Contacts of the helix formed by residues 192 - 202 (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 ASN 192 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B GLY 4.1 6.7 + - - -
86B ASN* 2.9 27.7 + - - -
87B MET 3.8 17.1 + - - +
88B GLY* 5.1 0.8 - - - -
93B CYS* 4.0 17.8 - - - +
190B ILE 3.3 1.2 + - - -
191B VAL* 1.3 73.1 - - - +
193B TRP* 1.3 60.9 + - - +
194B LYS* 3.1 25.6 + - - +
195B GLU* 3.1 21.1 + - - +
196B VAL* 3.3 14.9 + - - +
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Residues in contact with TRP 193 (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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93B CYS* 5.5 0.8 - - - +
94B GLY 3.2 25.7 + - - -
95B GLY 3.0 19.5 + - - -
96B GLU* 3.7 9.8 - - - +
97B PRO* 3.6 25.6 - - + -
101B LEU* 3.9 19.7 - - + -
105B ILE* 4.7 2.2 - - + -
112B PHE* 3.7 21.8 - + - -
115B PHE* 3.8 26.0 - + - -
134B LEU* 5.6 1.6 - - + -
163B LEU* 4.0 21.5 - - + -
188B TRP* 3.8 16.3 + + - -
191B VAL* 3.4 23.6 + - + +
192B ASN* 1.3 70.3 + - - +
194B LYS* 1.3 61.6 + - + +
196B VAL* 3.8 13.2 - - + +
197B GLU* 2.7 51.2 + - - +
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Residues in contact with LYS 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B GLU 5.5 6.1 - - - +
93B CYS* 6.5 0.2 - - - -
98B SER* 5.4 3.4 + - - -
192B ASN* 3.1 12.5 + - - +
193B TRP* 1.3 80.8 - - + +
195B GLU* 1.3 58.1 + - - +
197B GLU* 3.3 22.4 + - - +
198B LYS* 2.9 28.6 + - - +
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Residues in contact with GLU 195 (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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85B GLY* 3.3 27.4 - - - +
86B ASN* 4.4 1.6 - - - -
192B ASN* 3.1 18.8 + - - +
193B TRP 3.2 0.2 - - - -
194B LYS* 1.3 81.2 - - - +
196B VAL* 1.3 57.0 + - - +
198B LYS* 3.1 20.1 + - - +
199B ARG* 2.9 72.0 + - - +
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Residues in contact with VAL 196 (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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86B ASN* 3.7 18.2 - - + -
101B LEU* 3.7 21.8 - - + -
134B LEU* 5.0 1.6 - - + -
162B LEU* 3.5 40.1 - - + +
163B LEU* 3.9 20.6 - - + -
191B VAL* 4.8 1.3 - - + -
192B ASN 3.5 14.8 - - - +
193B TRP* 3.3 20.3 + - + +
195B GLU* 1.3 71.5 - - - +
197B GLU* 1.3 67.5 + - - +
199B ARG* 3.2 4.0 + - - +
200B PHE* 2.9 23.2 + - - +
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Residues in contact with GLU 197 (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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97B PRO* 3.3 9.7 - - - +
98B SER* 2.9 50.5 + - - +
101B LEU* 4.0 20.4 - - + +
193B TRP* 2.7 31.9 + - - +
194B LYS* 3.3 26.6 + - - +
196B VAL* 1.3 73.3 - - - +
198B LYS* 1.3 59.4 + - - +
200B PHE* 3.2 6.7 + - - +
201B GLU* 2.8 36.2 + - - +
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Residues in contact with LYS 198 (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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194B LYS 2.9 17.4 + - - +
195B GLU* 3.1 25.9 + - - +
197B GLU* 1.3 72.0 - - - +
199B ARG* 1.3 65.8 + - + +
201B GLU* 3.0 19.9 + - - +
202B ASP* 3.2 30.2 + - - +
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Residues in contact with ARG 199 (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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81B LEU 4.8 0.2 + - - -
82B PHE* 2.8 56.1 + - + +
85B GLY* 3.6 8.7 - - - -
86B ASN* 2.9 33.1 + - - +
161B ILE 3.8 12.1 - - - +
162B LEU* 2.7 53.8 + - + +
163B LEU* 4.2 0.4 - - - +
195B GLU* 2.9 43.9 + - - +
196B VAL* 3.2 6.0 + - - +
198B LYS* 1.3 76.6 - - + +
200B PHE* 1.3 63.1 + - - +
201B GLU 3.3 0.5 + - - -
202B ASP* 3.3 19.8 + - - +
203B ILE* 3.9 9.0 + - - +
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Residues in contact with PHE 200 (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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100B LYS* 4.0 9.6 - - + -
101B LEU* 3.7 42.8 - - + -
104B TYR* 3.5 50.5 - + + -
136B TYR* 4.1 18.8 - + - -
143B LEU* 3.9 16.4 - - + -
162B LEU* 3.5 25.5 - - + +
196B VAL 2.9 15.9 + - - +
197B GLU* 3.6 7.0 - - - +
198B LYS 3.1 0.2 - - - -
199B ARG* 1.3 77.7 - - - +
201B GLU* 1.3 64.9 + - + +
203B ILE* 3.4 16.2 + - + +
204B LEU 3.5 20.0 + - - +
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Residues in contact with GLU 201 (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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100B LYS* 4.9 27.6 + - + +
197B GLU* 2.8 32.4 - - - +
198B LYS* 3.0 11.4 + - - +
200B PHE* 1.3 78.3 - - + +
202B ASP* 1.3 60.1 + - - +
203B ILE 3.1 9.0 + - - -
204B LEU* 3.2 14.5 + - - +
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Residues in contact with ASP 202 (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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198B LYS* 3.2 34.1 - - - +
199B ARG* 3.3 10.4 + - - +
200B PHE 3.3 1.4 - - - -
201B GLU* 1.3 80.5 - - - +
203B ILE* 1.3 67.7 + - + +
204B LEU 3.6 0.2 - - - -
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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