Contacts of the strand formed by residues 142 - 149 (chain C) 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 ARG 142 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107C LYS* 4.6 2.0 - - - +
108C ASP* 3.7 16.7 + - - +
136C TYR* 3.4 6.7 - - - -
137C CYS* 2.8 35.4 + - - +
140C THR* 3.1 35.4 - - - +
141C ASP* 1.3 78.0 - - - +
143C LEU* 1.3 62.6 + - - +
144C PHE* 3.6 15.8 + - + -
5E LYS* 4.1 13.5 - - - +
6E LYS 2.7 39.4 + - - +
7E PHE* 4.0 7.9 - - - -
48E LEU* 3.9 34.1 + - - +
52E ASP* 2.7 41.6 + - - -
55E ARG* 5.2 4.6 - - - +
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Residues in contact with LEU 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C LEU* 4.3 7.4 - - + -
104C TYR* 3.7 27.4 - - + +
105C ILE* 3.8 30.1 - - + +
108C ASP* 2.9 20.2 + - - +
109C PHE* 3.9 26.0 - - + -
134C LEU* 4.2 11.7 - - + -
135C THR 3.3 14.8 - - - +
136C TYR* 4.1 3.8 - - + -
142C ARG* 1.3 73.3 - - - +
144C PHE* 1.3 68.1 + - - +
162C LEU* 3.7 22.2 - - + -
200C PHE* 3.9 19.1 - - + -
55E ARG* 5.6 3.5 + - - -
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Residues in contact with PHE 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C LEU* 3.3 4.9 - - - +
135C THR* 2.8 46.6 + - + +
137C CYS* 3.5 17.5 - - + -
140C THR* 3.9 6.7 - - - -
142C ARG* 3.6 21.2 + - + -
143C LEU* 1.3 84.2 - - - +
145C ILE* 1.3 67.6 + - - +
156C ILE* 4.4 9.6 - - + -
159C PHE* 3.6 22.0 - + - -
8E TYR* 3.2 30.3 - + - -
48E LEU* 3.8 27.6 - - + -
70E LEU* 4.2 17.5 - - + -
74E VAL* 4.2 11.4 - - + -
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Residues in contact with ILE 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C PHE* 3.7 33.2 - - + -
115C PHE* 4.3 2.9 - - + -
118C GLU* 4.1 11.4 - - + +
119C PHE* 3.9 43.1 - - + +
122C ALA* 4.0 13.2 - - + -
133C VAL 3.4 9.9 - - - +
134C LEU* 4.1 9.0 - - + -
144C PHE* 1.3 81.6 - - - +
146C MET* 1.3 69.3 + - - +
55E ARG* 5.7 0.4 - - - +
63E ILE* 6.0 0.4 - - + -
67E LEU* 3.3 44.8 - - + +
70E LEU* 4.5 6.0 - - - +
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Residues in contact with MET 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C ALA* 3.7 2.6 - - - +
133C VAL* 2.9 49.5 + - + +
135C THR* 3.7 26.7 - - + -
144C PHE* 5.5 0.4 - - + -
145C ILE* 1.3 80.7 - - - +
147C GLN* 1.3 61.4 + - - +
148C VAL* 3.8 7.4 + - + -
154C ASN 4.2 11.9 - - - +
155C VAL* 4.2 11.7 - - - -
156C ILE* 3.2 62.1 - - + +
159C PHE* 4.3 8.1 - - + +
67E LEU* 4.3 4.0 - - - +
71E SER* 5.3 5.4 - - - -
157E PRO* 5.9 3.4 - - - -
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Residues in contact with GLN 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C ALA* 2.9 32.8 + - + +
125C SER* 3.2 21.4 + - - -
126C ALA* 3.4 25.9 - - + +
131C TRP 3.5 8.5 - - - +
132C ALA* 4.8 0.9 - - - +
146C MET* 1.3 74.5 - - - +
148C VAL* 1.3 62.6 + - - +
149C GLU* 3.6 5.9 + - + +
154C ASN* 3.6 26.0 + - - +
64E LYS* 3.5 28.6 - - - +
67E LEU* 4.2 24.5 + - + +
68E LYS* 3.9 19.1 - - + +
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Residues in contact with VAL 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C LEU* 4.7 4.3 - - + -
126C ALA* 5.3 0.9 - - - +
130C GLY* 2.9 4.0 - - - -
131C TRP* 2.7 45.1 + - + +
133C VAL* 4.0 25.8 - - + -
146C MET* 4.6 9.0 - - + +
147C GLN* 1.3 74.1 - - - +
149C GLU* 1.3 75.0 + - - +
150C LYS 3.9 3.6 - - - +
151C HIS* 3.6 9.2 - - - +
152C ASN 3.4 18.4 - - - +
153C VAL 3.3 10.8 - - - +
154C ASN 4.6 2.2 - - - +
155C VAL* 4.2 20.9 - - + -
157E PRO* 5.5 4.9 - - + -
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Residues in contact with GLU 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C ALA* 5.9 2.0 - - + -
127C GLU* 3.8 20.0 + - - +
129C SER 3.5 9.0 - - - +
130C GLY* 4.1 0.2 - - - -
147C GLN* 3.6 8.0 + - + +
148C VAL* 1.3 73.5 - - - +
150C LYS* 1.3 73.9 + - + +
151C HIS 3.1 0.2 + - - -
152C ASN 3.2 1.0 + - - -
153C VAL* 3.0 47.2 + - + +
154C ASN* 3.8 17.1 + - - +
150D LYS* 2.7 42.9 + - + +
68E LYS* 3.2 22.8 + - - -
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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