Contacts of the helix formed by residues 192 - 202 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85E GLY 4.0 10.1 + - - -
86E ASN* 2.9 27.2 + - - -
87E MET 3.8 15.2 + - - -
88E GLY* 5.1 1.0 - - - -
93E CYS* 4.0 17.6 - - - -
190E ILE 3.3 1.2 + - - -
191E VAL* 1.3 72.3 - - - +
193E TRP* 1.3 61.1 + - - +
194E LYS* 3.2 25.4 + - - +
195E GLU* 3.2 21.1 + - - +
196E VAL* 3.4 15.1 + - - +
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Residues in contact with TRP 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E CYS* 5.5 0.8 - - - +
94E GLY 3.2 25.0 + - - +
95E GLY 2.9 20.7 + - - -
96E GLU* 3.6 11.8 - - - +
97E PRO* 3.5 24.5 - - + -
101E LEU* 3.8 20.4 - - + -
105E ILE* 4.8 1.8 - - + -
112E PHE* 3.7 20.9 - + - -
115E PHE* 3.9 25.6 - + - -
134E LEU* 5.6 1.6 - - + -
163E LEU* 3.9 23.3 - - + -
188E TRP* 3.8 16.7 + + - -
191E VAL* 3.4 21.9 + - + +
192E ASN* 1.3 69.4 + - - +
194E LYS* 1.3 59.4 + - + +
196E VAL* 3.8 13.9 - - + +
197E GLU* 2.7 53.6 + - - +
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Residues in contact with LYS 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E GLU 5.5 6.7 - - - +
98E SER* 5.4 3.4 + - - -
192E ASN* 3.2 12.5 + - - +
193E TRP* 1.3 80.8 - - + +
195E GLU* 1.3 57.5 + - - +
197E GLU* 3.4 21.2 + - - +
198E LYS* 2.9 28.5 + - - +
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Residues in contact with GLU 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E GLY* 3.3 29.2 - - - +
86E ASN* 4.4 0.9 - - - -
192E ASN* 3.2 17.9 + - - +
193E TRP 3.2 0.2 - - - -
194E LYS* 1.3 77.7 - - - +
196E VAL* 1.3 59.2 + - - +
198E LYS* 3.2 21.5 + - - +
199E ARG* 2.9 73.4 + - - +
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Residues in contact with VAL 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E ASN* 3.8 17.3 - - + -
101E LEU* 3.6 21.3 - - + -
134E LEU* 5.0 1.8 - - + -
162E LEU* 3.5 39.4 - - + +
163E LEU* 3.9 20.9 - - + -
191E VAL* 4.8 1.3 - - + -
192E ASN 3.5 14.1 - - - +
193E TRP* 3.3 20.3 + - + +
195E GLU* 1.3 74.3 - - - +
197E GLU* 1.3 64.0 + - - +
199E ARG* 3.2 4.5 + - - +
200E PHE* 2.9 21.8 + - - +
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Residues in contact with GLU 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E PRO* 3.4 9.9 - - - +
98E SER* 3.0 50.0 + - - +
101E LEU* 4.1 19.7 - - + +
193E TRP* 2.7 33.3 + - - +
194E LYS* 3.4 25.5 + - - +
196E VAL* 1.3 73.3 - - - +
198E LYS* 1.3 59.8 + - - +
200E PHE* 3.2 6.7 + - - +
201E GLU* 2.8 36.9 + - - +
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Residues in contact with LYS 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E LYS 2.9 15.1 + - - +
195E GLU* 3.2 25.9 + - - +
197E GLU* 1.3 75.9 - - - +
199E ARG* 1.3 63.5 + - + +
201E GLU* 3.0 20.9 + - + +
202E ASP* 3.3 29.7 + - - +
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Residues in contact with ARG 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E LEU 4.8 0.2 + - - -
82E PHE* 2.9 54.7 + - + +
85E GLY* 3.5 9.3 - - - -
86E ASN* 2.9 34.9 + - - +
161E ILE* 3.9 12.5 - - - +
162E LEU* 2.9 43.1 + - + +
163E LEU* 4.3 0.2 - - - +
195E GLU* 2.9 44.5 + - - +
196E VAL* 3.5 6.1 - - - +
198E LYS* 1.3 76.6 - - - +
200E PHE* 1.3 62.3 + - - +
201E GLU 3.3 0.3 + - - -
202E ASP* 3.3 18.0 + - - +
203E ILE* 3.9 9.9 + - - +
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Residues in contact with PHE 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E LYS* 3.9 9.6 - - + -
101E LEU* 3.7 39.7 - - + -
104E TYR* 3.4 50.0 - + + -
136E TYR* 4.0 18.2 - + - -
143E LEU* 3.9 16.6 - - + -
162E LEU* 3.6 27.1 - - + -
196E VAL 2.9 17.4 + - - +
197E GLU* 3.6 7.0 - - - +
198E LYS 3.2 0.2 - - - -
199E ARG* 1.3 77.1 - - - +
201E GLU* 1.3 63.6 - - + +
203E ILE* 3.4 15.9 + - + +
204E LEU 3.5 20.7 + - - +
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Residues in contact with GLU 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ASP* 5.4 4.2 - - - +
100E LYS* 4.7 27.3 + - + +
197E GLU* 2.8 32.2 - - + +
198E LYS* 3.0 10.2 + - + +
200E PHE* 1.3 82.5 - - + +
202E ASP* 1.3 62.0 + - - +
203E ILE 3.1 0.7 - - - -
204E LEU* 3.2 18.8 + - - +
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Residues in contact with ASP 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E LYS* 3.3 32.8 - - - +
199E ARG* 3.3 10.3 + - - +
200E PHE 3.3 1.0 - - - -
201E GLU* 1.3 80.0 - - - +
203E ILE* 1.3 66.5 + - + +
204E 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