Contacts of the helix formed by residues 137 - 144 (chain C) in PDB entry 6CM9
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 137 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135C ASN* 3.2 16.7 - - - +
136C ALA* 1.3 80.9 - - - +
138C GLU* 1.3 61.8 + - - +
139C ILE 3.4 1.1 - - - -
140C THR* 3.7 5.7 - - - -
141C ASP* 3.0 37.8 + - - +
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Residues in contact with GLU 138 (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 MET* 3.3 36.2 - - + +
135C ASN* 2.8 21.3 + - - +
137C ALA* 1.3 71.4 - - - +
139C ILE* 1.3 60.7 + - - +
141C ASP* 3.3 6.8 + - - +
142C LYS* 2.9 46.8 + - + +
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Residues in contact with ILE 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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92C VAL* 4.6 10.8 - - + -
94C SER* 3.4 27.8 - - - +
125C ALA* 4.5 19.1 - - + -
128C GLN* 5.1 2.0 - - - +
134C MET* 3.7 27.6 - - + +
135C ASN 3.4 20.3 + - - +
137C ALA 3.4 0.2 - - - -
138C GLU* 1.3 74.8 - - - +
140C THR* 1.3 57.9 + - - +
142C LYS* 3.4 5.2 + - - +
143C LEU* 2.9 51.8 + - + +
155C ILE* 4.0 17.0 - - + -
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Residues in contact with THR 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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136C ALA 3.3 19.4 + - - -
137C ALA* 3.6 9.5 + - - -
139C ILE* 1.3 78.8 - - - +
141C ASP* 1.3 62.2 + - - +
143C LEU 3.8 0.2 - - - -
144C GLY* 2.9 24.4 + - - -
145C LEU* 3.4 25.2 + - + +
146C HIS* 5.1 2.0 - - + +
153C TRP* 3.6 32.7 - - + -
155C ILE* 3.4 20.7 - - - +
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Residues in contact with ASP 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 ALA* 3.0 23.2 + - - +
138C GLU* 3.3 7.0 + - + +
140C THR* 1.3 82.6 - - - +
142C LYS* 1.3 65.2 + - + +
144C GLY* 3.8 6.7 + - - -
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Residues in contact with LYS 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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97C ARG* 5.8 8.5 - - - +
100C VAL* 6.1 4.0 - - - +
101C ASN* 5.9 0.4 + - - -
104C ARG* 2.8 33.9 + - - +
138C GLU* 2.9 33.2 + - + +
139C ILE* 3.9 6.7 - - - +
140C THR 3.3 0.2 - - - -
141C ASP* 1.3 80.9 - - + +
143C LEU* 1.3 62.1 + - + +
144C GLY 3.4 0.5 + - - -
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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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90C PHE* 4.8 10.3 - - + -
92C VAL* 4.2 17.9 - - + -
100C VAL* 4.7 17.5 - - + -
104C ARG* 4.0 37.0 - - + +
107C LEU* 5.0 13.8 - - + +
108C MET* 3.4 24.6 - - - +
123C VAL* 4.9 8.3 - - + -
139C ILE* 2.9 40.5 + - + +
140C THR 4.3 1.6 - - - +
142C LYS* 1.3 79.1 - - + +
144C GLY* 1.3 63.6 + - - +
145C LEU* 4.4 19.1 - - + +
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Residues in contact with GLY 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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104C ARG* 4.7 6.1 - - - -
108C MET* 4.9 3.2 - - - +
140C THR 2.9 11.6 + - - -
141C ASP* 3.8 6.0 + - - -
142C LYS 3.2 3.8 - - - -
143C LEU* 1.3 80.6 - - - +
145C LEU* 1.3 61.0 + - - -
146C HIS 3.4 3.4 - - - -
147C SER* 3.1 23.1 + - - -
148C LEU* 3.8 11.1 - - - +
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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