Contacts of the helix formed by residues 136 - 146 (chain C) in PDB entry 5UWS
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 GLU 136 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C ARG* 4.7 5.4 + - - -
133C ASN 5.4 0.3 - - - +
134C TRP* 3.5 21.8 + - + -
135C PRO* 1.3 93.9 - - + +
137C PHE* 1.3 63.3 + - - +
138C ILE 3.4 2.2 - - - -
139C PRO* 3.6 10.8 - - + -
140C GLU* 2.9 56.1 + - + +
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Residues in contact with PHE 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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95C VAL* 6.3 0.2 - - + -
122C LEU* 4.3 12.6 - - + -
126C LEU* 3.6 39.7 - - + -
130C TRP* 3.7 16.8 - + + -
134C TRP* 3.2 52.9 + + + +
135C PRO 3.3 1.6 - - - -
136C GLU* 1.3 78.4 - - - +
138C ILE* 1.3 71.9 + - + +
140C GLU* 3.6 2.8 - - - +
141C LEU* 2.7 65.5 + - + +
158C VAL* 4.1 13.9 - - + -
159C LEU* 5.2 0.7 - - + -
162C LEU* 5.0 4.7 - - + -
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Residues in contact with ILE 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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130C TRP* 4.0 20.3 - - + +
135C PRO 4.8 0.2 + - - -
137C PHE* 1.3 91.9 - - + +
139C PRO* 1.3 65.8 - - - +
141C LEU* 3.1 6.5 + - + +
142C ILE* 2.9 30.3 + - + +
159C LEU* 4.1 15.9 - - + -
162C LEU* 5.1 4.0 - - + -
189C GLU* 3.3 35.0 + - + +
192C GLN* 3.8 26.2 - - + +
193C ILE* 3.9 29.8 - - + -
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Residues in contact with PRO 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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135C PRO 3.9 8.7 - - - +
136C GLU* 3.5 18.2 - - + +
138C ILE* 1.3 96.7 - - + +
140C GLU* 1.3 57.3 + - + +
142C ILE* 3.4 8.1 + - + +
143C GLY* 2.9 24.4 + - - -
189C GLU* 3.6 12.6 - - - +
192C GLN* 4.4 9.2 - - - +
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Residues in contact with GLU 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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134C TRP* 4.8 5.9 + - - -
136C GLU* 2.9 51.1 + - + +
137C PHE* 3.9 2.5 - - - +
139C PRO* 1.3 70.8 - - + +
141C LEU* 1.3 61.0 + - - +
143C GLY* 3.9 1.7 - - - +
144C SER* 3.0 30.3 + - - -
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Residues in contact with LEU 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 PHE* 2.7 53.4 + - + +
138C ILE* 3.5 8.3 - - + +
140C GLU* 1.3 71.6 - - - +
142C ILE* 1.3 68.4 + - + +
144C SER* 2.9 18.4 + - - -
145C SER* 2.9 18.9 + - - -
155C ASN* 3.3 39.2 + - + +
158C VAL* 4.7 5.4 - - + -
159C LEU* 4.0 35.0 - - + -
193C ILE* 6.3 0.4 - - + -
196C LEU* 4.0 13.5 - - + -
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Residues in contact with ILE 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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138C ILE* 2.9 26.3 + - + +
139C PRO* 3.8 5.8 - - + +
141C LEU* 1.3 79.4 - - + +
143C GLY* 1.3 64.4 + - - +
145C SER* 3.3 19.4 + - - -
146C SER* 3.8 5.7 + - - -
192C GLN* 3.4 53.6 - - + +
193C ILE* 4.1 2.7 - - + +
196C LEU* 4.1 30.0 - - + +
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Residues in contact with GLY 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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139C PRO 2.9 16.9 + - - -
140C GLU* 3.9 2.5 - - - -
142C ILE* 1.3 78.3 - - - +
144C SER* 1.3 58.7 + - - +
145C SER 3.2 0.2 + - - -
146C SER* 2.9 25.8 + - - -
147C SER* 3.9 5.0 + - - -
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Residues in contact with SER 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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140C GLU 3.0 14.8 + - - -
141C LEU* 2.9 18.5 + - - -
143C GLY* 1.3 74.4 - - - +
145C SER* 1.3 64.1 + - - +
147C SER* 3.1 23.3 + - - -
148C SER 3.9 3.1 + - - -
151C VAL* 3.8 17.9 - - - +
155C ASN* 3.3 12.5 + - - -
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Residues in contact with SER 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 LEU 2.9 11.4 + - - -
142C ILE 3.5 10.3 - - - -
143C GLY 3.1 0.6 - - - -
144C SER* 1.3 77.6 + - - +
146C SER* 1.3 61.4 + - - +
147C SER 3.1 1.7 + - - -
148C SER 3.2 18.5 + - - +
152C CYS* 3.4 31.9 - - - +
155C ASN* 2.8 29.0 + - - +
196C LEU* 3.8 26.6 - - - +
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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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142C ILE 3.8 5.0 + - - -
143C GLY* 2.9 17.5 + - - -
145C SER* 1.3 78.0 - - - +
147C SER* 1.3 61.0 + - - +
148C SER 3.5 0.4 + - - -
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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