Contacts of the helix formed by residues 134 - 151 (chain A) 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 SER 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A ILE* 1.3 66.4 + - - +
136A TYR* 3.4 8.1 + - - +
137A GLN* 3.1 50.4 + - - +
138A ASP* 3.0 30.7 + - - +
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Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A SER* 1.3 70.9 + - - +
136A TYR* 1.3 67.9 + - - +
138A ASP* 2.9 28.4 + - + +
139A GLN* 2.9 32.0 + - + +
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Residues in contact with TYR 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A SER* 3.4 8.0 + - - +
135A ILE* 1.3 80.7 - - - +
137A GLN* 1.3 69.6 + - - +
139A GLN* 3.3 7.5 + - + +
140A GLU* 2.9 59.5 + - - +
174A ARG* 5.6 3.4 - - + -
175A VAL* 3.7 29.2 - - + +
178A SER* 3.2 30.5 + - - -
182A LYS* 5.4 1.3 - - - -
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Residues in contact with GLN 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A SER* 3.1 40.1 + - - +
135A ILE 3.2 0.4 - - - -
136A TYR* 1.3 87.4 - - - +
138A ASP* 1.3 67.3 + - - +
140A GLU* 3.2 18.4 + - - +
141A GLN* 2.9 35.6 + - + +
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Residues in contact with ASP 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A SER 3.0 23.5 + - - +
135A ILE* 2.9 24.7 + - + +
137A GLN* 1.3 76.2 - - - +
139A GLN* 1.3 55.0 + - + +
141A GLN* 3.0 18.6 + - - +
142A ARG* 2.7 47.7 + - + +
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Residues in contact with GLN 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ILE* 2.9 33.4 + - + +
136A TYR* 3.7 8.5 - - + +
138A ASP* 1.3 72.6 - - - +
140A GLU* 1.3 67.3 + - - +
142A ARG* 2.7 46.6 + - - +
143A ILE* 2.9 34.6 + - + +
165A LEU* 4.9 1.7 - - + +
167A THR* 3.4 30.6 + - + +
171A GLU* 5.3 3.2 + - - +
172A ILE* 6.2 1.3 - - + -
175A VAL* 4.8 12.1 - - + -
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Residues in contact with GLU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A TYR* 2.9 46.7 + - - +
137A GLN* 3.2 22.3 + - - +
139A GLN* 1.3 76.0 - - - +
141A GLN* 1.3 59.4 + - + +
143A ILE* 3.0 6.2 + - - +
144A LEU* 2.9 33.6 + - + +
175A VAL* 3.5 24.0 - - + +
179A LEU* 3.6 18.9 - - + +
182A LYS* 2.9 29.2 + - - -
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Residues in contact with GLN 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLN* 2.9 24.6 + - + +
138A ASP* 3.4 20.1 - - - +
140A GLU* 1.3 78.7 - - + +
142A ARG* 1.3 56.5 + - + +
144A LEU* 3.7 11.7 - - + +
145A LYS* 2.8 33.5 + - - +
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Residues in contact with ARG 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ASP* 2.7 34.7 + - + +
139A GLN* 2.7 51.4 + - - +
141A GLN* 1.3 72.3 - - + +
143A ILE* 1.3 58.1 + - - +
145A LYS* 3.9 7.3 - - - +
146A PHE* 3.0 28.4 + - - +
164A LYS 5.0 0.2 + - - -
165A LEU* 2.9 67.1 + - + +
166A GLY 5.1 0.2 + - - -
167A THR* 3.6 7.1 + - - -
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Residues in contact with ILE 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A GLN* 2.9 16.9 + - + +
140A GLU* 3.3 7.2 - - - +
142A ARG* 1.3 75.5 - - - +
144A LEU* 1.3 67.0 + - - +
146A PHE* 3.1 4.2 + - - +
147A LEU* 3.0 26.0 + - + +
161A LEU* 4.3 12.1 - - + -
165A LEU* 3.8 19.7 - - + -
172A ILE* 4.1 27.4 - - + +
175A VAL* 3.5 37.0 - - + -
176A LEU* 3.9 23.3 - - + -
179A LEU* 4.4 4.9 - - + -
185A LEU* 4.3 13.5 - - + -
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A GLU* 2.9 23.5 + - + +
141A GLN* 3.7 10.8 - - + +
143A ILE* 1.3 76.0 - - - +
145A LYS* 1.3 57.9 + - - +
147A LEU* 3.4 2.8 + - - +
148A GLU* 2.9 47.6 + - - +
179A LEU* 4.3 24.7 - - + -
184A LYS* 4.7 26.0 - - + +
185A LEU* 4.4 13.5 - - + -
197A ILE* 3.8 23.3 - - + +
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Residues in contact with LYS 145 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A GLN 2.8 21.7 + - - +
142A ARG* 3.9 6.3 - - - +
144A LEU* 1.3 70.6 - - - +
146A PHE* 1.3 67.2 + - - +
148A GLU* 3.3 9.9 + - - +
149A GLU* 3.0 60.6 + - + +
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Residues in contact with PHE 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ARG 3.0 19.3 + - - +
143A ILE* 3.1 4.2 + - - +
145A LYS* 1.3 77.9 - - - +
147A LEU* 1.3 62.3 + - + +
149A GLU* 3.9 11.9 - - - +
150A LEU* 2.9 45.3 + - + +
156A THR* 4.6 1.3 - - + -
160A ASP* 4.2 13.0 - - - -
161A LEU* 3.5 27.8 - - + -
164A LYS* 3.5 47.8 - - + -
165A LEU* 4.2 15.0 - - + -
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Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ILE* 3.0 24.4 + - + +
144A LEU 4.0 0.9 - - - +
146A PHE* 1.3 81.3 - - + +
148A GLU* 1.3 63.0 + - - +
149A GLU 3.2 0.2 - - - -
150A LEU* 3.4 28.2 - - + +
151A GLY 3.2 23.0 + - - +
154A LYS 5.1 1.2 - - - +
156A THR* 3.9 14.4 - - + -
161A LEU* 4.6 11.9 - - + -
185A LEU* 3.4 37.5 - - + -
195A TRP* 3.8 18.4 - - + +
196A LYS* 4.2 11.7 - - - +
197A ILE* 3.7 22.3 + - + +
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Residues in contact with GLU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LEU* 2.9 40.6 + - - +
145A LYS* 3.8 8.3 - - - +
147A LEU* 1.3 76.4 - - - +
149A GLU* 1.3 63.5 + - + +
151A GLY* 3.5 10.4 + - - -
152A GLU* 4.6 11.5 + - + +
197A ILE* 4.0 21.8 - - + +
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Residues in contact with GLU 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A LYS* 3.0 52.9 + - + +
146A PHE* 3.9 11.1 - - - +
148A GLU* 1.3 75.8 - - + +
150A LEU* 1.3 68.6 + - - +
151A GLY* 3.1 1.8 + - - -
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Residues in contact with LEU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A PHE* 2.9 31.8 + - + +
147A LEU* 3.4 31.6 - - + +
149A GLU* 1.3 79.5 - - - +
151A GLY* 1.3 57.7 + - - +
154A LYS* 3.7 25.7 - - + +
155A ALA 3.9 32.3 - - - +
156A THR* 4.2 10.3 - - + -
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Residues in contact with GLY 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LEU 3.2 8.3 + - - +
148A GLU 3.5 6.4 + - - -
149A GLU 3.1 4.3 - - - -
150A LEU* 1.3 79.9 - - - +
152A GLU* 1.3 57.2 + - - -
153A GLY 3.2 2.5 - - - -
154A LYS* 2.7 40.0 + - - +
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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