Contacts of the helix formed by residues 179 - 188 (chain E) in PDB entry 1MA1
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 VAL 179 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176E TYR* 2.8 25.9 + - + +
177E ARG* 3.2 1.1 - - + -
178E ASN* 1.3 93.5 - - - +
180E ARG* 1.3 64.5 + - - +
181E PRO* 3.2 9.9 - - + -
182E ASP* 3.0 47.1 + - + +
183E TYR 3.6 2.9 + - - -
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Residues in contact with ARG 180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E ALA 3.3 9.1 + - - -
124E ILE* 3.0 32.5 + - + +
126E ALA* 2.9 26.5 + - - +
128E GLY* 3.2 22.6 + - - +
167E VAL* 3.0 48.0 + - + +
169E GLU* 4.6 6.3 + - - +
172E TYR* 2.8 43.8 + - + +
178E ASN 2.9 10.2 + - - +
179E VAL* 1.3 72.0 - - - +
181E PRO* 1.3 64.0 - - + +
183E TYR* 3.2 4.8 + - + +
184E VAL* 2.9 31.4 + - + +
168F TRP* 6.1 0.2 - - - -
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Residues in contact with PRO 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E ILE* 4.0 40.1 - - + +
178E ASN 4.7 1.1 - - - +
179E VAL* 3.2 12.6 - - + -
180E ARG* 1.3 95.6 - - + +
182E ASP* 1.3 59.4 + - - +
184E VAL* 3.5 1.9 + - + +
185E GLU* 2.9 30.0 + - - +
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Residues in contact with ASP 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176E TYR* 3.6 22.6 - - + -
179E VAL* 3.0 32.8 + - + +
181E PRO* 1.3 75.5 - - - +
183E TYR* 1.3 61.6 + - - +
185E GLU* 3.3 5.7 + - - +
186E ALA* 2.8 29.8 + - - +
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Residues in contact with TYR 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E HIS 5.3 0.4 - - - -
24E ILE* 4.3 23.0 - - + +
28E GLN* 6.3 0.2 - - + -
83E PHE* 3.4 23.9 - - - -
165E LEU* 3.9 15.6 - - + +
166E ASP 3.0 28.6 + - - -
167E VAL* 4.7 4.0 - - + -
171E ALA* 3.5 27.1 - - + +
172E TYR* 3.3 34.5 - + + -
176E TYR* 3.6 34.6 - + + -
179E VAL 3.6 2.0 + - - -
180E ARG 3.2 10.7 + - - +
182E ASP* 1.3 76.4 - - - +
184E VAL* 1.3 72.7 + - + +
186E ALA* 3.2 5.1 + - + +
187E PHE* 3.0 25.4 + + + +
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Residues in contact with VAL 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E SER* 3.8 37.7 - - - +
123E ALA* 3.8 22.2 - - + -
124E ILE* 3.9 17.7 - - + -
165E LEU* 4.2 14.4 - - + -
167E VAL* 4.5 1.3 - - + -
180E ARG* 2.9 33.4 + - + +
181E PRO 3.8 4.0 - - - +
183E TYR* 1.3 81.1 - - + +
185E GLU* 1.3 63.3 + - - +
187E PHE* 3.2 20.3 + - - +
188E TRP* 3.3 12.9 + - + +
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Residues in contact with GLU 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E ARG* 2.9 40.5 + - - -
120E SER* 5.8 0.2 + - - -
181E PRO 2.9 20.0 + - - +
182E ASP* 3.6 8.1 - - - +
183E TYR 3.2 0.2 - - - -
184E VAL* 1.3 76.6 - - - +
186E ALA* 1.3 65.5 + - - +
187E PHE 3.2 0.7 + - - -
188E TRP* 3.4 14.6 + - - +
189E ASN* 3.8 8.6 + - - +
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Residues in contact with ALA 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E HIS* 4.0 21.3 + - + +
24E ILE* 6.2 0.4 - - + -
176E TYR* 3.2 27.8 - - + +
182E ASP 2.8 17.4 + - - +
183E TYR* 3.2 6.3 + - + +
185E GLU* 1.3 73.7 - - - +
187E PHE* 1.3 63.1 + - - +
189E ASN* 3.0 31.6 + - - +
190E ILE* 4.0 4.7 + - - +
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Residues in contact with PHE 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E ILE* 5.7 2.2 - - + -
83E PHE* 4.1 5.6 - + - -
86E ASN* 4.1 2.5 - - - -
87E MET* 3.6 38.8 - - + -
119E PHE* 4.5 5.8 - + - -
163E LEU* 4.0 17.5 - - + -
164E VAL 3.9 16.6 - - - -
165E LEU* 3.5 45.5 - - + -
183E TYR* 3.0 15.3 + + + +
184E VAL 3.3 12.1 - - - +
185E GLU 3.1 0.6 - - - -
186E ALA* 1.3 78.0 - - - +
188E TRP* 1.3 71.5 + + - +
189E ASN 3.0 0.2 - - - -
190E ILE* 2.9 31.8 + - + +
191E VAL* 3.2 29.3 + - + +
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Residues in contact with TRP 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E GLY* 3.4 18.2 - - - -
95E GLY 4.2 5.5 + - - +
112E PHE* 4.6 6.3 - + - -
115E PHE* 3.8 20.2 - + - -
116E ARG* 3.5 71.9 - - + +
119E PHE* 3.5 34.8 - + + -
120E SER* 3.1 19.2 + - - -
163E LEU* 4.7 3.1 - - + -
184E VAL* 3.3 28.3 + - + +
185E GLU* 3.4 10.7 + - - +
186E ALA 3.1 1.2 + - - -
187E PHE* 1.3 84.4 - + - +
189E ASN* 1.3 60.4 + - - +
190E ILE 3.3 0.2 - - - -
191E VAL* 3.6 23.9 - - + +
193E TRP* 3.8 27.6 - + - -
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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
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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