Contacts of the helix formed by residues 135 - 149 (chain A) in PDB entry 1A16
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 ALA 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A TYR* 1.3 72.0 - - - +
136A TYR* 1.3 57.8 + - - +
138A ASP* 3.3 9.6 + - - +
139A VAL* 3.0 35.4 + - + +
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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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28A PHE* 3.6 24.6 - + + +
29A ALA* 2.6 42.1 + - - +
30A ALA 4.9 0.8 + - - -
31A PRO* 4.1 24.7 - - + -
59A GLU* 4.9 4.9 + - + -
60A ALA 4.1 7.3 + - - -
110A PHE* 4.1 22.2 - + - -
134A TYR* 3.3 22.6 - + + -
135A ALA* 1.3 79.5 - - - +
137A ALA* 1.3 65.5 + - + +
139A VAL* 3.5 7.3 + - - +
140A ILE* 3.2 38.9 + - + +
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Residues in contact with ALA 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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28A PHE* 3.6 45.3 - - + -
129A HIS* 4.3 7.6 - - + -
130A ALA 5.9 0.7 - - - +
133A GLU* 6.1 0.7 - - + -
134A TYR* 3.1 24.6 + - + +
136A TYR* 1.3 80.6 - - + +
138A ASP* 1.3 59.6 + - - +
140A ILE* 3.2 3.8 + - - +
141A VAL* 2.9 34.7 + - - +
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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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129A HIS* 2.9 28.7 + - - -
130A ALA 4.2 0.9 - - - +
131A GLN* 3.8 8.8 - - - +
132A GLY* 3.0 34.9 + - - -
133A GLU 4.6 0.3 + - - -
134A TYR 3.1 14.0 + - - +
135A ALA* 3.3 9.9 + - - +
137A ALA* 1.3 75.9 - - - +
139A VAL* 1.3 57.6 + - + +
141A VAL 4.5 0.2 - - - +
142A ASN* 2.8 48.7 + - - +
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Residues in contact with VAL 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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135A ALA* 3.0 23.5 + - + +
136A TYR* 3.8 8.1 - - - +
137A ALA 3.3 0.2 - - - -
138A ASP* 1.3 74.7 - - + +
140A ILE* 1.3 61.6 + - + +
142A ASN* 3.9 5.5 - - - +
143A SER* 2.8 40.3 + - - +
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Residues in contact with ILE 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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28A PHE* 4.0 20.4 - - + -
110A PHE* 4.1 12.1 - - + -
113A ILE* 4.0 31.6 - - + -
114A ASN* 4.1 27.3 + - - +
117A LEU* 3.7 26.5 - - + +
136A TYR* 3.2 29.7 + - + +
137A ALA 3.5 7.2 - - - +
139A VAL* 1.3 80.0 - - + +
141A VAL* 1.3 64.1 + - - +
143A SER* 3.4 17.2 + - - -
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Residues in contact with VAL 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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26A LEU* 3.7 19.3 - - + -
28A PHE* 3.7 16.6 - - + -
117A LEU* 4.5 6.6 - - + +
121A LEU* 5.4 2.7 - - + +
127A VAL* 5.0 3.6 - - + -
129A HIS* 3.5 33.7 - - + +
137A ALA 2.9 20.7 + - - +
138A ASP 4.0 2.5 - - - +
140A ILE* 1.3 72.9 - - - +
142A ASN* 1.3 68.4 + - - +
143A SER 3.3 0.3 + - - -
145A LEU* 3.3 31.4 + - + +
162A MET* 3.9 27.8 - - + -
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Residues in contact with ASN 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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131A GLN* 4.2 17.9 + - - +
138A ASP* 2.8 36.8 + - - +
139A VAL* 4.0 5.2 - - - +
141A VAL* 1.3 78.3 - - - +
143A SER* 1.3 56.6 + - - +
145A LEU* 3.8 10.3 - - - +
146A GLU* 3.0 35.5 + - + +
149A ARG* 4.8 2.4 + - - +
162A MET* 5.2 0.2 - - - +
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Residues in contact with SER 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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114A ASN* 4.4 14.9 + - - -
118A TYR* 5.7 1.8 - - - -
139A VAL* 2.8 28.6 + - - +
140A ILE* 3.6 13.4 - - - -
141A VAL 3.2 1.0 - - - -
142A ASN* 1.3 80.3 - - - +
145A LEU 3.1 25.4 + - - -
146A GLU* 4.1 5.5 - - - +
147A LYS* 3.2 42.5 + - - +
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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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118A TYR* 5.0 4.0 - - - +
121A LEU* 4.1 19.2 - - + +
127A VAL* 4.6 6.1 - - + -
141A VAL* 3.3 29.6 + - + +
142A ASN* 3.8 9.4 - - - +
143A SER 3.1 24.9 + - - -
146A GLU* 1.3 63.2 + - - +
147A LYS* 3.2 3.1 - - - +
148A LEU* 3.3 18.5 + - + +
149A ARG* 2.8 61.4 + - - +
158A ALA* 3.9 5.2 - - + +
159A PRO* 3.7 38.8 - - + +
162A MET* 3.9 28.5 - - + -
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Residues in contact with GLU 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 ASN* 3.0 22.8 + - + +
143A SER* 3.4 6.5 + - - +
145A LEU* 1.3 74.8 - - - +
147A LYS* 1.3 62.8 + - + +
149A ARG* 2.8 36.6 + - - +
150A LYS* 2.9 70.7 + - - +
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Residues in contact with LYS 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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114A ASN* 2.8 38.0 + - - +
115A GLN* 4.8 5.5 - - - +
118A TYR* 3.9 39.1 - - + -
143A SER* 3.2 24.5 + - - +
145A LEU 3.2 0.4 - - - -
146A GLU* 1.3 77.6 - - + +
148A LEU* 1.3 59.3 + - - +
150A LYS* 3.8 2.3 - - - +
151A GLY* 3.0 25.8 + - - -
156A LEU* 4.4 5.8 - - + +
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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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118A TYR* 3.4 44.0 - - + +
121A LEU* 3.7 30.5 - - + +
122A ASN* 3.8 13.0 - - + +
145A LEU* 3.3 14.5 + - + +
146A GLU 3.3 0.2 - - - -
147A LYS* 1.3 74.7 - - - +
149A ARG* 1.3 66.3 + - - +
151A GLY* 3.0 10.4 + - - -
156A LEU* 3.5 46.7 - - + +
157A THR* 3.9 4.9 - - - +
158A ALA* 3.4 27.1 - - + +
159A PRO* 4.2 2.9 - - + -
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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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142A ASN* 4.8 2.6 + - - +
145A LEU* 2.8 47.9 + - - +
146A GLU* 2.8 52.2 + - - +
148A LEU* 1.3 73.9 - - - +
150A LYS* 1.3 61.6 + - + +
151A GLY 3.7 0.2 + - - -
152A SER* 4.6 7.4 + - - -
158A ALA* 3.9 17.3 - - + +
159A PRO 5.7 3.0 + - - -
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Residues in contact with LYS 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 GLU* 2.9 48.7 + - - +
147A LYS* 3.8 2.7 - - - +
149A ARG* 1.3 78.6 - - + +
151A GLY* 1.3 58.1 + - - +
152A SER* 3.5 4.6 + - - -
153A ARG* 5.0 4.5 + - - -
154A GLN* 4.9 2.1 - - - +
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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