Contacts of the helix formed by residues 143 - 148 (chain A) in PDB entry 3DGR
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 TRP 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A HIS* 6.1 0.9 - - + +
23A TYR* 3.7 28.5 - - + +
26A TYR* 4.5 12.2 - - + -
97A ASN* 3.7 19.9 - - + +
100A GLY* 3.8 23.5 - - - -
101A TRP* 3.5 51.4 - + - -
104A ILE* 3.7 24.5 - - + -
140A GLU 3.2 26.2 + - - -
141A CYS* 3.8 7.5 - - - +
142A TYR* 1.3 100.4 - + + +
144A LEU* 1.3 78.0 + - + +
145A THR 3.4 0.6 + - - -
146A ASN* 3.8 3.5 + - - +
147A TRP* 3.4 33.4 + + - +
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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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101A TRP* 4.1 24.0 - - + -
104A ILE* 4.0 8.5 - - + -
112A LEU* 4.2 10.8 - - + -
113A PRO* 3.4 36.1 - - + +
114A ILE* 3.5 24.2 - - + -
141A CYS* 2.9 18.6 + - + +
143A TRP* 1.3 98.4 - - + +
145A THR* 1.3 66.1 + - - +
146A ASN 3.2 0.5 + - - -
147A TRP* 3.2 14.5 + - + +
148A ILE* 3.5 26.0 + - + +
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Residues in contact with THR 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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33A VAL* 2.7 40.3 + - + +
35A SER* 3.7 13.0 - - - +
114A ILE* 3.8 10.3 - - - +
134A VAL* 3.4 25.8 - - + +
135A GLU 3.6 0.5 - - - -
136A ASN* 3.1 24.6 + - - +
142A TYR 3.8 0.9 + - - -
143A TRP 3.4 0.4 - - - -
144A LEU* 1.3 80.5 - - - +
146A ASN* 1.3 72.7 + - - +
148A ILE* 3.3 17.2 + - - +
149A GLU 3.9 2.9 + - - -
399A PHE* 3.9 7.1 - - - -
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Residues in contact with ASN 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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19A LYS* 2.7 27.5 + - - +
22A HIS* 5.6 2.5 - - + +
26A TYR* 3.5 22.6 + - - +
33A VAL* 3.9 4.1 - - - +
35A SER* 2.7 25.4 + - - -
142A TYR 5.0 0.4 + - - -
143A TRP 3.8 4.2 + - - +
145A THR* 1.3 83.2 - - - +
147A TRP* 1.3 66.6 + - - +
148A ILE 3.1 1.6 - - - -
149A GLU* 3.2 21.9 + - - +
399A PHE* 3.6 13.5 + - - -
400A LYS* 5.4 0.6 - - - +
401A CYS 5.0 2.6 - - - +
246B GLU* 2.8 25.4 + - - +
248B SER* 3.6 12.5 + - - -
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Residues in contact with TRP 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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11A ILE* 3.2 23.1 + - + -
12A LEU* 3.2 25.6 - - - -
14A ALA 4.9 2.3 - - - +
15A THR* 2.7 46.8 + - + -
19A LYS* 4.2 15.9 - - - +
20A VAL* 3.7 40.6 - - + -
23A TYR* 6.3 0.4 - + - -
96A PHE* 4.4 11.7 - + - -
97A ASN* 5.6 5.4 - - + -
101A TRP* 3.5 40.7 - + - -
143A TRP* 3.4 31.9 + + + +
144A LEU* 3.2 17.2 + - + +
146A ASN* 1.3 77.2 - - - +
148A ILE* 1.3 70.8 + - + +
149A GLU 3.3 0.7 + - - -
150A THR* 4.2 2.4 + - - -
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Residues in contact with ILE 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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11A ILE* 4.1 26.0 - - + -
70A LEU* 4.3 14.4 - - + -
112A LEU* 4.3 4.9 - - + -
114A ILE* 4.1 23.8 - - + -
116A ILE* 4.8 0.4 - - + -
134A VAL* 3.8 16.8 - - + -
144A LEU* 3.5 22.0 - - + +
145A THR 3.3 14.1 - - - +
147A TRP* 1.3 81.2 - - + +
149A GLU* 1.3 66.5 + - - +
150A THR 3.2 2.0 - - - -
151A ILE* 3.5 14.2 - - + +
152A LEU* 3.2 44.6 + - + +
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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