Contacts of the helix formed by residues 168 - 180 (chain M) in PDB entry 1JJ2
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 LEU 168 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71M TRP* 5.4 2.8 - - - -
143M ARG 4.8 0.2 - - - +
147M ILE* 6.6 0.2 - - - -
163M PHE* 4.1 20.3 - - + -
164M ASP* 3.3 18.1 + - + +
167M ASP* 1.3 94.1 - - - +
169M PRO* 1.3 63.3 - - - +
170M GLU* 2.9 24.2 + - + +
171M HIS* 3.3 36.0 + - + +
172M PHE* 3.8 3.5 + - - +
174M GLU* 5.8 1.3 - - - +
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Residues in contact with PRO 169 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143M ARG* 3.4 50.0 + - + +
144M GLY* 3.9 22.2 - - - +
145M ALA* 4.1 5.8 - - + +
147M ILE* 5.6 0.4 - - + -
148M ALA* 3.9 17.7 - - + -
167M ASP* 4.0 6.1 - - + +
168M LEU* 1.3 85.1 - - - +
170M GLU* 1.3 73.2 + - - +
171M HIS 3.3 0.2 - - - -
172M PHE* 3.0 19.1 - - + +
173M ASP* 3.0 14.6 - - - +
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Residues in contact with GLU 170 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143M ARG* 3.7 15.6 + - - +
168M LEU* 3.4 25.2 - - + +
169M PRO* 1.3 94.6 - - - +
171M HIS* 1.3 63.8 + - - +
172M PHE 3.0 2.0 - - - -
173M ASP* 3.1 14.9 + - - +
174M GLU* 3.0 32.6 + - + +
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Residues in contact with HIS 171 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70M GLY 2.8 22.5 + - - -
71M TRP* 3.7 17.0 - + + -
72M GLU* 3.3 44.2 - - + -
73M ALA* 4.4 1.1 - - - +
163M PHE* 3.1 25.4 - + + -
168M LEU* 3.3 29.2 + - + +
170M GLU* 1.3 78.7 - - - +
172M PHE* 1.3 61.3 + - - +
174M GLU* 3.4 23.4 + - + +
175M LEU* 3.2 20.3 + - + +
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Residues in contact with PHE 172 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71M TRP* 4.1 9.4 - - + -
79M PRO* 3.6 31.2 - - + -
82M TYR* 3.8 22.0 - + - -
83M LEU* 3.7 31.2 - - + -
139M TRP* 3.8 24.0 - + - -
142M THR* 4.1 10.3 - - + -
143M ARG* 3.4 48.9 - - + +
168M LEU 3.8 1.9 + - - +
169M PRO* 3.0 12.4 + - + +
171M HIS* 1.3 77.0 - - - +
173M ASP* 1.3 68.2 + - - +
175M LEU* 3.1 5.2 + - - +
176M ARG* 2.9 32.4 + - + +
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Residues in contact with ASP 173 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139M TRP* 5.2 5.2 + - - -
143M ARG* 2.4 38.5 + - - +
169M PRO 3.0 10.0 - - - +
170M GLU* 3.1 14.3 + - - +
172M PHE* 1.3 83.2 - - - +
174M GLU* 1.3 56.2 - - + +
176M ARG* 3.8 6.4 - - - +
177M GLU* 2.7 38.7 + - - +
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Residues in contact with GLU 174 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168M LEU* 5.8 1.6 - - - +
170M GLU* 3.0 19.6 + - + +
171M HIS* 3.4 30.0 - - + +
173M ASP* 1.3 76.2 - - + +
175M LEU* 1.3 52.1 + - - +
177M GLU* 3.3 9.1 - - - +
178M THR* 2.7 36.8 + - - -
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Residues in contact with LEU 175 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66M LEU* 4.0 18.8 - - + -
69M TYR* 3.5 40.4 - - + +
70M GLY 4.6 5.8 - - - +
71M TRP* 3.1 35.9 - - + -
83M LEU* 3.4 21.8 - - + -
171M HIS* 3.2 11.3 + - + +
172M PHE 3.1 8.6 + - - +
173M ASP 3.1 0.4 - - - -
174M GLU* 1.3 76.8 - - - +
176M ARG* 1.3 68.1 + - - +
177M GLU 3.1 1.1 - - - -
178M THR* 2.9 19.4 + - - +
179M LEU* 2.9 20.6 + - + +
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Residues in contact with ARG 176 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82M TYR* 2.6 36.3 + - + -
83M LEU* 3.9 18.1 - - + +
86M LEU* 4.4 9.8 - - + +
124M ASP* 3.9 15.0 + - - +
139M TRP* 3.0 38.5 - - - -
172M PHE* 2.9 23.4 + - + +
173M ASP* 3.8 7.4 - - - +
175M LEU* 1.3 74.1 - - - +
177M GLU* 1.3 65.8 + - - +
179M LEU* 3.1 10.8 + - - +
180M LEU* 3.2 44.9 + - + +
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Residues in contact with GLU 177 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173M ASP 2.7 19.6 + - - +
174M GLU* 3.3 9.9 - - - +
176M ARG* 1.3 80.6 - - - +
178M THR* 1.3 59.6 + - - +
180M LEU* 3.3 15.0 + - - +
181M ASP* 2.8 24.7 - - - +
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Residues in contact with THR 178 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69M TYR* 4.5 25.9 + - + +
174M GLU 2.7 22.0 + - - -
175M LEU* 2.9 18.9 + - + +
177M GLU* 1.3 77.8 - - - +
179M LEU* 1.3 63.7 + - + +
180M LEU 3.0 1.7 + - - -
181M ASP* 3.1 24.8 + - - +
183M ASP* 4.1 10.2 - - + +
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Residues in contact with LEU 179 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66M LEU* 5.0 3.6 - - + -
69M TYR* 4.1 28.0 - - + -
83M LEU* 4.1 31.6 - - + +
86M LEU* 4.0 28.5 - - + -
87M LEU* 4.3 13.2 - - + +
90M LEU* 3.2 24.7 - - + +
175M LEU* 2.9 26.3 + - + +
176M ARG 3.6 6.3 - - - +
178M THR* 1.3 75.6 - - + +
180M LEU* 1.3 57.6 + - - +
181M ASP 3.1 6.8 + - - -
183M ASP* 4.1 3.2 - - - +
186M LEU* 3.7 28.2 - - + +
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Residues in contact with LEU 180 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86M LEU* 4.2 27.1 - - + -
90M LEU* 5.2 7.2 - - + -
124M ASP* 5.1 7.6 - - + +
176M ARG* 3.2 46.9 + - + +
177M GLU* 3.7 15.5 - - - +
178M THR 3.0 3.0 + - - -
179M LEU* 1.3 77.8 - - - +
181M ASP* 1.3 65.8 + - - +
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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