Contacts of the helix formed by residues 140 - 153 (chain D) in PDB entry 4J4L
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 140 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138D THR 3.6 3.6 + - - -
139D PRO* 1.3 69.2 - - - +
141D PRO* 1.4 71.2 - - - +
142D THR* 3.1 18.9 + - - -
143D THR* 2.8 45.4 + - - +
144D ASN* 3.4 22.7 + - - +
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Residues in contact with PRO 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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139D PRO 3.1 10.0 - - - +
140D ASP* 1.4 89.0 - - - +
142D THR* 1.3 61.7 + - - +
144D ASN* 3.5 19.7 - - + +
145D ALA* 3.5 9.4 + - - +
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Residues in contact with THR 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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140D ASP* 3.1 14.5 + - - -
141D PRO* 1.3 74.5 - - - +
143D THR* 1.3 68.3 + - - +
144D ASN 2.9 2.4 + - - -
145D ALA* 3.0 17.5 + - + +
146D SER* 3.5 11.0 + - - -
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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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140D ASP* 2.8 35.0 + - + +
142D THR* 1.3 72.4 - - - +
144D ASN* 1.3 66.0 + - - +
146D SER* 3.2 19.6 + - - -
147D LEU* 3.3 15.7 + - + +
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Residues in contact with ASN 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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92D LEU 5.7 1.2 + - - -
93D GLU* 6.3 0.2 - - - +
96D VAL* 3.7 39.6 - - + +
139D PRO* 3.8 25.0 + - - +
140D ASP 3.4 14.0 + - - +
141D PRO* 3.5 14.1 - - + +
142D THR 2.9 1.4 - - - -
143D THR* 1.3 83.9 - - - +
145D ALA* 1.3 57.5 + - - +
147D LEU* 3.3 10.9 + - - +
148D LEU* 3.1 28.7 + - - +
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Residues in contact with ALA 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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141D PRO 3.5 8.7 + - - +
142D THR* 3.0 11.9 + - + +
144D ASN* 1.3 75.6 - - - +
146D SER* 1.3 66.5 + - - +
148D LEU* 3.6 10.8 - - - +
149D THR* 3.2 24.1 + - - -
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Residues in contact with SER 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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142D THR 3.5 5.9 + - - -
143D THR* 3.2 17.5 + - - -
145D ALA* 1.3 78.9 - - - +
147D LEU* 1.3 57.2 + - - +
149D THR* 3.0 8.7 + - - +
150D LYS* 2.9 29.5 + - - +
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Residues in contact with LEU 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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62D LEU* 5.6 7.0 - - + -
63D ASN* 5.8 4.3 - - - +
96D VAL* 3.9 27.4 - - + -
97D TYR* 3.7 31.4 - - + +
143D THR* 3.3 16.5 + - + +
144D ASN* 3.3 14.6 - - - +
145D ALA 3.2 0.2 - - - -
146D SER* 1.3 80.5 + - - +
148D LEU* 1.3 57.3 + - - +
150D LYS* 3.2 20.1 - - + +
151D LEU* 3.0 34.0 + - + +
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Residues in contact with LEU 148 (chain D).
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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96D VAL* 4.0 16.6 - - + +
99D GLU* 4.7 17.9 - - + +
100D TYR* 3.9 40.2 - - + +
144D ASN 3.1 13.8 + - - +
145D ALA* 3.6 10.8 - - - +
147D LEU* 1.3 77.7 - - - +
149D THR* 1.3 64.0 + - - +
151D LEU* 3.4 6.3 + - + +
152D GLN* 3.2 46.3 + - - +
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Residues in contact with THR 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 ALA 3.2 11.8 + - - -
146D SER* 3.0 13.2 + - - -
148D LEU* 1.3 76.3 - - - +
150D LYS* 1.3 65.5 + - - +
152D GLN* 3.3 10.8 + - - +
153D ALA* 3.0 26.5 + - + +
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Residues in contact with LYS 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 SER 2.9 11.5 + - - +
147D LEU* 3.2 23.0 - - + +
149D THR* 1.3 77.2 - - - +
151D LEU* 1.3 66.0 + - + +
153D ALA* 3.3 17.4 + - - +
154D GLN* 3.8 14.5 + - + +
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Residues in contact with LEU 151 (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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62D LEU* 4.3 17.5 - - + -
97D TYR* 4.3 22.4 - - + -
100D TYR* 3.5 45.9 + - + -
147D LEU* 3.0 24.6 + - + +
148D LEU* 3.4 8.7 + - + +
149D THR 3.4 0.4 - - - -
150D LYS* 1.3 80.3 - - + +
152D GLN* 1.3 60.3 + - - +
153D ALA 3.6 0.2 + - - -
154D GLN* 3.6 25.8 + - - +
159D GLN* 3.3 22.9 + - - +
162D THR* 4.1 19.7 - - + +
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Residues in contact with GLN 152 (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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99D GLU 5.8 0.6 + - - -
100D TYR* 4.2 19.3 - - + +
103D ASN* 3.9 26.7 + - - +
148D LEU* 3.2 38.3 + - - +
149D THR* 3.3 8.4 + - - +
151D LEU* 1.3 76.3 - - - +
153D ALA* 1.3 58.5 + - - +
154D GLN 3.2 4.9 - - - +
159D GLN* 3.1 21.7 - - - +
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Residues in contact with ALA 153 (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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149D THR* 3.0 20.2 + - + +
150D LYS* 3.3 11.1 + - - +
152D GLN* 1.3 76.2 - - - +
154D GLN* 1.3 61.4 + - - +
155D ASN 4.1 0.2 + - - -
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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