Contacts of the helix formed by residues 131 - 153 (chain A) in PDB entry 4AD7
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 GLY 131 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A PHE* 1.3 88.1 - - - +
132A GLU* 1.3 58.9 + - - -
133A LEU* 3.0 16.2 + - - -
134A TYR* 3.2 17.3 + - - +
135A THR* 4.0 2.9 + - - +
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Residues in contact with GLU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A GLY* 1.3 67.6 - - - -
133A LEU* 1.3 74.3 + - + +
134A TYR 3.2 0.7 - - - -
135A THR* 3.1 16.1 + - - +
136A GLN* 2.9 44.6 + - + +
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Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PHE* 6.2 2.7 - - + -
131A GLY* 3.0 5.3 + - - +
132A GLU* 1.3 85.7 - - + +
134A TYR* 1.3 57.4 + - - +
136A GLN* 3.9 2.6 - - - +
137A ASN* 3.0 44.2 + - - +
173A ARG 5.3 4.0 - - - +
174A LEU* 4.1 27.4 - - + -
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Residues in contact with TYR 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LEU* 3.5 24.1 - - + +
123A GLN* 3.6 29.3 + - - +
126A PHE* 3.8 20.6 - + + +
127A PRO* 3.4 43.9 - - + +
130A PHE* 4.6 17.6 - - + -
131A GLY 3.2 10.8 + - - +
132A GLU 3.2 0.4 - - - -
133A LEU* 1.3 79.5 - - - +
135A THR* 1.3 68.2 + - + +
137A ASN 2.9 3.8 + - - -
138A ALA* 2.8 42.1 + - + +
141A PHE* 3.4 33.4 - + + -
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Residues in contact with THR 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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127A PRO* 4.1 17.3 - - + +
130A PHE 5.7 0.4 - - - +
131A GLY 4.0 2.9 + - - +
132A GLU* 3.1 25.6 + - - +
134A TYR* 1.3 97.9 - - + +
136A GLN* 1.3 70.7 + - - +
138A ALA* 3.9 13.1 - - - +
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Residues in contact with GLN 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 GLU* 2.9 42.8 + - + +
133A LEU* 3.9 4.5 - - - +
135A THR* 1.3 90.2 + - - +
137A ASN* 1.3 65.1 + - - +
138A ALA 3.3 2.7 + - - -
139A ARG* 4.8 3.8 + - - +
173A ARG* 3.3 25.1 + - - +
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Residues in contact with ASN 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 LEU* 3.0 28.1 + - - +
134A TYR 2.9 4.0 + - - -
136A GLN* 1.3 77.1 - - - +
138A ALA* 1.3 58.1 + - - +
139A ARG 3.2 2.9 - - - -
140A ALA* 2.9 30.2 + - + +
141A PHE* 2.9 30.5 + - + -
170A LEU* 3.4 24.9 - - + +
173A ARG* 3.2 40.0 + - - +
174A LEU* 4.8 7.9 - - - +
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Residues in contact with ALA 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 TYR* 2.8 27.6 + - + +
135A THR* 3.9 15.5 - - - +
136A GLN 3.3 2.8 - - - -
137A ASN* 1.3 76.9 - - - +
139A ARG* 1.3 57.0 + - - +
141A PHE* 3.3 11.0 + - - +
142A ARG* 2.9 40.3 + - - +
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Residues in contact with ARG 139 (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 GLN 4.8 3.5 + - - +
137A ASN 3.2 0.4 - - - -
138A ALA* 1.3 78.6 - - - +
140A ALA* 1.3 57.3 + - - +
142A ARG* 3.4 36.6 + - - +
143A ASP* 2.9 51.2 + - - +
173A ARG* 5.3 10.4 - - - +
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Residues in contact with ALA 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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137A ASN* 2.9 21.9 + - + +
139A ARG* 1.3 77.1 - - - +
141A PHE* 1.3 59.5 + - + +
143A ASP* 3.3 10.5 + - - +
144A LEU* 2.9 26.9 + - - +
166A PHE* 3.7 18.0 - - + -
169A ARG 6.5 1.1 - - - -
170A LEU* 5.7 4.5 - - + -
173A ARG* 5.0 13.9 - - - +
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Residues in contact with PHE 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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122A LEU* 4.9 15.5 - - + -
126A PHE* 5.4 7.6 - + - -
133A LEU 5.9 0.2 - - - -
134A TYR* 3.4 44.9 - + + -
137A ASN* 2.9 40.6 + - + -
138A ALA* 3.3 6.0 + - - +
140A ALA* 1.3 74.6 - - + +
142A ARG* 1.3 65.4 + - + +
144A LEU* 3.0 14.0 + - + +
145A TYR* 2.9 30.6 + - + +
166A PHE* 4.0 26.0 - + - -
170A LEU* 4.8 16.4 - - + -
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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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119A GLU* 4.0 22.0 - - - +
123A GLN* 4.5 11.0 - - + +
138A ALA* 2.9 23.9 + - - +
139A ARG* 3.5 40.2 - - - +
141A PHE* 1.3 75.7 - - - +
143A ASP* 1.3 60.3 + - - +
145A TYR* 3.3 5.0 + - - +
146A SER* 2.9 34.0 + - - +
149A ARG* 5.0 1.0 + - - -
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Residues in contact with ASP 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 ARG* 2.9 48.4 + - - +
140A ALA* 3.5 9.6 - - - +
141A PHE 3.2 0.2 - - - -
142A ARG* 1.3 77.3 + - - +
144A LEU* 1.3 60.3 + - - +
146A SER* 3.8 6.7 + - - -
147A GLU* 2.9 39.7 + - + +
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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 ALA 2.9 14.2 + - - +
141A PHE* 3.0 16.8 + - + +
143A ASP* 1.3 75.9 - - - +
145A TYR* 1.3 70.0 + - + +
147A GLU* 3.3 10.1 + - + +
148A LEU* 2.9 39.7 + - + +
163A LEU* 3.7 29.8 - - + -
166A PHE* 3.6 42.1 - - + -
167A TRP* 6.2 0.4 - - + -
317A VAL* 5.5 6.1 - - + +
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Residues in contact with TYR 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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115A LEU* 3.6 25.2 - - + +
118A SER* 3.2 22.6 + - - -
119A GLU* 3.4 58.1 - - + +
122A LEU* 4.2 14.8 - - + +
141A PHE* 2.9 17.2 + - + +
142A ARG 3.8 5.8 - - - +
144A LEU* 1.3 85.2 - - + +
146A SER* 1.3 57.7 + - - +
148A LEU* 3.1 12.6 + - + +
149A ARG* 2.9 34.4 + - - +
317A VAL* 3.5 24.9 - - + -
318A HIS* 3.4 26.0 + - - +
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Residues in contact with SER 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* 2.9 20.7 + - - +
143A ASP* 3.8 9.5 + - - -
145A TYR* 1.3 75.3 - - - +
147A GLU* 1.3 58.1 + - - +
149A ARG* 3.1 25.5 + - - +
150A LEU* 2.9 34.8 + - - +
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Residues in contact with GLU 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 ASP* 2.9 26.9 + - + +
144A LEU* 3.3 8.5 + - + +
146A SER* 1.3 76.7 - - - +
148A LEU* 1.3 58.2 + - + +
150A LEU* 3.3 27.1 + - - +
151A TYR* 2.9 26.3 + - - +
156A ASN* 5.1 8.5 + - - +
162A THR* 3.5 33.7 - - - +
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Residues in contact with LEU 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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115A LEU* 4.2 10.5 - - + -
144A LEU* 2.9 28.0 + - + +
145A TYR* 3.1 22.4 + - + +
147A GLU* 1.3 76.5 - - + +
149A ARG* 1.3 59.7 + - - +
151A TYR* 3.2 21.9 + - + +
152A TYR* 2.9 28.1 + - - +
159A LEU* 5.0 12.3 - - + -
163A LEU* 5.4 8.1 - - + -
213A ALA* 5.2 9.2 - - + -
217A PHE* 4.0 24.2 - - + -
317A VAL* 3.6 30.5 - - + -
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Residues in contact with ARG 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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112A GLN* 4.1 19.1 - - - +
115A LEU* 3.6 22.9 - - + +
116A ASN* 2.5 45.3 + - - +
119A GLU* 2.9 32.7 + - - -
142A ARG 5.0 0.4 + - - -
145A TYR* 2.9 18.6 + - - +
146A SER* 3.1 28.1 + - - +
148A LEU* 1.3 77.2 - - - +
150A LEU* 1.3 56.0 + - + +
152A TYR* 3.2 8.6 + - - +
153A ARG* 2.9 40.6 + - - +
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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 SER* 2.9 19.2 + - - +
147A GLU* 3.5 33.9 - - - +
148A LEU 3.3 0.2 - - - -
149A ARG* 1.3 73.4 - - + +
151A TYR* 1.3 65.0 + - - +
153A ARG* 3.3 30.3 + - - +
154A GLY 3.2 3.3 + - - -
155A ALA* 3.1 39.9 + - + +
156A ASN* 3.5 11.0 + - + -
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Residues in contact with TYR 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 GLU 2.9 14.5 + - - +
148A LEU* 3.2 17.7 + - + +
150A LEU* 1.3 78.3 - - - +
152A TYR* 1.3 59.9 + - - +
154A GLY* 3.3 10.4 + - - -
156A ASN* 3.0 32.7 - - + +
157A LEU* 4.0 18.6 + - - -
158A HIS 5.2 0.2 - - - -
159A LEU* 3.7 42.4 - - + +
213A ALA 4.4 0.7 - - - -
214A THR* 3.3 21.2 - - - +
217A PHE* 3.8 33.6 - + + +
218A VAL* 3.2 22.7 - - + +
221A ARG* 3.5 30.4 + - - -
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Residues in contact with TYR 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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108A ASP* 2.7 29.8 + - - -
111A PHE* 3.5 28.1 - + + +
112A GLN* 3.6 31.0 - - + -
115A LEU* 5.9 0.7 - - + -
148A LEU 2.9 13.2 + - - +
149A ARG* 3.2 10.3 + - + +
151A TYR* 1.3 79.4 - - - +
153A ARG* 1.3 61.7 + - + +
154A GLY 3.1 0.4 - - - -
217A PHE* 3.7 28.3 - + + -
220A ALA* 3.9 29.6 - - + -
221A ARG* 3.1 39.7 - - + +
224A VAL* 3.5 17.9 - - + +
314A ILE* 6.1 1.1 - - + -
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Residues in contact with ARG 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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112A GLN* 4.5 18.4 - - - +
149A ARG* 2.9 26.7 + - - +
150A LEU* 3.3 32.3 + - - +
151A TYR 3.3 0.4 - - - -
152A TYR* 1.3 80.7 - - + +
154A GLY* 1.3 60.6 + - - +
155A ALA* 4.1 10.9 - - + +
221A ARG* 4.7 2.7 - - - +
225A GLN* 5.7 0.7 + - - -
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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