Contacts of the strand formed by residues 141 - 147 (chain C) in PDB entry 1DXO
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 LYS 141 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95C ASP 3.0 6.5 + - - -
96C LEU* 3.3 7.6 - - + +
97C VAL* 2.9 25.3 + - - +
140C LYS* 1.3 79.8 - - - +
142C ALA* 1.3 60.4 + - - +
181C PHE* 3.9 2.8 - - - -
182C GLN* 3.1 42.9 + - + +
184C LEU* 4.1 31.0 - - + +
215C TRP* 2.7 69.0 + - + +
217C GLU 4.0 14.1 + - - -
219C PRO* 5.1 2.0 - - - +
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Residues in contact with ALA 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 VAL* 3.3 9.2 - - + +
99C PHE* 4.3 8.5 - - + -
141C LYS* 1.3 73.4 - - - +
143C VAL* 1.3 66.5 + - - +
176C LEU* 4.0 24.0 - - + -
181C PHE* 3.7 30.4 - - + -
182C GLN 2.9 6.4 + - - +
183C VAL* 3.4 8.4 - - + +
184C LEU 3.1 23.4 + - - -
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Residues in contact with VAL 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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96C LEU* 4.2 10.1 - - + -
97C VAL 3.0 7.9 + - - +
98C ILE* 3.6 8.3 - - + +
99C PHE* 2.9 28.8 + - - +
142C ALA* 1.3 73.4 - - - +
144C LEU* 1.3 76.1 + - - +
145C SER 4.0 0.3 + - - -
183C VAL* 5.2 0.7 - - - -
184C LEU* 3.2 47.6 - - + +
185C GLU 3.5 24.2 - - - +
187C GLN 4.5 0.4 - - - +
207C TRP* 4.6 14.4 - - + -
210C ARG* 4.1 10.8 - - - +
214C ILE* 4.2 6.7 - - + -
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Residues in contact with LEU 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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99C PHE* 3.3 35.4 - - + -
101C PHE* 3.7 14.1 - - + -
108C VAL* 5.9 0.9 - - + -
116C PHE* 6.0 1.6 - - + -
143C VAL* 1.3 77.8 - - - +
145C SER* 1.3 54.7 + - - +
146C ILE* 3.8 17.2 + - + -
168C LEU* 4.4 10.8 - - + -
171C ILE* 3.4 33.4 - - + -
172C GLN* 3.6 33.2 - - + +
176C LEU* 4.3 12.3 - - + -
184C LEU 5.0 0.2 + - - -
186C PRO* 3.3 6.0 - - + +
187C GLN* 2.7 32.4 + - - +
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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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21C MET* 3.2 21.3 - - - +
98C ILE* 4.6 4.5 - - - -
99C PHE 3.0 11.0 + - - +
100C GLN* 2.6 43.2 + - - -
101C PHE 3.1 14.2 + - - -
143C VAL 4.0 0.8 + - - -
144C LEU* 1.3 71.0 - - - +
146C ILE* 1.3 59.8 + - - +
187C GLN* 3.4 13.8 - - - +
207C TRP* 4.0 19.1 - - - -
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Residues in contact with ILE 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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21C MET* 6.2 0.2 - - - -
101C PHE* 3.3 40.6 - - + +
103C LEU* 3.7 26.2 - - + +
144C LEU* 4.1 12.1 - - + -
145C SER* 1.3 76.7 - - - +
147C THR* 1.3 77.0 + - - +
148C THR* 4.6 6.2 - - + +
164C MET* 5.4 3.8 - - + -
168C LEU* 3.4 32.8 - - + -
171C ILE* 6.1 1.1 - - + -
187C GLN 2.9 7.8 + - - +
188C LEU* 3.6 19.4 - - + -
189C THR* 3.0 29.3 + - - +
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Residues in contact with THR 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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17C PHE* 4.2 19.3 - - + -
18C ASN* 3.1 34.3 + - - +
21C MET* 5.0 2.7 - - + -
100C GLN* 4.2 7.0 - - - +
101C PHE 3.4 2.2 + - - -
102C PRO* 3.2 3.3 - - - +
103C LEU 2.8 25.8 + - - -
146C ILE* 1.3 75.3 - - - +
148C THR* 1.3 65.0 + - - +
189C THR* 3.3 23.1 - - - +
192C ILE* 4.0 9.9 - - + -
301C FAD 2.5 27.0 + - - +
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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