Contacts of the helix formed by residues 192 - 202 (chain B) in PDB entry 1MNG
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B LEU* 2.9 26.4 + - - +
91B THR* 2.8 34.2 + - - +
92B PRO 4.2 2.0 + - - -
94B GLY* 3.4 25.2 - - - +
95B ALA 3.9 2.5 - - - -
190B VAL 3.5 0.2 + - - -
191B LEU* 1.3 70.6 - - - +
193B TRP* 1.3 59.3 + - - +
194B ASP* 3.0 22.4 + - - +
195B VAL* 3.0 27.5 + - + +
196B ALA* 3.1 21.0 + - - +
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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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95B ALA* 3.0 22.7 + - + +
96B LYS 3.5 10.0 + - - -
97B GLU 3.1 35.2 - - - +
98B PRO* 3.6 32.3 - - + -
99B VAL* 4.0 6.4 + - - +
102B LEU* 3.8 21.8 - - + +
106B ILE* 4.2 5.6 - - + -
113B PHE* 3.5 26.6 - + - -
116B LEU* 4.1 14.4 - - + -
120B LEU* 5.6 0.7 - - + -
135B LEU* 4.8 1.3 - - + -
163B VAL* 3.9 22.4 - - + -
188B TRP* 4.3 7.5 + + - -
191B LEU* 3.7 37.7 + - + +
192B ASN* 1.3 69.0 - - - +
194B ASP* 1.3 61.4 + - - +
195B VAL 3.3 0.2 - - - -
196B ALA* 3.7 18.3 - - + +
197B GLU* 2.9 27.0 + - - +
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Residues in contact with ASP 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLY* 3.4 7.4 - - - -
95B ALA* 2.9 29.0 + - - +
99B VAL* 3.7 17.4 - - - +
192B ASN* 3.0 8.8 + - - +
193B TRP* 1.3 78.1 - - - +
195B VAL* 1.3 62.7 + - + +
197B GLU* 3.3 9.1 + - - +
198B GLU* 3.2 19.6 + - - +
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Residues in contact with VAL 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ARG* 3.7 48.9 - - + +
89B LEU* 4.2 3.8 - - + -
91B THR* 4.7 4.7 - - + -
192B ASN* 3.0 30.4 + - - +
194B ASP* 1.3 76.5 - - + +
196B ALA* 1.3 66.0 + - - +
198B GLU* 3.0 12.8 + - - +
199B PHE* 3.0 50.8 + - + -
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Residues in contact with ALA 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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89B LEU* 4.1 10.7 - - + +
102B LEU* 3.7 9.2 - - + -
162B ILE* 3.5 14.8 - - + +
163B VAL* 4.1 17.0 - - + -
192B ASN 3.1 12.2 + - - +
193B TRP* 3.7 33.4 - - + +
195B VAL* 1.3 76.4 - - - +
197B GLU* 1.3 58.2 + - - +
199B PHE* 3.3 2.1 + - - +
200B PHE* 3.0 25.3 + - - +
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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
----------------------------------------------------------
99B VAL* 3.5 16.9 - - + +
100B GLY* 3.7 4.3 - - - -
101B GLU* 2.9 23.9 + - - +
102B LEU* 2.8 32.4 + - + +
193B TRP 2.9 18.5 + - - +
194B ASP* 3.4 10.5 - - - +
195B VAL 3.1 0.4 - - - -
196B ALA* 1.3 73.6 - - - +
198B GLU* 1.3 58.7 + - - +
200B PHE* 3.2 5.9 + - - +
201B LYS* 2.9 64.0 + - - +
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Residues in contact with GLU 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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88B ARG* 3.1 40.2 + - - -
194B ASP 3.2 11.0 + - - +
195B VAL* 3.0 15.5 + - - +
197B GLU* 1.3 75.1 - - - +
199B PHE* 1.3 71.9 + - + +
201B LYS* 3.9 9.2 - - - +
202B LYS* 3.1 27.8 + - + +
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Residues in contact with PHE 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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85B LEU* 4.1 31.9 - - + -
88B ARG* 3.8 37.0 - - + -
89B LEU* 3.9 17.9 - - + -
160B THR* 5.0 0.3 - - - +
161B PRO 4.3 5.8 - - - +
162B ILE* 3.4 34.4 - - - +
195B VAL* 3.0 36.8 + - + -
196B ALA 3.6 6.3 - - - +
198B GLU* 1.3 84.5 - - - +
200B PHE* 1.3 61.9 + - - +
202B LYS* 3.1 39.2 + - + +
203B ALA* 3.2 9.5 + - - +
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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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101B GLU* 3.6 33.0 - - + -
102B LEU* 3.7 29.4 - - + -
105B ALA* 3.9 22.7 - - + -
137B LYS* 3.1 49.4 + - + -
141B GLY 6.0 0.9 - - - -
143B LEU* 4.2 15.0 - - + -
162B ILE* 3.7 24.6 - - + +
196B ALA 3.0 17.2 + - - +
197B GLU* 3.2 6.3 + - - +
199B PHE* 1.3 76.5 - - - +
201B LYS* 1.3 61.7 + - + +
203B ALA* 3.1 12.1 + - - +
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Residues in contact with LYS 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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101B GLU* 4.4 15.3 - - + -
137B LYS* 5.2 1.0 + - - +
197B GLU* 2.9 50.8 + - - +
198B GLU* 4.0 7.4 - - - +
200B PHE* 1.3 81.2 - - + +
202B LYS* 1.3 60.5 + - - +
203B ALA* 3.0 8.4 + - - +
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Residues in contact with LYS 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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160B THR* 3.6 25.5 - - - +
161B PRO 4.9 1.4 + - - -
198B GLU* 3.1 14.7 + - + +
199B PHE* 3.1 48.4 + - + +
201B LYS* 1.3 76.9 - - - +
203B ALA* 1.3 67.7 + - - +
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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