + - - +
148B GLU* 2.8 33.3 + - - +
179B LEU* 3.4 30.3 - - + -
184B LYS* 3.5 36.6 - - + +
185B LEU* 3.5 26.0 - - + -
197B ILE* 4.0 13.8 - - + +
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Residues in contact with LYS 145 (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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141B GLN* 2.8 24.1 + - - +
142B ARG* 3.6 10.5 - - + +
144B LEU* 1.3 73.0 - - - +
146B PHE* 1.3 58.2 + - - +
148B GLU* 3.4 7.0 + - - +
149B GLU* 3.0 53.0 + - + +
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Residues in contact with PHE 146 (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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142B ARG 3.1 13.5 + - - +
143B ILE 3.4 8.5 - - - +
144B LEU 3.1 0.4 - - - -
145B LYS* 1.3 73.6 - - - +
147B LEU* 1.3 64.6 + - + +
148B GLU 3.0 4.5 - - - -
149B GLU* 3.0 29.0 + - + +
150B LEU* 3.1 39.4 + - + +
156B THR* 4.9 2.0 - - - -
160B ASP* 5.2 4.7 - - - -
161B LEU* 4.1 28.3 - - + -
164B LYS* 3.7 38.1 - - + -
165B LEU* 3.7 24.5 - - + -
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Residues in contact with LEU 147 (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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143B ILE* 3.0 36.4 + - + +
144B LEU 3.8 0.2 - - - +
146B PHE* 1.3 78.2 - - + +
148B GLU* 1.3 60.1 + - - +
150B LEU* 3.8 8.3 + - + +
151B GLY 3.7 18.9 - - - +
152B GLU* 4.6 0.2 - - - -
154B LYS 5.2 3.9 - - - +
155B ALA 4.9 2.0 - - - +
156B THR* 3.1 35.7 - - + -
161B LEU* 4.5 7.0 - - + -
176B LEU* 4.9 2.9 - - + -
185B LEU* 3.3 35.9 - - + -
195B TRP* 3.6 9.6 - - + +
196B LYS* 4.5 4.5 - - - -
197B ILE* 3.5 30.7 + - + +
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Residues in contact with GLU 148 (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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144B LEU 2.8 16.5 + - - +
145B LYS* 3.6 8.1 - - - +
147B LEU* 1.3 76.5 - - - +
149B GLU* 1.3 60.3 + - + +
150B LEU 3.1 5.6 + - - -
151B GLY* 3.8 9.5 + - - -
152B GLU* 2.5 41.9 + - - +
197B ILE* 4.2 10.4 - - - +
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Residues in contact with GLU 149 (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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145B LYS* 3.0 43.7 + - + +
146B PHE* 3.0 13.8 + - + +
148B GLU* 1.3 76.7 - - + +
150B LEU* 1.3 59.7 + - - +
151B GLY 3.6 1.6 + - - -
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Residues in contact with LEU 150 (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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146B PHE* 3.1 38.9 + - + +
147B LEU* 3.8 6.9 + - + +
148B GLU 3.1 1.2 - - - -
149B GLU* 1.3 82.6 - - - +
151B GLY* 1.3 68.2 + - - +
154B LYS* 3.2 47.0 - - + +
155B ALA 4.2 18.2 - - - +
156B THR* 4.8 6.5 - - + +
160B ASP* 5.3 4.5 - - - +
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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