Contacts of the helix formed by residues 179 - 188 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176F TYR* 2.9 25.7 + - + +
177F ARG* 3.2 1.0 - - + -
178F ASN* 1.3 97.0 - - - +
180F ARG* 1.3 62.9 + - - +
181F PRO* 3.2 9.6 - - + -
182F ASP* 3.0 48.0 + - + +
183F TYR 3.6 3.3 + - - -
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Residues in contact with ARG 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E TRP* 6.1 0.2 - - - -
123F ALA 3.4 7.5 + - - -
124F ILE* 2.9 33.2 + - + +
126F ALA* 2.8 25.9 + - - +
128F GLY* 3.2 23.6 + - - +
167F VAL* 3.1 48.1 + - + +
169F GLU* 4.6 6.3 + - - +
172F TYR* 2.9 43.4 + - + +
178F ASN 2.9 10.1 + - - +
179F VAL* 1.3 70.9 - - - +
181F PRO* 1.3 64.7 - - + +
183F TYR* 3.2 5.0 + - + +
184F VAL* 2.9 30.9 + - + +
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Residues in contact with PRO 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124F ILE* 3.9 41.5 - - + +
178F ASN 4.7 0.9 - - - +
179F VAL* 3.2 12.1 - - + -
180F ARG* 1.3 95.4 - - + +
182F ASP* 1.3 59.4 + - - +
184F VAL* 3.5 2.0 + - + +
185F GLU* 2.9 29.8 + - - +
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Residues in contact with ASP 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176F TYR* 3.5 22.4 - - + -
179F VAL* 3.0 33.2 + - + +
181F PRO* 1.3 80.2 - - - +
183F TYR* 1.3 57.8 + - - +
185F GLU* 3.3 7.0 + - - +
186F ALA* 2.8 30.0 + - - +
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Residues in contact with TYR 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F HIS 5.3 0.2 - - - -
24F ILE* 4.2 22.6 - - + +
83F PHE* 3.3 24.7 - + - -
165F LEU* 3.8 17.0 - - + +
166F ASP 2.9 29.1 + - - -
167F VAL* 4.7 3.4 - - + -
171F ALA* 3.5 26.7 + - + +
172F TYR* 3.3 34.3 - + + -
176F TYR* 3.6 33.9 - + + -
179F VAL 3.6 1.8 + - - -
180F ARG 3.2 10.4 + - - +
182F ASP* 1.3 77.1 - - - +
184F VAL* 1.3 74.5 + - + +
186F ALA* 3.2 4.6 + - + +
187F PHE* 3.0 22.5 + + + +
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Residues in contact with VAL 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F SER* 3.7 39.5 - - - +
123F ALA* 3.8 20.0 - - + -
124F ILE* 3.9 17.3 - - + -
165F LEU* 4.3 13.7 - - + -
167F VAL* 4.5 1.8 - - + -
180F ARG* 2.9 33.3 + - + +
181F PRO 3.8 4.0 - - - +
183F TYR* 1.3 79.5 - - + +
185F GLU* 1.3 64.7 + - - +
187F PHE* 3.2 17.2 + - - +
188F TRP* 3.3 15.2 - - - +
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Residues in contact with GLU 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F ARG* 2.9 38.9 + - - -
120F SER* 5.6 0.3 + - - -
181F PRO 2.9 18.7 + - - +
182F ASP* 3.5 8.5 - - - +
184F VAL* 1.3 76.8 - - - +
186F ALA* 1.3 63.6 + - - +
187F PHE 3.1 0.9 + - - -
188F TRP* 3.4 14.4 + - - +
189F ASN* 3.7 9.3 + - - +
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Residues in contact with ALA 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F HIS* 4.0 25.2 + - + +
24F ILE* 6.2 0.2 - - + -
176F TYR* 3.3 27.1 - - + +
182F ASP 2.8 18.5 + - - +
183F TYR* 3.6 6.1 - - + +
185F GLU* 1.3 74.3 - - - +
187F PHE* 1.3 62.9 + - - +
189F ASN* 3.0 30.9 + - - +
190F ILE* 4.0 1.6 + - - +
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Residues in contact with PHE 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F ILE* 5.7 1.6 - - + -
83F PHE* 4.1 5.4 - + - -
86F ASN* 4.3 2.5 - - - -
87F MET* 3.7 38.1 - - + -
119F PHE* 4.6 6.5 - + - -
163F LEU* 4.0 17.0 - - + -
164F VAL 3.9 16.4 - - - -
165F LEU* 3.5 45.5 - - + -
183F TYR* 3.0 16.5 + + + +
184F VAL 3.3 11.0 - - - +
185F GLU 3.1 0.6 - - - -
186F ALA* 1.3 77.2 - - - +
188F TRP* 1.3 72.7 + + - +
190F ILE* 3.0 27.6 + - + +
191F VAL* 3.2 32.4 + - + +
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Residues in contact with TRP 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F GLY* 3.3 18.7 - - - -
95F GLY 4.2 5.7 + - - +
112F PHE* 4.6 5.8 - + - -
115F PHE* 3.8 21.3 - + - -
116F ARG* 3.5 70.1 - - + +
119F PHE* 3.5 34.8 - + + -
120F SER* 3.1 21.4 + - - -
163F LEU* 4.6 3.8 - - + -
165F LEU* 5.6 0.2 - - + -
184F VAL* 3.3 28.0 + - + +
185F GLU* 3.4 8.7 + - - +
186F ALA 3.2 1.0 - - - -
187F PHE* 1.3 83.8 - + - +
189F ASN* 1.3 60.0 + - - +
190F ILE 3.3 0.4 - - - -
191F VAL* 3.6 23.0 - - + +
193F TRP* 3.8 27.1 - + - -
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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