Contacts of the helix formed by residues 137 - 146 (chain A) in PDB entry 3C3P
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 ASN 137 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A PHE* 1.3 68.8 - - - +
138A GLY* 1.3 64.2 + - - +
139A ALA* 3.3 19.6 + - - +
140A ASP* 3.0 41.9 + - + +
141A VAL* 3.0 20.5 + - - +
180A GLU* 3.7 19.3 + - - +
181A PHE* 6.1 0.3 - - - -
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Residues in contact with GLY 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A MSE 4.1 12.3 - - - -
133A CYS* 6.2 0.4 - - - -
136A PHE 3.2 6.8 + - - -
137A ASN* 1.3 71.8 + - - +
139A ALA* 1.3 56.7 + - - +
141A VAL* 3.1 3.7 + - - +
142A LEU* 2.9 26.3 + - - +
181A PHE* 3.3 48.3 - - - +
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Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ASN* 3.3 11.6 + - - +
138A GLY* 1.3 75.1 - - - +
140A ASP* 1.3 62.5 + - - +
142A LEU* 3.5 2.3 + - - +
143A GLU* 3.0 29.3 + - - +
180A GLU* 4.9 6.5 - - - +
181A PHE* 3.4 5.8 - - - +
184A HIS* 3.7 47.1 + - + +
188A ARG* 5.3 0.9 + - - -
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Residues in contact with ASP 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LEU* 5.7 2.5 - - + -
137A ASN* 3.0 42.8 + - + +
139A ALA* 1.3 80.7 - - - +
141A VAL* 1.3 65.1 + - + +
143A GLU* 3.3 7.1 + - - +
144A ARG* 3.3 21.5 + - - +
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Residues in contact with VAL 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A PRO* 6.0 1.1 - - + -
117A LEU* 3.9 27.4 - - + -
129A LEU* 4.3 9.0 - - + -
131A MSE 4.1 31.2 - - + -
136A PHE* 3.4 38.1 - - + -
137A ASN 3.0 12.5 + - - +
138A GLY 3.5 7.4 - - - +
140A ASP* 1.3 76.7 - - + +
142A LEU* 1.3 59.1 + - - +
144A ARG* 3.3 2.4 + - - +
145A MSE 2.8 50.8 + - + +
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Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A LEU* 5.5 1.3 - - + -
131A MSE 5.5 1.1 - - + -
138A GLY 2.9 16.2 + - - +
139A ALA* 3.9 4.9 - - - +
141A VAL* 1.3 74.9 - - + +
143A GLU* 1.3 61.2 + - - +
144A ARG 3.1 1.8 - - - -
145A MSE 4.3 4.3 - - + +
146A ASN* 2.8 46.4 + - + +
149A LEU* 4.3 9.9 - - + -
155A LEU* 4.8 16.2 - - + -
181A PHE* 4.3 11.2 - - + -
184A HIS* 4.7 0.4 - - - +
185A LEU* 3.6 30.7 - - + -
188A ARG* 3.6 35.2 + - - +
191A PHE* 3.9 21.1 - - + -
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Residues in contact with GLU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ALA 3.0 17.4 + - - +
140A ASP* 3.3 8.2 + - - +
142A LEU* 1.3 78.2 - - - +
144A ARG* 1.3 58.5 + - - +
146A ASN* 4.7 2.5 + - - +
147A ARG* 3.4 19.1 + - - +
188A ARG* 5.2 4.9 - - - +
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Residues in contact with ARG 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LEU* 5.6 8.1 - - + -
121A ALA* 5.1 7.0 - - + +
140A ASP 3.3 10.3 + - - +
141A VAL* 3.6 8.3 - - - +
142A LEU 3.1 0.2 - - - -
143A GLU* 1.3 81.0 - - - +
145A MSE 1.3 67.4 + - + +
146A ASN 3.7 0.4 - - - -
147A ARG* 3.1 31.9 + - - +
148A CYS* 4.3 7.6 - - - -
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Residues in contact with MSE 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LEU* 4.3 12.6 - - + +
120A ALA* 3.5 29.6 - - + +
121A ALA* 3.7 28.9 - - - -
126A ILE* 3.4 32.8 - - + -
129A LEU* 3.9 26.9 - - + -
141A VAL* 2.8 42.5 + - + +
142A LEU* 4.6 2.2 - - + -
144A ARG* 1.3 76.7 - - + +
146A ASN* 1.3 58.3 + - - +
147A ARG 3.0 4.0 - - - -
148A CYS* 2.7 35.4 + - + +
149A LEU* 3.4 7.7 + - - +
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Residues in contact with ASN 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A LEU* 2.8 30.1 + - + +
143A GLU 4.7 2.0 - - - +
144A ARG 3.7 0.6 - - - -
145A MSE 1.3 73.1 - - - +
147A ARG* 1.3 61.5 + - + +
149A LEU* 3.2 39.9 + - - +
188A ARG* 3.9 20.5 - - - +
190A ASP* 4.1 6.9 + - - -
191A PHE* 3.6 6.9 - - - -
207A ARG* 3.5 31.0 + - - +
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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