Contacts of the strand formed by residues 40 - 46 (chain B) 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 GLY 40 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B GLU 3.4 3.0 + - - -
39B PRO* 1.3 74.3 - - - +
41B LEU* 1.3 60.4 + - - -
42B GLN* 5.5 2.6 - - - +
71B LEU 3.7 1.2 - - - +
72B LYS* 3.6 13.4 - - - +
73B THR* 2.7 42.0 + - - +
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Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B GLY* 1.3 73.7 - - - -
42B GLN* 1.3 63.3 + - - +
43B ILE* 4.2 5.2 - - + -
59B TYR* 3.3 41.0 + - + -
70B ILE* 3.6 29.6 - - + -
71B LEU 3.5 7.2 - - - +
72B LYS* 4.2 13.9 - - + +
133B TYR* 3.8 34.1 - - + +
134B PHE* 4.1 22.2 - - + -
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Residues in contact with GLN 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LYS* 2.7 31.1 + - - +
35B ALA* 3.5 2.1 - - - +
36B GLY* 2.8 27.3 + - - -
37B LYS 5.4 0.8 - - - +
38B GLU 5.9 2.0 - - - -
40B GLY 5.5 1.6 - - - -
41B LEU* 1.3 78.7 - - - +
43B ILE* 1.3 67.4 + - - +
44B TRP* 3.8 26.0 - - + -
59B TYR* 3.5 4.9 - - - +
69B VAL 4.0 0.2 - - - +
70B ILE* 3.4 1.7 - - - +
71B LEU* 2.9 45.3 + - - +
73B THR* 4.7 1.7 + - - -
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Residues in contact with ILE 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 4.2 4.7 - - + -
42B GLN* 1.3 81.2 - - - +
44B TRP* 1.3 68.7 + - - +
53B PRO* 3.9 1.9 - - - +
54B VAL* 3.1 41.0 + - + +
59B TYR* 3.4 49.5 + - + -
62B PHE* 4.3 9.2 - - + -
68B TYR* 4.1 15.3 - - + -
69B VAL 3.5 3.4 - - - +
70B ILE* 3.9 25.8 - - + -
134B PHE* 3.9 29.6 - - + -
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Residues in contact with TRP 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B GLU* 2.9 46.9 + - + +
32B PHE* 6.5 0.4 - + - -
34B LYS* 5.1 2.2 - - + -
35B ALA* 3.8 22.7 - - + -
42B GLN* 3.8 38.6 - - + -
43B ILE* 1.3 77.9 - - - +
45B ARG* 1.3 59.8 + - - +
51B LEU* 3.9 37.2 - - + -
52B VAL 3.5 5.2 - - - +
53B PRO* 3.7 27.6 - - + +
54B VAL* 4.2 0.4 - - - -
68B TYR* 3.3 9.0 - - - +
69B VAL* 2.8 57.4 + - + +
71B LEU* 4.1 17.3 - - + -
108B LEU* 4.4 12.8 - - + -
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Residues in contact with ARG 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B TRP* 1.3 74.4 - - - +
46B VAL* 1.3 67.7 + - - +
47B GLU* 2.9 42.1 + - + +
50B ASP 3.5 0.2 - - - +
51B LEU* 3.8 1.1 - - - -
52B VAL* 2.9 34.1 + - - +
54B VAL* 3.9 7.0 - - + +
63B PHE* 3.6 16.1 - - - -
66B ASP* 2.7 29.1 + - + +
67B ALA 4.2 3.8 - - - +
68B TYR* 3.7 35.6 + - + -
144B GLY 3.6 2.6 - - - -
145B VAL* 3.5 17.4 - - - +
149B PHE 2.8 34.1 + - - -
150B LYS* 3.9 14.1 - - - +
151B HIS* 4.3 10.6 - - + +
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Residues in contact with VAL 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ARG* 1.3 73.2 - - - +
47B GLU* 1.3 64.5 + - - +
48B LYS 4.2 1.0 + - - +
49B PHE* 4.4 11.4 - - - +
50B ASP 3.4 7.6 - - - +
51B LEU* 4.3 8.1 - - + -
66B ASP* 5.1 1.4 - - - +
67B ALA* 2.9 31.9 + - + +
68B TYR* 4.5 0.2 - - - -
69B VAL* 4.1 17.0 - - + -
97B GLU* 4.0 18.6 - - + +
100B ALA* 3.8 26.7 - - + -
101B ALA* 3.9 28.0 - - + +
104B PHE* 4.5 3.8 - - + -
145B VAL* 3.9 9.4 - - - +
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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