Contacts of the helix formed by residues 137 - 154 (chain N) in PDB entry 5X6E
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 ASN 137 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133N ASP 4.0 3.5 + - - +
136N ILE* 1.3 104.6 - - + +
138N GLY* 1.3 65.4 + - - +
139N LYS 3.7 0.3 + - - -
140N LEU* 3.9 6.6 + - - +
141N GLY* 3.1 24.3 + - - -
216N ARG 5.0 2.6 + - - -
217N TYR* 3.2 44.6 + - + +
17P T 4.6 1.4 + - - -
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Residues in contact with GLY 138 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139M LYS* 4.4 14.2 - - - +
134N PHE 3.2 13.0 + - - +
135N SER 3.6 5.5 + - - -
136N ILE 3.5 2.8 + - - -
137N ASN* 1.3 77.8 - - - +
139N LYS* 1.3 55.3 + - - -
141N GLY 3.2 1.4 + - - -
142N SER* 2.7 40.1 + - - -
17P T 4.5 2.7 - - - -
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Residues in contact with LYS 139 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134M PHE 5.1 1.0 + - - -
135M SER* 3.3 28.4 + - - +
137M ASN 4.9 4.4 + - - -
138M GLY* 5.6 3.0 - - - -
138N GLY* 1.3 70.5 - - - -
140N LEU* 1.3 60.2 - - - +
142N SER* 3.0 13.4 + - - +
143N ILE* 2.9 33.8 + - - +
179N GLY* 3.6 27.3 - - - +
180N ILE* 3.8 17.9 - - + -
189N ILE* 4.3 11.9 - - + -
17P T 3.2 40.8 + - - +
18P G 3.7 24.4 + - - +
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Residues in contact with LEU 140 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137N ASN 4.2 4.9 - - - +
138N GLY 3.4 0.4 - - - -
139N LYS* 1.3 75.4 - - - +
141N GLY* 1.3 62.1 + - - +
143N ILE* 3.6 1.9 + - - +
144N CYS* 3.2 32.1 + - - -
189N ILE* 4.2 17.2 - - + +
192N LYS* 5.1 21.1 - - + +
193N LEU* 3.9 33.4 - - + -
213N TYR* 5.2 4.9 - - - +
217N TYR* 3.7 34.1 - - + +
16P T 5.8 2.7 - - - +
17P T 3.3 18.7 + - - +
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Residues in contact with GLY 141 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133N ASP 4.2 12.3 - - - +
134N PHE* 4.6 0.9 - - - -
137N ASN* 3.1 30.9 + - - +
138N GLY 3.5 4.3 - - - -
140N LEU* 1.3 76.6 - - - +
142N SER* 1.3 57.5 + - - +
143N ILE 3.3 0.2 + - - -
144N CYS* 3.3 3.9 + - - +
145N GLY* 2.9 27.0 + - - -
217N TYR* 4.3 14.0 - - - +
218N ALA* 4.9 0.3 - - - +
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Residues in contact with SER 142 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134N PHE* 3.4 47.3 + - - +
138N GLY 2.7 25.7 + - - -
139N LYS* 3.2 18.8 + - - +
141N GLY* 1.3 73.6 - - - +
143N ILE* 1.3 61.9 + - - +
146N GLN* 3.1 21.0 + - - +
178N SER* 3.9 21.2 - - - -
179N GLY 4.9 2.5 + - - -
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Residues in contact with ILE 143 (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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139N LYS 2.9 22.0 + - - +
140N LEU 4.0 4.0 - - - +
142N SER* 1.3 69.1 - - - +
144N CYS* 1.3 58.4 + - - +
146N GLN* 3.2 4.8 + - + +
147N LEU* 2.8 46.9 + - + +
174N LEU* 4.5 20.4 - - + +
175N GLY* 5.0 0.2 - - - -
178N SER* 3.3 24.9 - - - +
180N ILE* 3.7 22.2 - - + -
186N VAL* 4.9 9.4 - - + -
189N ILE* 4.1 15.9 - - + -
190N ILE* 4.3 9.4 - - + -
193N LEU* 3.7 25.8 - - + -
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Residues in contact with CYS 144 (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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140N LEU* 3.2 27.1 + - - +
141N GLY 3.7 4.3 - - - +
143N ILE* 1.3 79.5 - - - +
145N GLY* 1.3 57.3 + - - +
147N LEU* 4.3 0.7 - - - -
148N LEU* 3.0 29.8 + - - +
193N LEU* 4.0 27.4 - - - -
213N TYR* 4.4 3.1 - - - -
214N LEU* 3.7 30.8 - - + +
217N TYR* 3.7 37.0 - - + -
218N ALA* 4.5 2.2 - - - +
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Residues in contact with GLY 145 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134N PHE* 4.1 3.8 - - - -
141N GLY 2.9 15.2 + - - -
142N SER 3.8 1.8 - - - -
144N CYS* 1.3 72.9 - - - +
146N GLN* 1.3 65.5 + - - +
148N LEU* 3.0 5.5 + - - +
149N ILE* 3.0 24.3 + - - +
218N ALA* 3.6 23.6 - - - +
221N LEU* 3.7 15.7 - - - +
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Residues in contact with GLN 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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62N TYR* 3.8 18.6 - - - -
130N LYS* 3.7 24.8 + - - +
134N PHE* 4.0 7.0 - - + -
142N SER 3.1 16.3 + - - +
143N ILE* 3.8 4.7 - - + +
145N GLY* 1.3 73.1 - - - +
147N LEU* 1.3 62.7 + - - +
149N ILE* 3.2 12.9 + - - +
150N LEU* 3.0 53.1 + - + +
174N LEU* 3.7 20.2 - - + +
177N SER* 3.4 34.1 - - - +
178N SER* 5.3 4.0 - - - +
301N GSH 3.9 9.3 + - - -
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Residues in contact with LEU 147 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143N ILE* 2.8 42.0 + - + +
144N CYS 3.7 4.7 - - - +
146N GLN* 1.3 72.1 - - - +
148N LEU* 1.3 49.2 + - - +
150N LEU* 3.3 5.7 + - + +
151N THR* 2.6 42.0 + - - +
164N ILE* 4.2 21.4 - - + +
169N LEU* 5.8 0.2 - - + -
174N LEU* 4.2 24.5 - - + -
190N ILE* 4.7 3.1 - - + -
193N LEU* 4.3 4.5 - - + -
194N LYS* 4.2 20.0 - - - +
199N ILE* 4.5 12.1 - - + -
206N PHE* 4.8 10.5 - - + -
208N VAL* 5.2 4.3 - - + -
214N LEU* 4.1 20.4 - - + -
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Residues in contact with LEU 148 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144N CYS 3.0 18.8 + - - +
145N GLY* 3.0 5.8 + - - +
147N LEU* 1.3 76.5 - - - +
149N ILE* 1.3 58.4 + - - +
151N THR* 3.4 10.0 - - + -
152N TYR* 3.1 52.2 + - + +
211N LEU* 5.6 2.5 - - + -
214N LEU* 3.6 18.3 - - + +
215N LYS* 3.6 43.3 - - + +
218N ALA 4.4 4.3 - - - +
221N LEU* 4.3 11.9 - - + -
222N ASP* 4.0 26.7 - - + +
225N PHE* 4.4 3.1 - - + -
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Residues in contact with ILE 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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126N TYR* 3.3 20.4 - - + +
130N LYS* 4.2 13.7 - - - -
134N PHE* 5.2 0.2 - - + -
145N GLY 3.0 14.7 + - - +
146N GLN* 3.4 19.1 - - - +
147N LEU 3.2 0.4 - - - -
148N LEU* 1.3 75.5 - - - +
150N LEU* 1.3 60.7 + - - +
152N TYR* 3.2 1.9 + - - +
153N VAL* 3.0 30.7 + - + +
221N LEU* 3.9 32.5 - - + -
225N PHE* 4.3 19.9 - - + -
301N GSH 3.4 41.1 - - - +
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Residues in contact with LEU 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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62N TYR* 4.1 11.9 - - + -
146N GLN* 3.0 39.0 + - + +
147N LEU* 3.7 3.4 - - + +
149N ILE* 1.3 75.6 - - - +
151N THR* 1.3 63.0 + - - +
154N TYR* 3.0 60.7 + - + +
164N ILE* 3.6 28.0 - - + +
166N LEU* 5.4 4.3 - - + -
169N LEU* 3.7 38.1 - - + -
174N LEU* 4.2 16.8 - - + -
301N GSH 4.2 1.8 - - - +
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Residues in contact with THR 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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147N LEU 2.6 29.5 + - - -
148N LEU* 3.4 12.3 - - + +
150N LEU* 1.3 73.6 - - - +
152N TYR* 1.3 63.6 + - + +
155N GLY* 3.1 22.1 - - - -
162N ILE* 3.8 29.8 - - + +
163N LYS 4.5 0.5 - - - +
164N ILE* 4.1 9.0 - - - +
208N VAL* 4.0 4.7 - - + +
211N LEU* 4.3 26.0 - - + -
214N LEU* 3.7 13.8 - - + +
236N LEU* 4.0 9.9 - - + +
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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 LEU* 3.1 29.6 + - + +
149N ILE 3.8 2.0 - - - +
150N LEU 3.2 0.2 - - - -
151N THR* 1.3 82.9 - - + +
153N VAL* 1.3 67.2 + - - +
155N GLY* 3.2 12.0 + - - -
211N LEU* 3.5 30.3 - - + +
215N LYS* 4.3 5.4 - - - +
222N ASP* 2.9 24.7 + - - -
225N PHE* 3.4 44.6 - + + -
232N THR* 4.8 12.2 - - - +
233N TRP* 3.2 33.4 + + - -
236N LEU* 3.7 32.3 - - + +
237N ASN* 3.7 8.9 + - - -
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Residues in contact with VAL 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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64N LYS* 2.2 54.7 + - + +
149N ILE 3.0 12.4 + - - +
152N TYR* 1.3 77.4 - - - +
154N TYR* 1.3 87.2 + - + +
155N GLY 3.4 1.6 + - - -
225N PHE* 4.0 18.4 - - + -
229N CYS* 6.1 2.5 - - - -
232N THR* 5.2 13.7 - - + +
301N GSH 3.9 36.6 - - + +
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Residues in contact with TYR 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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45N ILE* 3.3 33.4 - - + +
62N TYR* 3.1 29.5 + + + +
64N LYS* 3.5 30.0 - - + +
150N LEU* 3.0 49.3 + - + +
153N VAL* 1.3 99.3 - - + +
155N GLY* 1.3 57.7 + - - +
164N ILE* 3.1 14.3 - - + -
165N THR* 2.5 52.6 + - + +
166N LEU* 4.1 20.4 - - + +
301N GSH 3.8 8.6 + - - -
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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
------------------------------------------------------------
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