Contacts of the helix formed by residues 133 - 148 (chain C) in PDB entry 3CMM
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 SER 133 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131C THR 4.1 2.0 + - - -
132C VAL* 1.3 77.9 - - - +
134C LEU* 1.3 53.0 + - - +
135C GLU* 3.8 10.3 + - - +
136C ASP* 3.0 33.1 + - - +
137C LYS* 2.7 31.2 + - - +
300C HIS* 4.5 8.1 - - - -
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Residues in contact with LEU 134 (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 VAL 3.7 0.4 + - - -
133C SER* 1.3 69.9 - - - +
135C GLU* 1.3 60.2 + - - +
137C LYS* 4.0 12.8 - - + -
138C VAL* 2.8 37.5 + - + +
155C GLU* 5.8 1.8 - - - +
269C LEU* 4.2 23.6 - - + -
273C LEU* 3.9 30.5 - - + -
296C PHE 5.6 0.2 - - - -
297C GLN* 4.2 22.4 - - + +
300C HIS* 3.6 47.5 + - + +
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Residues in contact with GLU 135 (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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133C SER* 3.2 9.1 + - - +
134C LEU* 1.3 79.4 - - - +
136C ASP* 1.3 68.4 + - - +
138C VAL* 3.4 5.8 + - - +
139C LYS* 3.2 55.5 + - - +
304C VAL* 4.8 16.5 - - + +
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Residues in contact with ASP 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C VAL* 3.5 18.8 - - + +
133C SER* 3.0 26.1 + - - +
135C GLU* 1.3 85.0 - - - +
137C LYS* 1.3 59.2 + - - +
139C LYS* 3.4 15.9 + - - +
140C ILE* 2.9 38.8 + - + +
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Residues in contact with LYS 137 (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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128C ALA* 3.8 15.9 - - + -
129C THR 3.5 14.2 + - - -
130C ASP* 4.8 0.6 - - - +
132C VAL* 3.4 32.6 + - + +
133C SER 2.7 18.4 + - - +
134C LEU* 3.2 19.0 + - + +
136C ASP* 1.3 71.2 - - - +
138C VAL* 1.3 60.5 + - - +
140C ILE* 3.8 4.1 - - - +
141C ASN* 2.8 33.4 + - - +
151C PHE* 4.0 5.0 - - + -
153C SER* 3.1 27.8 + - - +
154C SER 3.2 23.8 + - - -
155C GLU* 4.0 20.7 + - - +
162C ASN* 5.7 0.4 + - - -
269C LEU* 3.8 15.3 - - + -
300C HIS* 5.6 1.9 + - + +
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Residues in contact with VAL 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C LEU* 2.8 24.4 + - + +
135C GLU* 3.7 6.7 - - - +
136C ASP 3.3 0.2 - - - -
137C LYS* 1.3 75.4 - - - +
139C LYS* 1.3 58.7 + - + +
141C ASN* 3.6 3.5 + - - +
142C GLU* 3.0 30.3 + - + +
269C LEU* 4.2 14.4 - - + -
270C LYS* 4.1 36.7 + - + +
273C LEU* 4.1 26.0 - - + -
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Residues in contact with LYS 139 (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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723A TYR* 3.3 67.6 + - + +
759A LYS* 4.8 7.9 - - - +
117C VAL* 4.8 1.7 - - + +
135C GLU* 3.2 43.3 + - - +
136C ASP* 3.7 19.1 + - - +
137C LYS 3.2 0.2 - - - -
138C VAL* 1.3 77.0 - - + +
140C ILE* 1.3 66.5 + - + +
142C GLU* 3.3 5.2 + - - +
143C PHE* 3.3 18.4 + - - +
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Residues in contact with ILE 140 (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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42C LEU* 3.9 23.3 - - + -
114C LEU* 4.5 13.5 - - + -
117C VAL* 4.4 20.9 - - + -
120C LEU* 3.8 19.0 - - + +
126C VAL* 4.3 8.5 - - + -
128C ALA* 5.5 0.7 - - + -
132C VAL* 4.3 11.7 - - + -
136C ASP* 2.9 28.6 + - + +
137C LYS* 3.9 3.4 - - - +
139C LYS* 1.3 76.5 - - + +
141C ASN* 1.3 64.6 + - - +
143C PHE* 3.2 5.0 + - - +
144C CYS* 3.1 23.3 + - - -
151C PHE* 3.5 23.8 - - + -
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Residues in contact with ASN 141 (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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137C LYS 2.8 18.3 + - - +
138C VAL 4.0 2.7 - - - +
140C ILE* 1.3 76.8 - - - +
142C GLU* 1.3 59.0 + - - +
144C CYS* 4.3 0.7 - - - -
145C HIS* 2.8 30.2 + - - +
151C PHE* 3.3 43.2 - - + +
164C PHE* 4.2 0.4 - - - -
166C ASP* 2.7 29.5 + - - +
268C SER* 3.6 10.2 - - - -
269C LEU* 2.8 36.2 + - + +
270C LYS 4.4 1.0 + - - -
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Residues in contact with GLU 142 (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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721A ASP* 3.4 25.7 - - - +
723A TYR* 3.8 5.2 - - + +
724A ASN* 2.8 39.3 + - - +
138C VAL* 3.0 21.3 + - + +
139C LYS* 3.7 6.7 - - - +
140C ILE 3.2 0.2 - - - -
141C ASN* 1.3 78.9 - - - +
143C PHE* 1.3 53.2 + - - +
145C HIS* 4.7 5.4 - - - +
146C SER* 2.7 37.9 + - - -
268C SER* 4.2 19.1 + - - -
270C LYS* 4.9 10.7 - - - +
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Residues in contact with PHE 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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722A ILE 6.0 0.2 - - - -
723A TYR* 3.2 22.1 + - - +
725A ASN* 3.3 28.9 - - + -
728A PHE* 5.8 4.9 - + + -
729A HIS* 5.5 0.2 - - - -
117C VAL* 3.4 48.9 - - + -
118C THR* 4.0 18.8 - - - -
120C LEU* 3.7 22.7 - - + -
121C SER* 3.9 19.7 - - - -
139C LYS 3.3 7.1 + - - +
140C ILE 3.2 7.7 + - - +
141C ASN 3.2 0.2 - - - -
142C GLU* 1.3 75.4 - - - +
144C CYS* 1.3 55.8 + - - +
146C SER* 3.4 2.5 + - - -
147C SER* 2.8 53.3 + - - -
149C ILE* 4.0 8.1 - - + -
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Residues in contact with CYS 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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120C LEU* 4.0 20.9 - - - -
126C VAL* 4.1 21.3 - - - -
140C ILE* 3.1 27.6 + - - +
141C ASN 3.7 3.4 - - - +
143C PHE* 1.3 78.3 - - - +
145C HIS* 1.3 58.7 + - - +
147C SER* 2.9 2.2 + - - -
148C GLY 2.8 27.4 + - - -
149C ILE* 3.0 37.3 + - + +
151C PHE* 4.1 18.6 - - + -
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Residues in contact with HIS 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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141C ASN* 2.8 23.9 + - - +
142C GLU* 4.2 8.1 - - - +
144C CYS* 1.3 74.5 - - - +
146C SER* 1.3 64.9 + - - +
147C SER 3.2 0.5 + - - -
148C GLY* 3.4 8.9 + - - -
149C ILE 4.5 2.7 - - - -
166C ASP* 2.9 33.4 + - - +
168C GLY* 4.1 10.2 - - - -
169C ASP* 3.9 29.7 + - + +
266C PHE 3.2 28.0 - - - -
267C LYS* 4.3 0.4 - - - -
268C SER* 4.1 21.1 + - - -
271C GLN* 5.5 1.4 + - - -
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Residues in contact with SER 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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724A ASN* 3.7 25.2 - - - -
725A ASN* 2.9 34.1 + - - +
726A ASP* 4.4 14.0 - - - +
843A GLN* 5.1 1.6 - - - -
849A THR* 4.8 8.2 + - - -
142C GLU* 2.7 23.5 + - - -
143C PHE 3.4 4.9 + - - -
145C HIS* 1.3 81.3 - - - +
147C SER* 1.3 57.0 + - - +
148C GLY 3.5 0.2 - - - -
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Residues in contact with SER 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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725A ASN* 3.2 30.7 + - - +
121C SER* 5.5 1.8 - - - -
143C PHE* 2.8 29.3 + - - -
144C CYS 2.9 4.3 + - - -
146C SER* 1.3 78.6 - - - +
148C GLY* 1.3 57.4 + - - +
149C ILE* 3.3 25.2 + - - +
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Residues in contact with GLY 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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144C CYS 2.8 4.3 + - - -
145C HIS* 3.4 9.9 + - - -
146C SER 3.5 0.8 - - - -
147C SER* 1.3 77.9 - - - +
149C ILE* 1.3 62.6 + - - +
150C ARG* 3.7 19.2 + - - -
167C LEU 5.3 1.9 - - - +
168C GLY* 6.0 4.9 - - - -
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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