Contacts of the strand formed by residues 130 - 137 (chain M) in PDB entry 6MUO
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 ALA 130 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125M GLU* 4.0 1.6 - - - +
126M THR* 2.8 52.0 + - + +
127M GLU 3.6 16.4 - - - +
128M GLU* 3.2 1.1 - - + -
129M ASN* 1.3 72.9 - - - +
131M VAL* 1.3 60.3 + - - +
132M TRP* 4.3 5.6 - - - +
153M VAL* 4.2 9.2 - - + -
155M TYR* 3.6 25.4 - - + +
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Residues in contact with VAL 131 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104M PHE* 5.6 6.7 - - + -
105M LYS* 5.9 9.4 - - + -
122M SER 5.7 1.8 - - - +
124M ARG 4.8 5.4 - - - +
125M GLU* 5.0 13.2 - - + +
129M ASN 3.6 1.3 + - - +
130M ALA* 1.3 74.0 - - - +
132M TRP* 1.3 65.3 + - - +
133M ILE* 3.8 31.2 - - + -
152M VAL 3.4 3.3 - - - +
153M VAL* 3.4 24.9 - - - +
154M TYR* 3.2 38.5 + - + +
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Residues in contact with TRP 132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71M ILE* 3.8 28.5 - - + +
74M MET* 4.5 13.7 - - + -
75M GLN* 3.2 36.5 - - + +
78M GLN* 3.6 30.7 - - - -
83M TRP* 4.1 22.7 - + - -
122M SER* 3.7 13.5 - - - +
124M ARG* 3.7 20.3 + - - +
126M THR* 3.1 36.6 + - - +
130M ALA* 4.3 8.2 - - + +
131M VAL* 1.3 77.9 - - - +
133M ILE* 1.3 65.0 + - - +
134M ARG 4.2 0.2 - - - -
151M TYR* 4.8 12.6 - + + -
152M VAL 4.3 1.6 - - - -
153M VAL* 3.7 31.2 - - + -
198M LEU* 5.3 5.2 - - + -
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Residues in contact with ILE 133 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71M ILE* 5.2 0.7 - - - -
104M PHE* 5.3 12.6 - - + -
108M PHE* 5.2 15.0 - - + -
120M THR* 3.3 35.4 - - + +
122M SER* 3.7 14.1 - - - +
131M VAL* 3.8 28.0 - - + -
132M TRP* 1.3 80.6 - - - +
134M ARG* 1.3 57.4 + - - +
135M ILE* 3.3 26.6 + - + +
150M THR 3.7 1.4 - - - +
151M TYR* 3.9 5.1 - - - -
152M VAL* 3.6 22.8 + - + +
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Residues in contact with ARG 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8M PHE* 4.3 11.9 - - - -
67M ALA* 3.8 30.4 - - + +
70M ASP* 3.5 23.4 + - - +
71M ILE* 3.7 17.1 - - + +
119M VAL 5.0 0.6 + - - +
120M THR* 2.6 30.1 + - - +
121M VAL 4.8 0.6 - - - +
122M SER* 2.9 19.4 + - - +
132M TRP 4.2 0.2 - - - -
133M ILE* 1.3 69.0 - - - +
135M ILE* 1.3 55.7 + - - +
136M ALA* 3.6 10.6 + - - +
146M GLN* 2.6 67.4 + - - +
149M PRO* 3.6 23.6 - - + +
150M THR 3.9 2.2 - - - -
151M TYR* 4.1 15.5 - - + -
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Residues in contact with ILE 135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120M THR* 3.3 21.8 - - + +
133M ILE* 3.3 34.3 - - + +
134M ARG* 1.3 70.7 - - - +
136M ALA* 1.3 71.3 + - - +
137M TRP* 3.6 33.9 - - + +
149M PRO* 3.3 4.8 - - - +
150M THR* 2.6 55.1 + - - +
152M VAL* 3.7 30.5 - - + -
175M LEU* 4.5 11.2 - - + -
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Residues in contact with ALA 136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119M VAL* 4.0 22.8 - - + +
120M THR* 4.4 5.4 - - - +
134M ARG* 3.6 18.0 + - - +
135M ILE* 1.3 79.1 - - - +
137M TRP* 1.3 83.1 + - - +
144M PRO* 4.8 1.1 - - + -
145M ASN 3.8 13.7 - - - +
146M GLN* 3.5 24.7 - - - +
148M LYS 5.0 0.2 - - - -
149M PRO* 4.7 6.3 - - + -
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Residues in contact with TRP 137 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111M ILE* 5.6 9.4 - - + -
112M LEU* 5.6 9.4 - - + -
119M VAL* 4.5 5.6 - - + -
135M ILE* 3.6 24.6 - - + +
136M ALA* 1.3 88.0 - - - +
138M GLY* 1.3 66.0 + - - +
144M PRO* 3.3 5.7 - - - +
145M ASN* 3.0 32.4 + - - +
148M LYS 5.0 7.9 + - - +
150M THR* 3.8 22.7 + - - -
166M SER* 5.1 4.0 + - - -
168M LEU* 3.7 39.6 + - + +
171M ASN* 3.2 42.7 + - + +
174M LEU* 4.5 14.8 - - + -
175M LEU* 4.0 24.2 - - + -
178M ALA* 5.8 3.1 - - + -
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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