Contacts of the helix formed by residues 194 - 203 (chain B) in PDB entry 1MMM
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 TRP 194 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B THR* 3.2 25.7 + - - +
93B THR 4.0 15.7 - - - +
94B LEU* 3.5 60.3 - - + +
95B GLN 5.4 0.2 - - - +
98B LEU* 3.9 15.5 - - + +
102B ILE* 4.3 7.0 - - + -
112B PHE* 3.7 26.0 - + - -
113B LYS* 5.0 8.1 - - - +
131B LEU* 4.7 2.9 - - + -
164B MET* 4.2 20.9 - - + -
189B TRP* 4.2 19.3 + + - -
192B VAL* 3.0 41.9 + - + +
193B ASN* 1.3 70.6 - - - +
195B ASP* 1.3 60.7 + - - +
197B ALA* 3.7 9.0 - - + +
198B ALA* 2.8 30.7 + - - +
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Residues in contact with ASP 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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89B LYS* 4.0 14.6 + - - +
92B THR* 3.8 24.0 - - - +
93B THR 4.5 8.7 + - - +
95B GLN* 5.0 5.5 + - - +
193B ASN* 2.9 11.5 + - - +
194B TRP* 1.3 78.0 - - - +
196B GLU* 1.3 58.0 + - - +
198B ALA* 3.3 7.5 + - - +
199B ALA* 3.0 25.6 + - - +
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Residues in contact with GLU 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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83B LEU 5.9 0.2 - - - +
86B LYS* 3.5 45.6 - - + +
87B GLY* 4.6 4.5 - - - -
193B ASN* 3.0 19.3 + - + +
195B ASP* 1.3 74.4 - - - +
197B ALA* 1.3 60.9 + - - +
199B ALA* 3.2 13.3 + - - +
200B ARG* 3.0 49.9 + - - +
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Residues in contact with ALA 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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98B LEU* 3.8 15.7 - - + -
163B ILE* 3.5 33.4 - - + +
164B MET* 4.3 10.5 - - + -
193B ASN 3.1 18.1 + - - +
194B TRP* 3.7 17.0 - - + +
196B GLU* 1.3 76.1 - - - +
198B ALA* 1.3 58.3 + - - +
200B ARG* 3.5 0.5 + - - +
201B PHE* 3.0 27.5 + - - +
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Residues in contact with ALA 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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95B GLN 5.5 3.6 - - - +
98B LEU* 3.7 21.7 - - + +
194B TRP 2.8 19.3 + - - +
195B ASP* 3.5 7.4 - - - +
196B GLU 3.2 0.2 - - - -
197B ALA* 1.3 75.1 - - - +
199B ALA* 1.3 58.8 + - - +
201B PHE* 3.3 6.3 + - - +
202B ALA* 3.0 28.8 + - - +
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Residues in contact with ALA 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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195B ASP 3.0 14.2 + - - +
196B GLU* 3.5 21.8 - - - +
198B ALA* 1.3 75.9 - - - +
200B ARG* 1.3 61.8 + - - +
202B ALA* 3.2 7.3 + - - +
203B ALA* 3.0 24.7 + - - +
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Residues in contact with ARG 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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83B LEU* 3.6 36.3 - - - +
150B LEU* 5.6 3.0 - - - +
161B PHE* 3.4 40.6 - - + -
162B PRO* 2.8 34.8 + - - +
163B ILE* 3.3 24.1 + - - +
196B GLU* 3.0 39.3 + - - +
197B ALA 3.9 4.3 - - - +
199B ALA* 1.3 75.6 - - - +
201B PHE* 1.3 58.6 + - - +
203B ALA* 3.8 4.8 - - - +
204B LYS* 2.9 28.6 + - - -
205B LYS 5.4 0.2 - - - -
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Residues in contact with PHE 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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97B ASP* 3.9 19.3 - - + -
98B LEU* 3.8 28.3 - - + -
101B ALA* 3.4 29.6 - - + -
104B ARG* 5.5 2.2 - - - -
133B LEU* 4.0 24.0 - - + -
138B LEU* 4.0 29.4 - - + -
163B ILE* 3.9 9.8 - - + +
197B ALA 3.0 18.7 + - - +
198B ALA* 3.5 6.5 - - - +
199B ALA 3.2 0.2 - - - -
200B ARG* 1.3 77.2 - - - +
202B ALA* 1.3 57.9 + - - +
204B LYS* 3.0 50.0 + - - +
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Residues in contact with ALA 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 ALA 3.0 12.8 + - - +
199B ALA* 3.6 10.3 - - - +
201B PHE* 1.3 78.5 - - - +
203B ALA* 1.3 63.7 + - - +
204B LYS* 3.5 13.1 + - - +
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Residues in contact with ALA 203 (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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199B ALA 3.0 15.9 + - - +
200B ARG* 4.0 4.3 - - - +
202B ALA* 1.3 74.9 - - - +
204B LYS* 1.3 61.5 + - - +
205B LYS* 2.7 40.6 + - + +
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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