Contacts of the helix formed by residues 137 - 150 (chain D) in PDB entry 4O2E
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 ASP 137 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85D TYR* 2.7 33.9 + - - -
123D TYR* 5.1 1.1 - - - -
135D ALA* 3.4 0.6 - - - +
136D ALA* 1.3 83.1 - - - +
138D THR* 1.3 66.8 + - - +
139D ALA* 3.1 5.7 + - - -
140D ALA* 3.0 23.6 + - - +
141D GLN* 3.1 30.7 + - - +
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Residues in contact with THR 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D ASP* 1.3 76.5 - - - +
139D ALA* 1.3 64.5 + - - +
141D GLN* 3.2 34.8 + - - +
142D ILE* 3.3 13.2 + - - +
145D ARG* 4.7 1.7 + - - -
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Residues in contact with ALA 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D TYR* 3.7 27.9 - - + +
85D TYR* 3.4 40.8 - - + +
123D TYR* 3.2 11.6 + - - +
137D ASP* 3.1 1.9 + - - +
138D THR* 1.3 82.8 + - - +
140D ALA* 1.3 57.8 + - - +
142D ILE* 2.9 31.4 + - - +
143D THR 3.3 1.6 + - - -
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Residues in contact with ALA 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D TYR* 3.0 53.7 + - + +
124D ILE* 3.9 4.2 - - + +
135D ALA* 3.6 17.3 - - + +
136D ALA 3.8 1.3 - - - +
137D ASP* 3.0 16.2 + - - +
139D ALA* 1.3 75.8 - - - +
141D GLN* 1.3 57.4 + - - +
143D THR* 3.2 3.6 + - - -
144D GLN* 2.8 27.2 + - - +
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Residues in contact with GLN 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D ALA* 3.8 17.6 + - + +
137D ASP* 3.1 25.4 + - - +
138D THR* 3.3 24.9 - - - +
139D ALA 3.1 1.0 - - - -
140D ALA* 1.3 76.0 - - - +
142D ILE* 1.3 63.5 + - - +
144D GLN* 3.2 10.1 + - - +
145D ARG* 3.0 44.4 + - - +
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Residues in contact with ILE 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D TYR* 3.7 45.8 - - + +
138D THR 3.3 12.5 + - - +
139D ALA* 2.9 12.4 + - - +
141D GLN* 1.3 74.4 - - - +
143D THR* 1.3 65.5 + - - +
145D ARG* 3.3 29.2 + - - +
146D LYS* 3.1 25.7 + - + +
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Residues in contact with THR 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D TYR* 3.7 1.2 - - - -
123D TYR* 2.9 31.1 + - + -
124D ILE* 4.2 4.7 - - + -
139D ALA 3.3 0.8 + - - -
140D ALA 3.2 8.8 + - - -
142D ILE* 1.3 78.0 - - - +
144D GLN* 1.3 58.4 + - - +
146D LYS* 3.2 7.3 + - - +
147D TRP* 2.9 69.8 + - + +
9F LEU* 2.7 33.1 + - + +
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Residues in contact with GLN 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D ILE* 4.0 11.4 - - + -
133D TRP* 3.6 39.8 + - + +
135D ALA* 3.5 22.1 + - - +
140D ALA 2.8 12.5 + - - +
141D GLN* 3.4 15.3 - - - +
142D ILE 3.2 0.4 - - - -
143D THR* 1.3 77.1 - - - +
145D ARG* 1.3 57.8 + - + +
147D TRP* 3.3 3.8 + - - +
148D GLU* 2.8 63.4 + - + +
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Residues in contact with ARG 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D THR 4.7 1.2 + - - -
141D GLN* 3.0 42.9 + - - +
142D ILE* 3.6 34.8 - - - +
143D THR 3.3 0.2 - - - -
144D GLN* 1.3 71.1 - - + +
146D LYS* 1.3 66.5 + - - +
148D GLU* 4.0 12.9 - - - +
149D ALA* 3.1 23.4 + - - +
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Residues in contact with LYS 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ASN* 3.4 12.5 - - - +
84D TYR* 3.1 14.1 + - - -
142D ILE* 3.1 12.9 + - + +
143D THR* 3.3 9.0 - - - +
145D ARG* 1.3 79.9 - - - +
147D TRP* 1.3 62.9 + - + +
149D ALA* 3.2 8.3 + - - +
150D ALA* 3.1 26.7 + - - +
8F ALA* 3.8 11.5 + - - +
9F LEU* 2.8 41.2 + - - +
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Residues in contact with TRP 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D ASN* 5.0 0.2 - - - -
116D PHE* 3.4 40.6 - + - -
124D ILE* 3.8 20.9 - - + -
133D TRP* 3.7 37.5 - + + +
143D THR* 2.9 28.8 + - + +
144D GLN* 3.9 3.4 - - - +
146D LYS* 1.3 81.8 - - + +
148D GLU* 1.3 60.9 + - - +
150D ALA* 3.3 1.7 + - + -
151D ARG 2.9 6.9 + - - -
152D VAL* 2.9 56.0 + - + +
153D ALA 4.6 0.3 + - - -
7F ASN* 3.6 29.1 - - + +
8F ALA 3.0 20.6 + - - -
9F LEU* 3.6 26.2 - - + -
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Residues in contact with GLU 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D SER* 6.0 0.7 - - - -
133D TRP* 4.1 19.4 + - + +
144D GLN* 2.8 53.8 + - - +
145D ARG* 4.0 13.8 - - - +
147D TRP* 1.3 72.9 - - - +
149D ALA* 1.3 61.0 + - - +
151D ARG* 3.3 21.3 + - - +
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Residues in contact with ALA 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D ARG 3.1 18.5 + - - +
146D LYS* 3.4 6.3 - - - +
148D GLU* 1.3 76.7 - - - +
150D ALA* 1.3 60.0 + - - +
151D ARG* 3.3 8.3 + - - +
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Residues in contact with ALA 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D LYS 3.1 14.1 + - - +
147D TRP* 3.3 5.1 + - + +
148D GLU 3.2 0.2 - - - -
149D ALA* 1.3 76.9 - - - +
151D ARG* 1.3 71.3 + - - +
152D VAL* 3.2 13.1 + - + -
155D GLN* 3.3 13.9 - - - +
7F ASN* 4.3 10.1 - - - +
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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