Contacts of the helix formed by residues 144 - 158 (chain N) in PDB entry 3H1J
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 144 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140N GLU 5.0 0.2 - - - +
141N MET* 3.1 11.3 + - - +
142N ASP 3.1 1.2 - - - -
143N ASN* 1.3 80.5 - - - +
145N MET* 1.3 53.5 + - - +
146N THR* 3.1 21.0 + - - -
147N ASN* 2.7 64.5 + - - +
148N VAL* 2.9 12.7 + - - +
47V ARG* 5.1 4.9 - - - +
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Residues in contact with MET 145 (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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142N ASP 3.7 20.4 - - - +
143N ASN* 3.7 14.3 + - - +
144N ASP* 1.3 71.8 + - - +
146N THR* 1.3 56.9 + - - +
148N VAL* 3.6 7.5 - - + +
149N THR* 2.7 37.3 + - - +
248N LEU* 3.7 36.1 - - + -
250N VAL* 5.2 4.7 - - + +
252N HIS* 2.8 42.0 - - + +
425N VAL* 4.3 14.1 - - + -
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Residues in contact with THR 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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144N ASP* 3.1 12.3 + - - -
145N MET* 1.3 78.4 - - - +
147N ASN* 1.3 67.4 + - - +
149N THR* 3.4 1.2 + - - -
150N PHE* 2.9 53.9 + - + -
252N HIS* 3.6 20.3 - - - -
308N GLN* 4.7 4.5 - - - +
323N HIS* 3.8 15.3 - - + -
325N VAL* 5.2 0.2 - - - +
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Residues in contact with ASN 147 (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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141N MET* 4.0 30.8 + - + +
144N ASP* 2.7 47.4 + - + +
146N THR* 1.3 73.3 - - - +
148N VAL* 1.3 67.7 + - - +
149N THR 2.8 2.7 + - - -
150N PHE* 2.8 16.1 + - - +
151N ASP* 2.9 23.0 + - - +
2R HIS* 5.3 2.0 - - + -
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Residues in contact with VAL 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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141N MET 4.1 1.1 - - - +
142N ASP* 3.2 33.7 - - - +
144N ASP 2.9 19.3 + - - +
145N MET* 3.6 13.7 - - + +
147N ASN* 1.3 70.8 - - - +
149N THR* 1.3 57.8 + - - +
151N ASP* 3.9 0.7 - - - +
152N TYR* 3.1 55.3 + - + +
425N VAL* 4.3 14.1 - - + -
2R HIS* 3.7 33.0 + - + +
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Residues in contact with THR 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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145N MET 2.7 25.8 + - - -
146N THR* 3.6 6.1 - - - -
147N ASN 2.8 1.0 + - - -
148N VAL* 1.3 73.3 - - - +
150N PHE* 1.3 58.9 + - + +
152N TYR* 4.5 1.6 - - - -
153N LEU* 2.9 24.8 + - - +
252N HIS* 3.2 24.3 - - + +
254N ALA* 3.7 30.5 - - + +
323N HIS* 4.0 13.5 - - + -
423N ALA* 3.6 15.4 - - + +
425N VAL* 3.5 17.2 - - + +
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Residues in contact with PHE 150 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92N ARG* 4.8 0.7 - - - +
146N THR* 2.9 48.4 + - + +
147N ASN* 2.8 9.8 + - - +
149N THR* 1.3 74.7 - - + +
151N ASP* 1.3 68.0 + - - +
153N LEU* 3.3 15.7 - - + +
154N HIS* 2.8 42.5 + + + +
254N ALA* 5.0 2.2 - - + -
308N GLN* 3.7 13.7 - - - -
310N PHE* 3.5 36.8 - + + -
312N THR* 5.8 2.7 - - - -
319N LEU* 6.2 0.2 - - + -
323N HIS* 3.7 29.8 - + + -
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Residues in contact with ASP 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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92N ARG* 3.0 23.9 + - - +
147N ASN* 2.9 17.4 + - - +
150N PHE* 1.3 77.8 - - - +
152N TYR* 1.3 52.4 + - + +
154N HIS* 2.9 6.8 + - - +
155N ALA* 2.5 35.8 + - - +
164N ALA 5.1 0.5 - - - +
166N THR* 3.3 27.9 - - + +
167N VAL 5.3 0.7 + - - -
168N GLU* 4.3 8.2 - - - +
2R HIS* 2.4 43.0 + - + +
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Residues in contact with TYR 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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148N VAL* 3.1 31.1 + - + +
149N THR 3.8 4.5 - - - +
151N ASP* 1.3 78.3 - - + +
153N LEU* 1.3 66.3 + - - +
155N ALA* 3.1 10.6 - - + +
156N THR 2.9 19.9 + - - -
241N ILE* 3.7 35.1 - - + +
243N ALA* 3.4 27.7 - - + +
423N ALA* 4.2 6.3 - - + -
424N ALA 5.2 1.1 - - - -
425N VAL* 4.0 12.6 - - + -
238Q ARG* 4.9 1.4 + - - -
2R HIS* 3.4 48.3 - + + +
5R VAL* 3.7 30.1 - - + +
14T ILE* 4.3 6.7 - - + +
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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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149N THR 2.9 17.4 + - - +
150N PHE* 3.3 18.8 - - + +
151N ASP 3.1 0.4 - - - -
152N TYR* 1.3 77.6 - - - +
154N HIS* 1.3 52.6 + - - +
156N THR* 3.5 2.5 - - - +
157N ALA* 2.7 37.6 + - + +
254N ALA* 4.0 24.2 - - + +
256N ALA* 4.2 8.3 - - + +
310N PHE* 3.7 30.3 - - + -
319N LEU* 3.9 22.4 - - + -
421N ALA* 3.6 36.1 - - + +
422N LEU 4.5 0.4 - - - -
423N ALA* 3.8 9.8 - - + +
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Residues in contact with HIS 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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92N ARG* 3.6 37.0 + - - +
150N PHE* 2.8 38.6 + + + +
151N ASP 2.9 7.2 + - - +
153N LEU* 1.3 75.4 - - - +
155N ALA* 1.3 65.4 + - - +
157N ALA* 4.4 0.7 - - - -
158N PHE* 2.9 44.6 + + - +
163N LEU* 3.6 15.9 - - + +
164N ALA* 3.5 10.6 - - - +
312N THR* 4.8 7.3 - - + +
314N TYR* 2.7 33.6 + + - -
319N LEU* 3.8 18.1 - - + +
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Residues in contact with ALA 155 (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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151N ASP 2.5 18.7 + - - +
152N TYR* 3.1 26.5 - - + +
154N HIS* 1.3 72.7 - - - +
156N THR* 1.3 55.2 + - - +
159N GLN* 3.3 15.4 - - - -
164N ALA* 3.7 21.2 + - - +
241N ILE* 5.1 4.0 - - + -
5R VAL 4.9 11.9 - - - +
6R THR* 5.8 0.7 - - - -
7R VAL* 2.9 24.1 + - + +
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Residues in contact with THR 156 (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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152N TYR 2.9 5.4 + - - +
153N LEU* 3.5 8.1 - - - +
155N ALA* 1.3 75.8 - - - +
157N ALA* 1.3 72.3 + - - +
158N PHE 3.2 2.0 - - - -
159N GLN* 3.0 24.8 + - - +
237N THR 4.0 0.5 - - - +
239N SER* 3.0 39.1 + - - +
240N GLU 3.8 9.2 + - - -
241N ILE* 3.5 31.2 - - + +
421N ALA* 4.6 0.7 - - + -
422N LEU 3.5 18.8 - - - +
7R VAL* 3.5 16.7 - - - +
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Residues in contact with ALA 157 (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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153N LEU* 2.7 25.5 + - + +
156N THR* 1.3 74.7 - - - +
158N PHE* 1.3 63.3 + - + +
159N GLN 3.9 0.2 + - - -
235N ARG 3.7 0.3 - - - +
236N PHE* 3.2 19.1 - - + -
237N THR 2.8 31.6 + - - +
319N LEU* 4.1 16.4 - - + -
421N ALA* 3.4 28.7 - - + -
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Residues in contact with PHE 158 (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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154N HIS* 2.9 37.1 + + - +
157N ALA* 1.3 79.5 - - + +
159N GLN* 1.3 69.4 + - - +
161N THR* 2.9 27.6 + - - +
163N LEU* 3.8 13.2 - - + -
164N ALA* 3.1 10.7 - - - +
234N CYS* 4.0 22.7 - - + -
235N ARG 3.9 5.8 - - - -
236N PHE* 4.4 14.8 - + + -
314N TYR* 4.6 5.8 - + - -
317N THR* 3.3 40.4 - - + -
318N GLY* 3.8 7.4 - - - -
319N LEU* 3.5 41.7 - - + -
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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