Contacts of the helix formed by residues 179 - 188 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176B TYR* 2.8 24.9 + - + +
177B ARG* 3.2 1.5 - - + -
178B ASN* 1.3 94.5 - - - +
180B ARG* 1.3 64.0 + - - +
181B PRO* 3.1 10.1 - - + -
182B ASP* 3.0 44.3 + - + +
183B TYR 3.5 6.1 + - - -
6C LYS* 5.5 9.2 - - - +
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Residues in contact with ARG 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A TRP* 6.1 0.4 - - - -
123B ALA 3.4 8.3 + - - -
124B ILE* 3.0 33.9 + - - +
126B ALA* 2.8 27.7 + - - +
128B GLY* 3.3 21.2 + - - +
167B VAL* 3.0 47.5 + - + +
169B GLU* 4.6 7.5 + - - +
172B TYR* 2.9 44.4 + - + +
178B ASN 2.9 10.1 + - - +
179B VAL* 1.3 71.8 - - - +
181B PRO* 1.3 65.7 - - + +
183B TYR* 3.2 4.6 + - + +
184B VAL* 2.9 31.2 + - + +
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Residues in contact with PRO 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ILE* 3.9 40.6 - - + +
178B ASN 4.7 0.9 - - - +
179B VAL* 3.2 12.3 - - + -
180B ARG* 1.3 95.2 - - + +
182B ASP* 1.3 58.8 + - - +
184B VAL* 3.5 2.1 + - + +
185B GLU* 2.9 29.8 + - - +
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Residues in contact with ASP 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B TYR* 3.5 25.3 - - + -
179B VAL* 3.0 28.9 + - + +
181B PRO* 1.3 79.8 - - - +
183B TYR* 1.3 58.0 + - - +
185B GLU* 3.3 6.4 + - - +
186B ALA* 2.8 29.6 + - - +
6C LYS* 5.3 6.1 + - - -
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Residues in contact with TYR 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B HIS 5.4 0.2 - - - -
24B ILE* 4.3 21.5 - - + +
28B GLN* 5.9 0.4 - - + -
83B PHE* 3.3 25.0 - + - -
165B LEU* 3.8 17.2 - - + +
166B ASP 3.0 28.6 + - - -
167B VAL* 4.8 3.8 - - + -
171B ALA* 3.4 28.2 + - + +
172B TYR* 3.2 33.9 - + + -
176B TYR* 3.7 35.0 - + + -
179B VAL 3.5 1.8 + - - -
180B ARG 3.2 10.9 + - - +
182B ASP* 1.3 76.6 - - - +
184B VAL* 1.3 73.8 + - + +
186B ALA* 3.2 4.1 + - + +
187B PHE* 3.0 23.4 + + + +
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Residues in contact with VAL 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B SER* 3.7 38.6 - - - +
123B ALA* 3.8 22.9 - - + -
124B ILE* 3.9 17.0 - - + -
165B LEU* 4.4 12.8 - - + -
167B VAL* 4.6 1.6 - - + -
180B ARG* 2.9 29.6 + - + +
181B PRO 3.8 4.3 - - - +
183B TYR* 1.3 84.4 - - + +
185B GLU* 1.3 63.7 + - - +
187B PHE* 3.2 19.6 + - - +
188B TRP* 3.3 13.1 + - - +
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Residues in contact with GLU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ARG* 2.9 37.2 + - - -
120B SER* 5.6 0.5 + - - -
181B PRO 2.9 17.5 + - - +
182B ASP* 3.5 9.0 - - - +
183B TYR 3.2 0.2 - - - -
184B VAL* 1.3 76.2 - - - +
186B ALA* 1.3 65.2 + - - +
187B PHE 3.1 0.7 + - - -
188B TRP* 3.4 15.5 + - - +
189B ASN* 3.7 8.5 + - - +
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Residues in contact with ALA 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B HIS* 4.0 24.4 + - + +
24B ILE* 6.2 1.1 - - + -
176B TYR* 3.2 28.0 - - + +
182B ASP 2.8 17.2 + - - +
183B TYR* 3.2 5.6 + - + +
185B GLU* 1.3 73.9 - - - +
187B PHE* 1.3 64.6 + - - +
189B ASN* 3.0 31.9 + - - +
190B ILE 4.0 1.2 + - - -
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Residues in contact with PHE 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ILE* 5.7 1.8 - - + -
83B PHE* 4.0 4.7 - + - -
86B ASN* 4.3 2.9 - - - -
87B MET* 3.7 37.9 - - + -
119B PHE* 4.6 7.0 - + - -
163B LEU* 4.1 16.6 - - + -
164B VAL 3.8 17.9 - - - -
165B LEU* 3.5 46.0 - - + -
183B TYR* 3.0 15.7 + + + +
184B VAL 3.2 12.1 - - - +
185B GLU 3.1 0.6 - - - -
186B ALA* 1.3 78.3 - - - +
188B TRP* 1.3 71.8 + + - +
189B ASN 3.0 0.2 - - - -
190B ILE* 2.9 30.9 + - + +
191B VAL* 3.2 28.0 + - + +
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Residues in contact with TRP 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B GLY* 3.3 18.2 - - - -
95B GLY 4.2 5.0 + - - +
112B PHE* 4.5 6.3 - + - -
115B PHE* 3.9 19.3 - + - -
116B ARG* 3.4 71.4 - - + +
119B PHE* 3.6 33.7 - + + -
120B SER* 3.1 19.8 + - - -
163B LEU* 4.7 3.1 - - + -
165B LEU* 5.5 0.2 - - + -
184B VAL* 3.3 28.3 + - + +
185B GLU* 3.4 9.4 + - - +
186B ALA 3.1 0.8 + - - -
187B PHE* 1.3 83.8 - + - +
189B ASN* 1.3 60.6 - - - +
190B ILE 3.3 0.2 - - - -
191B VAL* 3.5 23.4 - - + +
193B TRP* 3.8 27.4 - + - -
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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