Contacts of the strand formed by residues 138 - 146 (chain M) in PDB entry 6K4Y
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 TYR 138 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106M ILE* 3.6 25.7 - - + +
110M MET* 3.5 35.2 - - + -
111M GLU* 2.5 32.7 + - - -
114M LYS* 3.8 34.0 - - + -
117M MET* 4.6 7.0 - - + -
131M VAL* 4.6 11.0 - - + -
132M GLU 3.3 3.4 - - - -
133M ILE* 3.6 35.9 - - + +
137M ASN* 1.3 76.2 - - - +
139M LEU* 1.3 61.7 + - - +
140M ALA 4.1 0.4 - - - -
153M GLU* 3.3 7.3 - - - +
154M ILE* 2.9 48.5 + - + +
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Residues in contact with LEU 139 (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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117M MET* 5.4 0.2 - - - -
130M LYS 3.1 13.3 - - - +
131M VAL* 3.2 13.7 - - - +
132M GLU* 3.1 40.8 + - + +
134M TYR* 3.7 29.6 - - + +
137M ASN* 4.2 6.5 - - + +
138M TYR* 1.3 83.6 - - - +
140M ALA* 1.3 57.6 + - - +
141M ILE* 3.0 28.9 + - + -
151M ASN* 4.0 12.8 - - - +
153M GLU* 3.5 29.8 - - + +
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Residues in contact with ALA 140 (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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117M MET* 3.7 25.4 - - + +
118M LEU* 5.5 1.3 - - + -
121M LEU* 3.8 15.0 - - + -
128M LEU* 3.5 13.9 - - + +
131M VAL* 4.7 5.8 - - + -
138M TYR 4.1 0.2 - - - -
139M LEU* 1.3 69.5 - - - +
141M ILE* 1.3 63.8 + - - +
142M LEU 3.4 1.7 + - - -
152M PHE* 2.8 56.5 + - + +
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Residues in contact with ILE 141 (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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128M LEU* 3.3 11.4 - - - +
129M LYS* 2.9 40.7 + - + -
130M LYS* 3.5 26.6 + - + +
132M GLU* 4.6 7.6 - - + +
139M LEU* 3.0 35.7 + - + -
140M ALA* 1.3 71.1 - - - +
142M LEU* 1.3 72.3 + - - +
150M ARG* 3.7 9.9 - - + +
151M ASN* 3.7 22.0 - - + +
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Residues in contact with LEU 142 (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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121M LEU* 5.7 0.2 - - + -
126M PHE* 4.6 16.2 - - + -
127M VAL 4.1 12.3 - - - +
128M LEU* 5.4 3.1 - - + -
129M LYS* 3.3 10.4 - - - +
140M ALA 3.4 1.4 + - - +
141M ILE* 1.3 82.7 - - - +
143M GLU* 1.3 67.4 + - - +
144M LYS 3.5 12.1 - - - +
146M THR* 3.3 24.9 - - + +
149M ILE* 3.7 29.8 - - + +
150M ARG 2.9 17.1 + - - +
152M PHE* 3.6 47.3 - - + -
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Residues in contact with GLU 143 (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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127M VAL* 3.5 36.2 + - + +
128M LEU 3.0 22.3 + - - +
129M LYS* 3.4 26.3 - - - +
142M LEU* 1.3 76.4 - - - +
144M LYS* 1.3 94.8 + - + +
146M THR* 5.9 0.4 - - + +
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Residues in contact with LYS 144 (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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142M LEU* 3.5 21.5 - - - +
143M GLU* 1.3 121.5 + - + +
145M ARG* 1.3 62.0 + - - +
146M THR* 2.8 26.3 + - + +
149M ILE 3.8 0.3 - - - +
150M ARG* 5.0 0.4 - - - +
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Residues in contact with ARG 145 (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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144M LYS* 1.3 72.2 - - - +
146M THR* 1.3 62.2 + - - +
147M ASN 3.8 1.7 + - - -
148M GLY* 3.6 23.0 + - - +
149M ILE 3.3 17.0 - - - +
150M ARG* 4.7 5.8 - - + +
165M TYR* 2.9 48.4 + - + -
166M LYS* 4.1 8.9 + - - +
40T A 3.0 48.4 + - - -
41T T 3.3 29.9 + - - +
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Residues in contact with THR 146 (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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126M PHE* 5.4 7.8 - - - -
142M LEU* 3.3 23.1 - - + +
143M GLU 5.9 0.2 - - - +
144M LYS* 2.8 34.2 + - + +
145M ARG* 1.3 70.5 - - - +
147M ASN* 1.3 72.6 + - - +
148M GLY 3.1 0.7 - - - -
149M ILE* 3.0 24.6 + - - +
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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