Contacts of the strand formed by residues 179 - 184 (chain C) in PDB entry 1L3C
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 VAL 179 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C THR* 5.5 3.4 - - + -
18C ALA* 5.9 3.8 - - + +
21C VAL* 4.1 40.4 - - + -
133C THR* 4.3 12.8 - - + -
134C ALA 3.8 9.6 - - - +
135C ILE* 4.0 17.5 - - + -
157C THR 3.9 0.7 - - - +
158C GLU* 3.5 3.0 - - - -
159C LEU* 2.8 35.0 + - - +
161C ILE* 6.0 1.8 - - + -
176C ARG* 6.3 0.2 - - + -
177C ASN* 3.5 11.7 - - + +
178C PRO* 1.3 80.1 - - - +
180C ALA* 1.3 70.6 + - - +
181C LEU* 4.5 3.2 - - + +
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Residues in contact with ALA 180 (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 3.6 1.0 - - - +
134C ALA* 2.9 35.1 + - + +
140C LYS* 3.7 36.5 - - + +
156C ILE* 4.3 5.8 - - + -
157C THR 3.4 5.4 - - - +
158C GLU* 3.8 16.8 - - + +
179C VAL* 1.3 74.8 - - - +
181C LEU* 1.3 68.7 + - - +
182C ILE* 4.0 7.2 - - + -
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Residues in contact with LEU 181 (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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21C VAL* 4.0 26.0 - - + -
24C LEU* 3.7 37.7 - - + -
25C ILE* 4.0 21.8 - - + -
28C LEU* 4.1 17.9 - - + -
131C ILE* 4.5 7.2 - - + -
132C VAL 3.4 4.9 - - - +
133C THR* 4.0 18.8 - - - +
156C ILE* 3.2 4.5 - - - -
157C THR* 2.8 36.4 + - - +
159C LEU* 5.5 3.6 - - + -
179C VAL* 4.5 5.2 - - + +
180C ALA* 1.3 83.1 - - - +
182C ILE* 1.3 61.6 + - - +
183C TYR* 3.8 5.7 - - + -
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Residues in contact with ILE 182 (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 ILE 4.0 0.5 - - - +
131C ILE* 3.4 1.6 - - - -
132C VAL* 2.7 46.3 + - + +
134C ALA* 3.8 29.4 - - + -
140C LYS* 4.0 13.7 - - - -
143C ALA* 4.1 19.7 - - + -
144C MSE 4.2 14.4 - - + +
147C LEU* 3.8 15.6 - - + +
154C VAL* 3.5 28.3 - - + -
155C ASN 3.3 4.0 - - - +
156C ILE* 3.9 23.6 - - + -
180C ALA* 4.2 3.8 - - + +
181C LEU* 1.3 75.7 - - - +
183C TYR* 1.3 60.9 + - - +
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Residues in contact with TYR 183 (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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20B GLU* 5.7 0.3 + - - -
28C LEU* 3.7 43.4 - - + +
130C ILE 3.3 12.6 - - - +
131C ILE* 4.2 14.6 - - + -
147C LEU* 5.1 0.7 - - - -
154C VAL* 3.7 3.7 - - - -
155C ASN* 3.0 74.3 + - + +
156C ILE 5.3 0.3 + - - -
157C THR* 3.7 25.1 + - - -
181C LEU 3.8 12.8 - - - -
182C ILE* 1.3 74.6 - - - +
184C THR* 1.3 71.9 + - - +
185C GLY* 5.7 0.7 - - - -
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Residues in contact with THR 184 (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 GLY 4.5 1.4 + - - -
129C ARG* 4.1 5.9 - - - +
130C ILE* 3.1 37.3 + - + +
147C LEU* 4.0 23.6 - - + -
152C PHE* 3.5 48.1 - - + -
153C ASP 3.4 4.9 - - - +
154C VAL* 5.2 1.1 - - + -
155C ASN* 4.6 0.2 - - - -
183C TYR* 1.3 88.1 - - - +
185C GLY* 1.3 72.2 + - - +
186C VAL* 4.9 3.8 - - - +
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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