Contacts of the helix formed by residues 192 - 202 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85F GLY 4.0 8.9 + - - -
86F ASN* 2.9 27.6 + - - -
87F MET 3.9 14.8 + - - -
88F GLY* 5.2 0.6 - - - -
93F CYS* 3.9 18.6 - - - -
190F ILE 3.3 1.0 + - - -
191F VAL* 1.3 71.2 - - - +
193F TRP* 1.3 61.0 + - - +
194F LYS* 3.1 17.8 + - - +
195F GLU* 3.0 29.7 + - - +
196F VAL* 3.3 14.6 + - - +
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Residues in contact with TRP 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F CYS* 5.5 0.8 - - - +
94F GLY 3.2 24.8 + - - +
95F GLY 3.0 21.2 + - - -
96F GLU* 3.7 10.7 - - - +
97F PRO* 3.6 24.2 - - + -
101F LEU* 3.9 19.5 - - + -
105F ILE* 4.8 2.7 - - + -
112F PHE* 3.8 15.9 - + - -
115F PHE* 3.9 24.0 - + - -
134F LEU* 5.6 1.6 - - + -
163F LEU* 3.9 23.8 - - + -
188F TRP* 3.8 20.8 + + - -
191F VAL* 3.4 21.5 + - + +
192F ASN* 1.3 69.9 - - - +
194F LYS* 1.3 58.0 + - + +
196F VAL* 4.0 12.8 - - + +
197F GLU* 2.7 54.3 + - - +
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Residues in contact with LYS 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F GLU 5.5 6.7 - - - +
93F CYS* 6.4 0.4 - - - -
98F SER* 5.3 3.4 + - - -
192F ASN* 3.1 11.9 + - - +
193F TRP* 1.3 80.1 - - + +
195F GLU* 1.3 56.5 + - - +
197F GLU* 3.3 23.4 + - - +
198F LYS* 2.9 28.4 + - - +
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Residues in contact with GLU 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F GLY* 3.3 29.4 - - - +
86F ASN* 4.4 0.9 - - - -
192F ASN* 3.0 21.6 + - - +
194F LYS* 1.3 73.3 - - - +
196F VAL* 1.3 61.3 + - - +
198F LYS* 3.1 22.6 + - - +
199F ARG* 2.9 72.6 + - - +
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Residues in contact with VAL 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F ASN* 3.8 18.8 - - + -
101F LEU* 3.7 20.9 - - + -
134F LEU* 5.0 1.8 - - + -
162F LEU* 3.4 41.8 - - + +
163F LEU* 3.9 20.4 - - + -
191F VAL* 4.7 0.9 - - + -
192F ASN 3.5 14.1 - - - +
193F TRP* 3.2 19.8 + - + +
195F GLU* 1.3 75.2 - - - +
197F GLU* 1.3 64.0 + - - +
199F ARG* 3.3 4.1 + - - +
200F PHE* 2.9 22.3 + - - +
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Residues in contact with GLU 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F PRO* 3.4 9.7 - - - +
98F SER* 3.0 50.9 + - - +
101F LEU* 4.0 20.8 - - + +
193F TRP* 2.7 30.8 + - - +
194F LYS* 3.3 28.7 + - - +
196F VAL* 1.3 72.8 - - - +
198F LYS* 1.3 59.2 + - - +
200F PHE* 3.2 5.3 + - - +
201F GLU* 2.8 37.5 + - - +
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Residues in contact with LYS 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194F LYS 2.9 14.4 + - - +
195F GLU* 3.1 25.4 + - - +
197F GLU* 1.3 74.3 - - - +
199F ARG* 1.3 65.4 + - + +
201F GLU* 3.0 20.0 + - - +
202F ASP* 3.3 29.5 + - - +
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Residues in contact with ARG 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F PHE* 2.9 54.1 + - + +
85F GLY* 3.5 9.5 - - - -
86F ASN* 2.9 35.2 + - - +
161F ILE* 3.8 13.4 - - - +
162F LEU* 2.9 44.2 + - + +
163F LEU 4.3 0.2 - - - +
195F GLU* 2.9 44.0 + - - +
196F VAL* 3.5 6.1 - - - +
198F LYS* 1.3 76.1 - - - +
200F PHE* 1.3 62.3 + - - +
201F GLU 3.3 0.5 + - - -
202F ASP* 3.4 18.6 + - - +
203F ILE* 3.9 10.0 + - - +
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Residues in contact with PHE 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F LYS* 3.9 10.1 - - + -
101F LEU* 3.7 42.4 - - + -
104F TYR* 3.5 50.7 - + + -
136F TYR* 4.0 19.1 - + - -
143F LEU* 3.9 15.7 - - + -
162F LEU* 3.5 27.1 - - + -
196F VAL 2.9 16.0 + - - +
197F GLU* 3.6 7.2 - - - +
198F LYS 3.1 0.2 - - - -
199F ARG* 1.3 76.9 - - - +
201F GLU* 1.3 64.3 + - + +
203F ILE* 3.4 15.5 + - + +
204F LEU 3.5 21.2 + - - +
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Residues in contact with GLU 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F LYS* 4.8 26.5 + - + +
197F GLU* 2.8 31.9 - - - +
198F LYS* 3.0 9.7 + - + +
200F PHE* 1.3 79.1 - - + +
202F ASP* 1.3 61.2 + - - +
203F ILE 3.1 5.2 - - - -
204F LEU* 3.2 18.8 + - - +
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Residues in contact with ASP 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198F LYS* 3.3 34.2 + - - +
199F ARG* 3.4 9.2 + - - +
200F PHE 3.3 0.8 - - - -
201F GLU* 1.3 80.1 - - - +
203F ILE* 1.3 66.5 + - + +
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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