Contacts of the helix formed by residues 132 - 155 (chain A) in PDB entry 4DYL
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 132 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A THR* 3.1 24.4 + - - +
130A THR 3.4 0.6 - - - -
131A HIS* 1.3 86.5 - - - +
133A GLN* 1.3 64.1 + - - +
134A ASP 3.6 1.1 - - - -
135A ILE* 3.7 3.0 - - - +
136A GLU* 2.9 38.5 + - - +
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Residues in contact with GLN 133 (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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125A GLN 4.7 0.3 - - - +
128A THR* 2.9 28.3 + - + +
129A LYS* 3.0 40.9 + - + +
132A SER* 1.3 72.4 - - - +
134A ASP* 1.3 69.3 + - - +
136A GLU* 3.2 7.5 + - - +
137A LYS* 3.0 26.7 + - + +
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Residues in contact with ASP 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LYS* 2.9 32.2 + - - +
130A THR* 3.7 21.8 + - - +
133A GLN* 1.3 76.4 - - - +
135A ILE* 1.3 60.0 + - + +
137A LYS* 3.2 8.5 + - - +
138A LEU* 3.0 39.8 + - + +
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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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130A THR 3.6 11.9 - - - +
131A HIS 3.4 23.1 - - - +
132A SER 3.7 8.5 - - - +
133A GLN 3.2 0.2 - - - -
134A ASP* 1.3 77.8 - - + +
136A GLU* 1.3 61.9 + - - +
138A LEU* 3.4 11.2 + - + +
139A LYS* 2.9 45.6 + - + +
186A TYR* 4.7 7.2 - - + +
189A GLY 3.6 31.2 - - - +
190A VAL* 4.0 15.0 - - + +
193A ALA* 3.8 11.4 - - + -
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Residues in contact with GLU 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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132A SER* 2.9 26.0 + - - +
133A GLN* 3.2 6.5 + - - +
135A ILE* 1.3 79.7 - - - +
137A LYS* 1.3 58.0 + - + +
139A LYS* 3.7 24.4 - - - +
140A SER* 3.0 31.9 + - - -
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Residues in contact with LYS 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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133A GLN* 3.0 14.2 + - + +
134A ASP* 3.2 11.9 + - - +
136A GLU* 1.3 78.2 - - + +
138A LEU* 1.3 62.0 + - + +
140A SER* 3.5 5.4 + - - -
141A GLN* 3.1 45.4 + - + +
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Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ASP* 3.0 28.6 + - + +
135A ILE* 3.7 9.2 - - + +
137A LYS* 1.3 73.3 - - + +
139A LYS* 1.3 54.7 + - - +
141A GLN* 3.3 7.8 + - - +
142A TYR* 2.8 20.1 + - - +
182A HIS* 2.7 43.1 + - + +
185A ARG* 4.3 13.9 - - + +
186A TYR* 3.7 30.5 - - + +
189A GLY* 4.2 25.8 - - - -
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Residues in contact with LYS 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 28.3 + - + +
136A GLU* 3.7 28.9 - - - +
138A LEU* 1.3 75.8 - - - +
140A SER* 1.3 61.6 + - - +
142A TYR* 3.3 8.6 + - - +
143A ARG* 3.1 30.5 + - + +
186A TYR* 3.7 30.3 - - + +
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Residues in contact with SER 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLU 3.0 18.3 + - - -
137A LYS* 3.8 6.3 - - - -
138A LEU 3.3 0.2 - - - -
139A LYS* 1.3 76.2 - - - +
141A GLN* 1.3 63.2 - - - +
143A ARG* 3.5 8.8 + - - +
144A ALA* 3.2 20.6 + - - +
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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 LYS* 3.1 37.0 + - + +
138A LEU* 3.7 6.2 - - - +
140A SER* 1.3 75.2 - - - +
142A TYR* 1.3 65.6 + - - +
144A ALA* 3.1 8.7 + - - +
145A LEU* 2.9 29.3 + - + +
182A HIS* 3.3 30.6 - - + +
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Residues in contact with TYR 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 LEU 2.8 17.4 + - - +
139A LYS* 3.4 8.5 - - - +
141A GLN* 1.3 77.3 - - - +
143A ARG* 1.3 57.3 + - + +
145A LEU* 3.2 3.5 + - - +
146A ALA* 2.9 33.0 + - + +
179A LEU* 3.7 25.5 - - + +
182A HIS* 3.3 16.5 + + + -
183A HIS* 2.7 42.6 + + + +
186A TYR* 3.5 42.8 - + + -
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Residues in contact with ARG 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 LYS* 3.1 19.3 + - + +
140A SER* 3.6 10.3 - - - +
141A GLN 3.2 0.2 - - - -
142A TYR* 1.3 77.0 - - + +
144A ALA* 1.3 57.0 + - - +
146A ALA* 3.4 6.6 + - - +
147A ARG* 3.0 29.5 + - - +
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Residues in contact with ALA 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 SER 3.2 10.2 + - - +
141A GLN* 3.1 12.0 + - - +
143A ARG* 1.3 78.9 - - - +
145A LEU* 1.3 59.2 + - + +
147A ARG* 3.3 6.2 + - - +
148A ASP* 2.9 29.2 + - - +
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Residues in contact with LEU 145 (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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141A GLN* 2.9 19.8 + - + +
142A TYR 3.7 3.6 - - - +
144A ALA* 1.3 76.0 - - + +
146A ALA* 1.3 59.9 - - - +
148A ASP* 3.6 11.6 - - + +
149A SER* 2.9 29.1 + - - -
175A SER* 5.0 2.5 - - - +
178A LYS* 3.9 31.9 - - + +
179A LEU* 4.0 17.2 - - + +
182A HIS* 3.4 42.0 - - + +
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Residues in contact with ALA 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 TYR* 2.9 22.8 + - + +
143A ARG* 3.7 7.6 - - - +
144A ALA 3.3 0.2 - - - -
145A LEU* 1.3 74.9 - - - +
147A ARG* 1.3 59.5 + - - +
149A SER* 3.1 3.5 + - - -
150A ALA* 2.8 29.9 + - - +
179A LEU* 3.8 21.0 - - + +
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Residues in contact with ARG 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 ARG 3.0 17.8 + - - +
144A ALA* 3.8 5.6 - - - +
146A ALA* 1.3 74.5 - - - +
148A ASP* 1.3 57.5 + - - +
150A ALA* 3.3 8.4 + - - +
151A GLN* 3.0 31.6 + - - +
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Residues in contact with ASP 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 ALA 2.9 18.1 + - - +
145A LEU* 3.6 15.8 - - + +
147A ARG* 1.3 76.3 - - - +
149A SER* 1.3 57.4 + - - +
151A GLN* 3.3 6.9 + - - +
152A ALA* 3.0 28.5 + - - +
175A SER* 3.9 17.0 - - - -
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Residues in contact with SER 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 LEU 2.9 19.5 + - - -
146A ALA 3.1 3.6 + - - -
148A ASP* 1.3 73.3 + - - +
150A ALA* 1.3 57.6 + - - +
152A ALA 3.7 0.2 - - - -
153A LYS* 2.8 30.7 + - - +
172A TYR* 3.6 5.3 - - - -
175A SER* 3.1 41.3 + - - -
176A LEU* 3.4 17.1 + - - +
179A LEU* 4.0 15.2 - - - +
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Residues in contact with ALA 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 ALA 2.8 19.5 + - - +
147A ARG* 3.5 9.2 - - - +
149A SER* 1.3 72.0 - - - +
151A GLN* 1.3 61.6 + - - +
153A LYS* 3.3 9.1 + - - +
154A ARG* 3.1 24.3 + - - +
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Residues in contact with GLN 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 ARG 3.0 17.5 + - - +
148A ASP* 3.6 7.2 - - - +
149A SER 3.3 0.2 - - - -
150A ALA* 1.3 77.2 - - - +
152A ALA* 1.3 57.4 + - - +
154A ARG* 3.4 11.9 + - - +
155A LYS* 2.8 31.7 + - + +
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Residues in contact with ALA 152 (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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148A ASP* 3.0 17.9 + - - +
149A SER 3.9 3.4 - - - +
151A GLN* 1.3 73.8 - - - +
153A LYS* 1.3 64.8 + - - +
154A ARG 3.5 0.2 + - - -
155A LYS* 3.5 11.3 + - - +
156A TYR* 3.3 19.4 - - - +
168A ALA 4.5 1.3 - - - +
171A LYS* 4.2 10.8 - - + +
172A TYR* 4.0 27.2 - - - +
175A SER* 4.2 9.6 - - - -
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Residues in contact with LYS 153 (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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149A SER 2.8 18.5 + - - +
150A ALA* 3.5 9.0 - - - +
152A ALA* 1.3 77.1 - - - +
154A ARG* 1.3 62.8 - - - +
156A TYR* 3.4 22.8 - - + +
172A TYR* 3.4 40.8 - - + +
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Residues in contact with ARG 154 (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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150A ALA 3.1 13.9 + - - +
151A GLN* 3.5 12.6 - - - +
153A LYS* 1.3 76.2 - - - +
155A LYS* 1.3 53.2 + - - +
156A TYR 2.7 24.4 + - - +
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Residues in contact with LYS 155 (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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151A GLN* 2.8 22.3 + - + +
152A ALA* 3.6 8.6 - - - +
153A LYS 3.4 0.2 - - - -
154A ARG* 1.3 69.1 - - - +
156A TYR* 1.3 59.5 + - - +
168A ALA* 3.4 15.6 - - - +
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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