Contacts of the helix formed by residues 140 - 151 (chain D) in PDB entry 1DE4
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 140 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123D HIS* 3.3 55.1 - - + +
124D LEU* 4.0 3.4 - - + +
135D ALA* 3.6 8.1 - - + -
137D GLU* 2.9 16.4 + - + +
138D PRO 2.9 0.6 + - - -
139D ARG* 1.3 75.6 - - - +
141D TRP* 1.3 64.6 + - - +
142D PRO* 3.3 4.1 - - - -
143D THR* 3.3 7.8 + - - -
144D LYS* 3.0 19.4 + - - +
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Residues in contact with TRP 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* 3.4 28.5 + - + +
137D GLU 3.5 10.8 + - - -
138D PRO* 3.1 21.8 + - + +
140D ALA* 1.3 74.7 - - - +
142D PRO* 1.3 72.4 - - + +
144D LYS* 3.3 39.2 - - + +
145D LEU* 3.0 47.3 + - + +
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Residues in contact with PRO 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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86D ASN* 3.9 33.2 - - + +
138D PRO 3.7 2.9 - - - +
139D ARG* 3.3 19.1 - - - +
140D ALA 3.3 5.4 - - - -
141D TRP* 1.3 94.2 - - + +
143D THR* 1.3 56.5 + - - +
145D LEU* 3.1 8.0 + - + +
146D GLU* 2.9 28.4 + - - +
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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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82D THR* 4.3 3.0 - - + +
83D ILE* 3.6 22.4 - - + +
86D ASN* 3.1 24.1 + - - +
87D HIS* 5.7 0.2 - - - -
123D HIS* 4.8 3.9 + - - -
124D LEU* 3.6 22.7 - - + -
139D ARG 5.4 1.0 + - - -
140D ALA 3.3 9.2 + - - -
142D PRO* 1.3 75.6 - - - +
144D LYS* 1.3 69.2 + - - +
146D GLU* 4.2 4.7 - - - -
147D TRP* 3.0 55.2 + - + +
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Residues in contact with LYS 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 LEU* 4.0 15.0 - - + +
132D ASP* 4.9 2.6 - - - +
133D TRP* 2.9 30.5 + - + +
134D ARG* 4.4 1.6 - - - +
135D ALA* 4.3 10.8 - - + +
140D ALA 3.0 14.8 + - - +
141D TRP* 3.3 55.3 - - + +
143D THR* 1.3 79.5 - - - +
145D LEU* 1.3 62.9 + - + +
147D TRP* 3.3 3.1 + - - +
148D GLU* 3.0 62.7 + - - +
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Residues in contact with LEU 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 TRP* 3.0 40.7 + - + +
142D PRO* 3.6 7.0 - - + +
144D LYS* 1.3 75.2 - - + +
146D GLU* 1.3 66.7 + - - +
148D GLU* 2.9 25.5 + - - +
149D ARG* 2.9 54.8 + - - +
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Residues in contact with GLU 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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82D THR* 3.8 7.2 - - - +
86D ASN* 3.1 16.6 + - - +
142D PRO 2.9 16.0 + - - +
143D THR* 3.8 5.6 - - - +
145D LEU* 1.3 75.4 - - - +
147D TRP* 1.3 59.8 + - + +
149D ARG* 3.9 13.7 + - - +
150D HIS 4.1 3.6 + - - -
629F ARG* 2.5 43.1 + - - -
638F SER* 4.7 10.4 + - - +
639F LEU 5.2 4.7 + - - -
640F GLN* 3.1 36.6 + - - +
643F TYR* 4.6 0.7 - - - -
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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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79D ASP* 3.7 25.7 + - + -
82D THR* 4.4 8.9 + - + +
83D ILE* 4.6 4.5 - - + -
116D TYR* 3.5 46.0 - + - -
124D LEU* 4.1 17.9 - - + -
133D TRP* 3.5 56.5 - + + -
143D THR* 3.0 39.6 + - + +
144D LYS 3.8 2.5 - - - +
146D GLU* 1.3 79.0 - - + +
148D GLU* 1.3 64.0 + - - +
149D ARG 3.3 1.6 + - - -
150D HIS* 3.5 15.9 - - - +
151D LYS* 3.8 4.0 + - - -
153D ARG* 3.4 32.2 - - - +
154D ALA* 5.4 0.3 + - - +
640F GLN* 3.4 26.1 + - - +
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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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131D LEU 5.1 2.9 - - - +
132D ASP* 2.8 32.8 - - + +
133D TRP* 3.1 24.3 + - + -
144D LYS* 3.0 56.5 + - - +
145D LEU* 2.9 14.8 + - - +
147D TRP* 1.3 77.2 - - - +
149D ARG* 1.3 73.3 + - - +
151D LYS* 3.3 31.1 + - - +
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Residues in contact with ARG 149 (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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900C NAG 3.8 9.7 - - - +
145D LEU* 2.9 65.1 + - - +
146D GLU* 4.2 9.0 - - - +
147D TRP 3.3 0.2 - - - -
148D GLU* 1.3 85.4 + - - +
150D HIS* 1.3 66.8 + - - +
151D LYS* 3.1 18.2 - - - +
638F SER* 5.9 6.5 - - - +
641F TRP* 4.4 3.6 - - + -
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Residues in contact with HIS 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 GLU 4.1 1.4 + - - -
147D TRP 3.5 12.1 - - - +
149D ARG* 1.3 79.4 - - - +
151D LYS* 1.3 58.3 + - - +
152D ILE* 2.8 33.1 + - + +
153D ARG* 3.1 36.8 - - + -
640F GLN* 3.0 58.9 + - + +
641F TRP* 3.1 55.4 + + - +
644F SER* 3.2 25.8 - - - -
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Residues in contact with LYS 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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900C NAG 3.5 30.5 - - + +
147D TRP 3.8 6.8 + - - -
148D GLU* 3.3 23.4 + - - +
149D ARG* 3.1 16.7 - - - +
150D HIS* 1.3 76.8 - - - +
152D ILE* 1.3 62.3 + - + +
153D ARG 3.5 0.7 - - - -
154D ALA* 3.8 10.1 + - - +
155D ARG* 3.0 31.1 + - - +
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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