Contacts of the strand formed by residues 45 - 51 (chain B) in PDB entry 3SDI
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 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B ALA* 2.9 28.9 + - - +
43B SER 3.6 0.2 - - - -
44B ASP* 1.3 79.6 - - - +
46B ILE* 1.3 65.9 + - - +
146B TYR* 3.4 14.6 - - - -
186B VAL* 3.3 14.5 - - - +
215B ILE 2.9 15.9 - - - -
216B ARG* 4.6 0.4 - - - -
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Residues in contact with ILE 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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40B ILE 3.4 11.4 - - - +
41B MET* 4.0 7.4 - - + -
45B GLY* 1.3 81.9 - - - +
47B VAL* 1.3 73.4 + - - +
48B LEU* 5.8 0.2 - - - -
139B ALA* 3.8 13.5 - - + -
140B GLY 3.6 17.9 - - - +
146B TYR* 3.6 17.0 - - + -
147B GLN 3.3 40.6 - - - +
148B LEU* 3.6 24.2 - - + -
186B VAL* 4.5 2.2 - - - +
213B ALA 4.0 0.2 - - - +
214B THR* 3.3 9.4 - - - -
215B ILE* 3.0 37.6 + - + +
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Residues in contact with VAL 47 (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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38B ILE 4.3 0.4 - - - +
39B GLY* 3.3 7.1 - - - -
40B ILE* 2.7 39.9 + - + +
46B ILE* 1.3 79.8 - - - +
48B LEU* 1.3 71.4 + - - +
186B VAL* 4.2 7.0 - - + +
189B ALA* 3.9 14.6 - - + +
190B ILE* 3.8 34.5 - - + +
193B ALA* 4.0 18.8 - - + -
212B PHE* 3.6 31.9 - - + -
213B ALA 3.7 2.7 - - - +
214B THR* 4.3 4.7 - - + -
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Residues in contact with LEU 48 (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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38B ILE 3.5 2.9 - - - +
39B GLY* 4.0 6.3 - - - -
47B VAL* 1.3 83.3 - - - +
49B ALA* 1.3 60.7 + - - +
67B LEU* 4.1 18.2 - - + +
75B ALA* 4.3 13.9 - - + +
76B VAL 4.1 7.0 - - - +
77B ALA* 4.0 27.8 - - + +
137B ILE* 3.8 29.6 - - + +
139B ALA* 3.7 31.0 - - + -
148B LEU* 4.4 1.3 - - + -
211B GLU 4.0 0.2 - - - +
212B PHE* 3.4 5.7 - - - -
213B ALA* 2.8 49.2 + - + +
215B ILE* 5.8 0.4 - - + -
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Residues in contact with ALA 49 (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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36B THR 4.2 0.3 - - - +
37B ALA* 3.4 1.4 - - - +
38B ILE* 2.8 35.7 + - + +
47B VAL 4.3 0.2 - - - -
48B LEU* 1.3 75.5 - - - +
50B ALA* 1.3 62.4 + - - +
67B LEU* 5.1 1.3 - - - -
77B ALA* 5.3 0.9 - - - +
193B ALA* 4.2 15.9 - - + -
197B LEU* 3.7 22.1 - - + +
210B LEU* 5.5 0.2 - - + -
211B GLU 3.4 5.2 - - - -
212B PHE* 3.4 28.0 - - + -
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Residues in contact with ALA 50 (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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36B THR 3.4 6.7 - - - +
37B ALA* 4.1 8.1 - - + -
49B ALA* 1.3 76.4 - - - +
51B GLU* 1.3 60.8 + - - +
52B ARG 3.9 0.2 + - - -
66B LYS* 3.8 37.9 - - + -
67B LEU* 4.4 11.4 - - + -
197B LEU* 4.3 3.0 - - - +
210B LEU* 3.3 12.7 - - - +
211B GLU* 2.9 34.9 + - + +
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Residues in contact with GLU 51 (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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35B GLY* 3.5 15.6 - - - -
36B THR* 3.0 26.8 + - - +
50B ALA* 1.3 71.4 - - - +
52B ARG* 1.3 67.9 + - - +
53B LYS 3.5 0.2 + - - -
66B LYS* 3.3 15.3 - - - +
197B LEU* 4.2 18.6 - - + +
200B THR* 5.2 1.2 + - - -
202B THR* 3.1 33.0 + - - +
203B ASP* 4.4 3.8 + - - +
204B SER* 4.1 1.4 + - - -
205B LEU* 4.4 8.5 - - + +
209B ARG* 2.7 42.7 + - - +
210B LEU* 4.5 2.7 - - + -
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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