Contacts of the helix formed by residues 139 - 149 (chain C) in PDB entry 5L26
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 139 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137C GLY 4.0 0.2 + - - -
138C THR* 1.3 73.6 - - - +
140C LYS* 1.3 59.6 + - - +
141C ALA* 4.0 3.9 + - - +
142C GLU* 3.0 33.8 + - - +
143C SER* 2.8 28.5 + - - -
172C GLU* 2.9 30.4 + - - -
227C THR* 4.3 10.1 - - - +
228C GLN 4.1 15.3 - - - -
229C ASN 5.5 0.4 - - - -
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Residues in contact with LYS 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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129C GLY 6.0 0.4 - - - +
133C GLN* 3.2 30.4 + - - +
139C SER* 1.3 74.9 - - - +
141C ALA* 1.3 61.9 + - - +
143C SER* 3.2 6.2 + - - -
144C MET* 3.0 51.4 + - + +
228C GLN 4.6 1.4 + - - +
229C ASN 3.8 17.4 + - - +
230C ASP* 5.0 1.6 - - - +
231C ALA* 3.7 34.5 - - + +
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Residues in contact with ALA 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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139C SER* 3.3 6.1 + - - +
140C LYS* 1.3 78.2 - - - +
142C GLU* 1.3 64.5 + - - +
144C MET* 3.1 3.4 + - - -
145C SER* 3.1 20.4 + - - -
161C VAL* 3.4 30.9 - - + +
164C TYR* 4.2 25.6 - - + -
168C MET* 4.4 11.9 - - + -
172C GLU* 5.8 2.0 - - - +
228C GLN 5.8 0.2 + - - -
231C ALA* 4.1 7.4 - - + +
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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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138C THR* 3.3 12.0 - - - -
139C SER* 3.0 41.4 + - - +
141C ALA* 1.3 79.2 - - - +
143C SER* 1.3 59.1 + - - +
145C SER* 3.9 2.1 - - - -
146C ALA* 3.2 26.0 + - - +
168C MET* 5.3 0.6 - - + +
172C GLU* 3.3 28.9 - - + +
175C ALA* 3.2 22.6 - - + +
176C VAL* 4.4 13.3 - - + +
214C LEU* 4.1 8.2 - - + +
218C LYS* 2.7 36.4 + - - -
223C GLU* 5.1 0.2 - - - +
227C THR* 6.0 0.3 - - - +
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Residues in contact with SER 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C GLY* 3.3 26.7 - - - -
132C LEU* 4.0 11.5 - - - +
133C GLN* 3.8 7.4 + - - -
138C THR* 2.6 29.3 + - - -
139C SER 2.8 15.6 + - - -
140C LYS* 3.2 6.0 + - - -
141C ALA 3.1 0.6 - - - -
142C GLU* 1.3 77.3 - - - +
144C MET* 1.3 59.0 + - - +
146C ALA* 3.9 4.9 - - - +
147C ALA* 3.0 30.0 + - - +
214C LEU* 5.0 2.8 - - - +
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Residues in contact with MET 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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125C ILE* 3.4 40.6 - - + +
126C LYS* 3.9 23.8 - - + +
129C GLY* 4.3 3.4 - - - -
130C GLY* 4.8 6.1 - - - +
133C GLN* 6.2 0.2 - - - +
140C LYS* 3.0 41.9 + - + +
141C ALA* 3.1 6.3 + - - +
143C SER* 1.3 77.7 - - - +
145C SER* 1.3 57.5 + - - +
147C ALA* 3.3 1.9 + - - -
148C ALA* 2.8 31.1 + - - +
160C VAL* 4.5 3.8 - - + -
161C VAL* 3.6 18.4 - - + -
231C ALA* 5.0 7.6 - - + +
232C GLU 5.8 1.3 - - - +
233C VAL* 5.2 17.3 - - + +
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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 ALA 3.1 13.8 + - - -
142C GLU 4.0 4.7 - - - -
144C MET* 1.3 78.2 - - - +
146C ALA* 1.3 58.3 + - - +
148C ALA* 3.3 6.4 + - - +
149C ASN* 2.9 40.5 + - - -
157C ALA* 3.9 5.6 - - - +
158C PRO* 4.0 9.9 - - - +
161C VAL* 4.1 17.8 - - - +
176C VAL* 3.5 34.8 - - - +
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Residues in contact with ALA 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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132C LEU* 4.5 1.1 - - + -
142C GLU 3.2 17.1 + - - +
143C SER 3.9 3.8 - - - +
145C SER* 1.3 78.8 - - - +
147C ALA* 1.3 61.7 + - - +
149C ASN* 3.4 20.6 + - - +
150C ILE* 3.8 3.5 - - - +
175C ALA 5.5 1.8 - - - +
179C GLY* 5.1 9.4 - - - -
210C ALA* 3.3 33.0 - - + +
214C LEU* 4.1 26.5 - - + -
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Residues in contact with ALA 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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125C ILE* 4.0 15.5 - - - +
128C ILE* 3.8 20.3 - - + +
129C GLY 3.8 22.7 - - - +
132C LEU* 4.7 1.8 - - + +
143C SER 3.0 18.8 + - - +
144C MET 3.7 3.6 - - - +
146C ALA* 1.3 76.9 - - - +
148C ALA* 1.3 62.2 + - - +
150C ILE* 3.3 29.2 + - - +
151C PHE* 4.5 1.6 + - - +
210C ALA* 4.6 2.0 - - - -
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Residues in contact with ALA 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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116C TYR* 4.5 4.7 + - - +
125C ILE* 3.6 29.1 - - + +
144C MET 2.8 17.8 + - - +
145C SER 3.3 4.5 + - - +
147C ALA* 1.3 72.8 - - - +
149C ASN* 1.3 62.7 + - - +
150C ILE 3.0 6.8 + - - -
151C PHE* 3.0 15.2 + - - +
152C VAL* 3.1 16.7 + - - +
157C ALA* 3.9 23.6 - - + +
160C VAL* 4.4 2.0 - - + -
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Residues in contact with ASN 149 (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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145C SER* 2.9 28.3 + - - +
146C ALA* 3.6 9.2 - - - +
147C ALA 3.3 0.6 - - - -
148C ALA* 1.3 76.3 - - - +
150C ILE* 1.3 62.3 + - - +
151C PHE 3.3 0.2 - - - -
152C VAL 3.0 5.3 - - - +
153C GLY 3.1 15.4 - - - +
154C GLN* 3.6 2.3 + - - +
157C ALA* 3.3 11.0 - - - +
158C PRO* 5.4 0.6 - - - +
176C VAL 4.0 3.0 + - - -
179C GLY* 3.2 10.9 - - - +
180C GLY* 3.1 29.3 - - - +
183C SER* 3.2 22.4 + - - +
184C VAL 3.1 4.9 - - - +
210C ALA* 6.2 0.7 - - - -
504C NA 2.3 41.0 - - - -
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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