Contacts of the strand formed by residues 81 - 89 (chain A) in PDB entry 1D0N
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 LEU 81 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLY 3.6 23.6 - - - +
37A LYS* 4.0 16.2 - - - +
38A GLU* 4.6 0.2 - - - -
39A PRO* 4.3 15.9 - - + -
73A THR* 3.9 15.0 - - + -
74A VAL 3.4 11.0 - - - +
75A GLN* 4.1 13.0 - - + +
76A LEU* 4.7 2.3 - - - +
79A GLY 4.6 5.2 - - - +
80A ILE* 1.3 94.1 - - - +
82A GLN* 1.3 59.9 + - - +
83A TYR* 3.7 27.1 - - + +
115A ARG* 4.6 8.8 + - - -
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Residues in contact with GLN 82 (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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72A LYS 3.6 0.5 - - - +
73A THR* 3.4 6.2 - - - +
74A VAL* 2.7 50.8 + - + +
76A LEU* 3.0 24.8 - - + +
80A ILE 4.1 0.2 + - - -
81A LEU* 1.3 75.0 - - - +
83A TYR* 1.3 68.1 + - - +
84A ASP* 3.5 20.6 + - - +
117A VAL* 6.1 0.2 - - + -
381A ALA 4.8 3.6 - - - +
382A TYR* 3.2 28.1 - - + -
383A LEU* 2.6 48.5 + - - -
385A SER 5.1 0.8 - - - +
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Residues in contact with TYR 83 (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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36A GLY* 3.0 29.2 + - - -
71A LEU* 3.9 15.9 - - + -
72A LYS 3.6 1.1 - - - -
73A THR* 3.4 33.4 - - + -
81A LEU* 3.7 27.0 - - + +
82A GLN* 1.3 82.2 - - - +
84A ASP* 1.3 64.7 + - - +
85A LEU 4.0 0.2 - - - -
112A LEU* 4.2 32.4 - - + +
115A ARG* 4.3 32.7 + - + +
116A ALA* 3.4 18.8 - - + +
117A VAL* 2.9 28.4 + - - +
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Residues in contact with ASP 84 (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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70A ILE 3.5 4.9 - - - +
71A LEU* 3.6 3.3 - - - -
72A LYS* 3.0 42.0 + - + +
74A VAL* 5.3 0.7 - - - +
82A GLN* 3.5 17.3 + - - +
83A TYR* 1.3 74.2 - - - +
85A LEU* 1.3 60.9 + - - +
86A HIS* 3.6 7.7 - - - +
117A VAL* 3.5 7.8 - - - +
119A HIS* 2.9 21.2 + - - +
129A THR* 4.7 4.0 - - - +
133A TYR* 3.6 22.8 + - - +
382A TYR* 2.8 31.0 + - - -
385A SER* 4.9 4.9 + - - -
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Residues in contact with LEU 85 (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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69A VAL* 4.0 19.3 - - + -
70A ILE 3.6 4.5 - - - +
71A LEU* 4.4 15.7 - - + -
83A TYR 4.0 0.6 - - - -
84A ASP* 1.3 72.1 - - - +
86A HIS* 1.3 57.9 + - - +
105A THR* 3.3 43.3 - - + +
108A LEU* 4.0 27.6 - - + -
109A ASP* 3.8 24.2 - - + +
112A LEU* 5.1 2.2 - - + -
116A ALA* 4.3 10.8 - - + -
117A VAL 2.7 14.3 + - - +
118A GLN* 3.2 5.0 - - + +
119A HIS* 2.5 35.2 + - - +
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Residues in contact with HIS 86 (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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69A VAL* 3.5 5.0 - - - +
70A ILE* 2.7 49.9 + - + +
84A ASP* 3.6 13.6 - - - +
85A LEU* 1.3 80.2 - - - +
87A TYR* 1.3 60.8 + - - +
105A THR* 4.9 2.0 - - - -
119A HIS* 3.0 33.6 - + + +
121A GLU* 2.8 34.8 + - + -
127A SER* 4.5 0.9 - - - -
129A THR* 4.2 3.4 - - + -
130A PHE* 3.5 23.8 - + + -
133A TYR* 2.7 45.2 + + - -
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Residues in contact with TYR 87 (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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68A TYR 3.0 12.3 - - - +
69A VAL* 4.6 2.0 - - + -
86A HIS* 1.3 75.5 - - - +
88A TRP* 1.3 58.6 + - - +
89A LEU* 4.1 18.8 - - + -
98A SER* 4.5 2.5 - - - -
101A ALA* 3.9 24.9 - - + +
102A ALA* 3.9 19.0 - - + +
105A THR* 3.4 28.0 - - + +
119A HIS 2.9 15.6 + - - -
120A ARG* 3.2 46.6 + - + -
121A GLU* 2.9 26.0 + - - +
332A LEU* 3.3 42.3 + - + +
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Residues in contact with TRP 88 (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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62A PHE* 3.6 33.4 - + + -
63A PHE 3.6 21.3 - - - -
64A THR* 4.5 1.3 - - - -
66A ASP 3.7 3.4 - - - -
67A ALA* 3.2 9.5 - - - +
68A TYR* 2.8 48.9 + + + +
70A ILE* 4.0 18.6 - - + -
86A HIS 4.2 0.2 - - - -
87A TYR* 1.3 73.7 - - - +
89A LEU* 1.3 66.5 + - - +
90A GLY* 3.3 29.2 - - - -
121A GLU* 3.4 19.1 - - + -
123A GLN* 3.7 30.4 - - + +
126A GLU* 3.1 21.9 + - - -
130A PHE* 3.8 28.0 - + + -
138A LEU* 5.3 0.2 - - - +
140A TYR* 4.0 11.3 - + - -
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Residues in contact with LEU 89 (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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66A ASP 4.3 1.3 - - - -
67A ALA* 4.4 6.3 - - + -
87A TYR* 4.1 23.3 - - + +
88A TRP* 1.3 84.9 - - - +
90A GLY* 1.3 65.8 + - - +
93A CYS* 4.7 4.3 - - + -
98A SER* 3.3 38.6 - - - -
120A ARG* 3.9 36.3 - - + +
121A GLU 2.9 14.4 + - - +
122A VAL* 3.7 14.1 - - + +
123A GLN* 3.0 25.3 + - - +
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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