Contacts of the strand formed by residues 141 - 147 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A ASP 3.1 4.6 + - - -
96A LEU* 3.4 10.6 - - + +
97A VAL 3.0 24.1 + - - -
140A LYS* 1.3 81.7 - - - +
142A ALA* 1.3 60.4 + - - +
181A PHE* 3.7 3.8 - - - -
182A GLN* 3.0 40.6 + - + +
184A LEU* 4.3 24.2 - - + -
215A TRP* 2.6 72.0 + - + +
216A ASP 5.2 0.2 - - - -
217A GLU 4.3 10.9 + - - -
219A PRO* 5.3 1.9 - - - +
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Residues in contact with ALA 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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97A VAL* 3.3 8.3 - - + +
99A PHE* 4.3 7.4 - - + -
141A LYS* 1.3 73.0 - - - +
143A VAL* 1.3 65.5 + - - +
176A LEU* 3.7 29.8 - - + -
181A PHE* 3.6 26.3 - - + -
182A GLN 2.8 7.0 + - - +
183A VAL* 3.4 8.2 - - - +
184A LEU 2.9 25.5 + - - -
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Residues in contact with VAL 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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96A LEU* 3.7 27.1 - - + -
97A VAL 3.0 6.9 + - - +
98A ILE* 3.5 13.4 - - + +
99A PHE* 2.9 29.6 + - - +
142A ALA* 1.3 79.4 - - - +
144A LEU* 1.3 72.1 + - - +
183A VAL* 5.3 0.7 - - - -
184A LEU* 3.9 18.4 - - + +
185A GLU 3.4 25.1 - - - +
207A TRP* 4.4 10.8 - - + -
210A ARG* 4.0 16.4 - - - +
214A ILE* 4.1 7.0 - - + -
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Residues in contact with LEU 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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99A PHE* 3.5 35.2 - - + -
101A PHE* 3.7 15.0 - - + -
108A VAL* 5.6 1.1 - - + -
112A LEU* 5.8 0.4 - - + -
116A PHE* 5.8 2.0 - - + -
143A VAL* 1.3 77.6 - - - +
145A SER* 1.3 55.3 + - - +
146A ILE* 3.8 25.0 + - + -
168A LEU* 4.5 3.8 - - + -
171A ILE* 3.9 23.3 - - + -
172A GLN* 3.4 38.7 + - + +
176A LEU* 4.4 13.0 - - + -
183A VAL* 5.6 0.8 - - + +
184A LEU 5.0 1.2 + - - -
186A PRO* 3.3 7.7 - - + +
187A GLN 2.8 30.8 + - - +
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Residues in contact with SER 145 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A MET* 3.3 21.8 - - - +
98A ILE* 4.4 4.0 - - - -
99A PHE 2.9 13.2 + - - +
100A GLN* 2.8 30.2 + - - -
101A PHE 3.2 24.3 + - - +
143A VAL 4.0 0.8 + - - -
144A LEU* 1.3 70.8 - - - +
146A ILE* 1.3 60.4 + - - +
187A GLN* 3.4 13.6 + - - +
207A TRP* 4.1 21.4 - - - -
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Residues in contact with ILE 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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21A MET* 6.3 0.2 - - - -
101A PHE* 3.3 37.5 - - + +
102A PRO 4.2 0.2 - - - -
103A LEU* 3.6 31.0 - - + +
144A LEU* 3.8 16.8 - - + +
145A SER* 1.3 78.8 - - - +
147A THR* 1.3 78.9 + - - +
148A THR* 4.3 5.1 - - + +
164A MET* 5.5 2.2 - - + -
168A LEU* 3.9 28.0 - - + -
171A ILE* 5.9 2.2 - - + -
186A PRO* 5.3 0.4 - - + -
187A GLN 2.8 9.3 + - - +
188A LEU* 3.7 17.1 - - + -
189A THR* 2.9 29.7 + - - +
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Residues in contact with THR 147 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A PHE* 4.1 21.3 - - + -
18A ASN* 3.2 16.9 + - - +
21A MET* 5.1 0.9 - - + -
100A GLN* 4.4 11.2 - - - +
101A PHE 3.4 1.7 + - - -
102A PRO* 3.1 12.8 - - - +
103A LEU 2.8 25.5 + - - -
146A ILE* 1.3 75.5 - - - +
148A THR* 1.3 67.7 + - - +
189A THR* 3.2 26.2 - - + +
192A ILE* 4.1 10.3 - - + -
301A FAD 2.8 22.8 + - - +
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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