Contacts of the helix formed by residues 145 - 154 (chain N) in PDB entry 3J0S
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 145 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68N TYR* 3.6 17.6 + - - -
141N GLU* 3.0 28.1 + - - +
142N GLU* 3.9 10.2 - - - +
143N VAL 3.4 1.0 - - - -
144N LYS* 1.3 84.4 - - - +
146N ARG* 1.3 64.9 + - - +
147N CYS* 3.2 10.4 + - + +
148N THR* 3.5 15.0 + - - +
149N LEU 4.1 0.2 + - - -
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Residues in contact with ARG 146 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66N ASP* 5.0 13.5 + - - -
68N TYR* 3.6 35.3 + - - +
69N ALA* 5.5 1.0 - - - +
144N LYS 3.5 12.5 + - - -
145N ASP* 1.3 70.6 - - - +
147N CYS* 1.3 65.7 + - - +
149N LEU* 3.3 2.8 + - - +
150N ALA* 3.1 8.7 + - - +
161N LEU* 3.1 54.3 - - + +
162N GLU* 5.5 3.6 - - - +
165N PRO* 3.1 43.6 - - + +
166N LEU* 4.0 17.5 - - + -
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Residues in contact with CYS 147 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C LYS* 6.3 0.9 - - - -
145N ASP* 3.2 7.4 - - + +
146N ARG* 1.3 80.1 - - - +
148N THR* 1.3 57.7 + - - +
150N ALA* 3.1 10.1 + - - +
151N GLU* 2.8 33.3 + - - +
166N LEU* 5.1 6.4 - - + +
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Residues in contact with THR 148 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68N TYR* 5.0 2.7 - - - +
135N LEU* 3.3 34.7 - - + +
136N GLN 5.6 6.7 - - - +
137N ALA* 6.0 2.0 - - + -
142N GLU* 3.2 37.0 + - + +
145N ASP* 3.5 9.8 + - - +
146N ARG 3.3 1.0 - - - -
147N CYS* 1.3 77.8 - - - +
149N LEU* 1.3 61.8 + - - +
151N GLU* 3.4 25.6 + - - +
152N LYS 3.9 0.5 + - - -
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Residues in contact with LEU 149 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68N TYR* 3.7 42.8 + - + +
85N TYR* 4.1 18.8 - - + -
87N ALA* 4.6 19.1 - - + +
89N TYR* 5.4 2.2 - - + -
100N VAL* 6.0 0.9 - - + -
135N LEU* 3.9 16.1 - - + +
145N ASP 4.1 0.8 + - - -
146N ARG 3.3 3.3 + - - +
148N THR* 1.3 77.6 - - - +
150N ALA* 1.3 61.3 + - - +
152N LYS* 3.3 38.0 - - + +
153N LEU* 3.7 10.9 - - + +
161N LEU* 3.4 32.3 - - + -
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Residues in contact with ALA 150 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146N ARG 3.1 12.7 + - - +
147N CYS* 3.1 13.1 + - - +
149N LEU* 1.3 75.5 - - - +
151N GLU* 1.3 62.3 + - - +
152N LYS 3.2 0.2 - - - -
153N LEU* 3.0 35.6 - - + +
154N GLY 3.2 5.2 + - - -
155N GLY* 3.4 16.7 + - - -
158N VAL* 5.4 2.0 - - + -
161N LEU* 4.0 2.2 - - + +
166N LEU* 3.8 23.8 - - + -
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Residues in contact with GLU 151 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291C LYS* 3.4 30.1 - - + +
292C ASP* 3.4 22.3 - - - +
326C LYS* 5.8 2.3 + - - -
135N LEU* 5.6 2.1 - - - +
147N CYS* 2.8 21.2 + - - +
148N THR* 3.4 22.9 - - - +
149N LEU 3.3 0.2 - - - -
150N ALA* 1.3 72.7 - - - +
152N LYS* 1.3 62.8 + - - +
154N GLY* 3.3 17.6 + - - +
155N GLY* 5.5 0.4 - - - -
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Residues in contact with LYS 152 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87N ALA* 4.9 2.5 - - + -
98N ASP* 4.1 21.1 - - + +
100N VAL* 3.1 36.8 - - + -
133N HIS* 4.1 30.0 + - + +
134N GLU 6.2 0.2 - - - +
135N LEU* 3.2 39.2 - - + +
148N THR 3.9 2.3 + - - +
149N LEU* 3.3 24.9 + - + +
151N GLU* 1.3 79.9 - - - +
153N LEU* 1.3 71.1 + - + +
154N GLY 3.5 0.3 + - - -
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Residues in contact with LEU 153 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89N TYR* 3.2 56.5 - - + +
98N ASP* 4.3 1.3 - - - +
149N LEU* 3.7 12.3 - - + +
150N ALA* 3.0 27.8 - - + +
152N LYS* 1.3 97.1 - - + +
154N GLY* 1.3 56.0 + - - +
155N GLY 3.7 0.4 - - - -
158N VAL* 3.5 40.1 - - + +
161N LEU* 5.3 5.2 - - + -
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Residues in contact with GLY 154 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150N ALA 3.2 4.5 + - - -
151N GLU* 3.3 10.6 + - - +
152N LYS 3.3 3.2 - - - -
153N LEU* 1.3 78.8 - - - +
155N GLY* 1.3 58.8 + - - +
156N SER* 3.4 8.0 + - - -
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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