Contacts of the helix formed by residues 145 - 153 (chain D) in PDB entry 3REO
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 TYR 145 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141D GLU* 3.5 32.4 + - - -
142D PRO 2.8 9.4 + - - +
144D PHE* 1.3 85.8 - - + +
146D LEU* 1.3 65.2 + - - +
147D LYS 3.4 2.2 - - - -
148D ASP* 3.2 21.5 + - + +
149D ALA* 3.0 22.7 + - - +
156D PRO* 3.7 18.2 - - + +
159D LYS* 3.7 29.2 + - + +
160D ALA* 3.6 30.9 + - + -
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Residues in contact with LEU 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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36B MET 4.3 0.9 - - - +
37B ALA* 4.1 14.8 - - + -
40B ALA* 3.6 24.7 - - + -
79B MET* 5.1 0.9 - - + -
83B VAL* 4.4 11.7 - - + -
142D PRO 3.5 2.6 + - - +
143D TRP* 3.4 46.4 + - + +
144D PHE 3.6 0.2 - - - -
145D TYR* 1.3 76.5 - - - +
147D LYS* 1.3 67.5 + - - +
149D ALA* 3.0 2.4 + - - -
150D ILE* 3.0 32.2 + - + +
156D PRO* 3.7 20.6 - - + -
324D LEU* 4.2 26.9 - - + -
325D ALA* 5.1 1.6 - - - -
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Residues in contact with LYS 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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40B ALA* 4.3 12.6 - - - +
43B GLU* 3.7 42.9 + - + +
44B LEU* 3.6 31.3 - - + +
143D TRP 5.1 0.2 + - - -
144D PHE 5.2 2.6 + - - +
145D TYR 3.4 0.2 - - - -
146D LEU* 1.3 76.5 - - - +
148D ASP* 1.3 76.1 + - - +
150D ILE* 3.2 4.0 + - - +
151D LEU* 2.9 51.7 + - + +
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Residues in contact with ASP 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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144D PHE 3.7 7.6 - - - +
145D TYR* 3.3 33.7 - - + +
146D LEU 3.1 0.2 - - - -
147D LYS* 1.3 95.3 - - - +
149D ALA* 1.3 53.2 + - - +
151D LEU* 4.7 4.3 - - - -
152D GLU* 2.6 41.7 + - + +
159D LYS* 4.0 16.6 - - + -
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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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73B ASN* 3.4 3.5 + - - -
79B MET* 3.6 11.3 - - + +
145D TYR 3.0 6.5 + - - +
146D LEU 3.0 3.1 + - - +
148D ASP* 1.3 75.8 - - - +
150D ILE* 1.3 58.8 + - - +
153D GLY* 2.8 28.5 + - - -
154D GLY 3.5 20.0 - - - +
156D PRO* 3.5 35.2 - - + -
159D LYS* 3.7 13.7 - - - +
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Residues in contact with ILE 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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40B ALA* 5.1 2.5 - - + -
44B LEU* 3.9 31.2 - - + -
69B LEU* 4.5 9.2 - - + -
71B THR* 3.8 0.2 + - - -
73B ASN* 2.9 20.3 + - - +
76B ALA* 3.6 19.8 - - + +
79B MET* 3.8 30.5 - - + +
80B LEU* 4.2 22.7 - - + -
83B VAL* 4.2 20.2 - - + -
146D LEU* 3.0 34.5 + - + +
147D LYS* 3.6 5.8 - - - +
149D ALA* 1.3 76.6 - - - +
151D LEU* 1.3 59.5 + - - +
324D LEU* 5.5 0.4 - - + -
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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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44B LEU* 3.6 27.1 - - + -
69B LEU* 4.1 26.7 - - + -
70B PRO* 4.1 29.1 - - + +
71B THR* 2.8 26.3 + - - -
72B THR 4.6 0.9 + - - -
73B ASN* 3.6 2.6 + - - +
147D LYS* 2.9 44.9 + - + +
148D ASP* 4.0 3.4 - - - +
150D ILE* 1.3 78.2 - - - +
152D GLU* 1.3 62.1 + - + +
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Residues in contact with GLU 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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73B ASN* 4.2 5.9 - - - +
148D ASP* 2.6 22.7 + - + +
151D LEU* 1.3 75.4 - - + +
153D GLY* 1.3 59.2 + - - +
159D LYS* 4.0 17.4 + - - +
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Residues in contact with GLY 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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73B ASN* 3.4 24.2 - - - +
75B GLU* 6.0 0.4 - - - -
79B MET* 5.3 0.9 - - - -
149D ALA 2.8 19.0 + - - +
152D GLU* 1.3 79.4 - - - +
154D GLY* 1.3 61.1 + - - -
159D LYS* 2.9 28.2 + - - -
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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