Contacts of the helix formed by residues 40 - 47 (chain B) in PDB entry 1S5E
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 ASN 40 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ASN* 3.7 19.4 + - - +
39B ILE* 1.3 76.1 - - - +
41B LEU* 1.3 60.6 + - - +
42B TYR 3.2 6.4 + - - -
43B ASP* 2.8 44.9 + - + -
44B HIS* 2.9 29.1 + - - +
57B ASP* 3.0 11.1 + - - +
59B TYR* 3.8 2.5 - - - -
164B LEU 5.3 0.4 - - - -
166B GLY* 3.0 33.1 + - - +
200B ASP* 4.8 9.9 + - - +
203B THR* 4.0 13.2 - - - +
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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 ASN* 1.3 69.7 + - - +
42B TYR* 1.3 60.8 + - - +
44B HIS* 3.2 15.5 + - + +
45B ALA* 2.8 29.9 + - + +
59B TYR* 3.4 46.1 - - + +
95B PHE* 5.0 9.6 - - + -
97B VAL* 4.3 20.4 - - + -
100B VAL* 3.6 37.7 - - + -
101B LEU* 3.9 17.7 - - + -
114B SER* 4.3 2.2 - - - -
161B GLY* 5.4 0.7 - - - +
164B LEU* 3.7 9.8 + - + +
165B ALA* 3.7 10.1 + - - +
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Residues in contact with TYR 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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40B ASN* 3.2 5.8 + - - +
41B LEU* 1.3 73.2 - - - +
43B ASP* 1.3 72.6 + - - +
45B ALA* 3.4 1.7 + - - +
46B ARG* 3.1 57.7 + - + +
101B LEU* 4.3 17.5 - - + -
104B TYR* 4.2 14.8 - - + -
106B PRO* 5.3 0.9 - - + -
165B ALA 2.9 22.8 + - - +
166B GLY 3.9 6.5 - - - -
167B PHE* 3.7 27.4 - + + +
168B PRO* 3.8 31.9 - - + -
171B HIS* 3.8 19.0 + + - -
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Residues in contact with ASP 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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38B ASN* 4.2 7.8 + - - -
40B ASN* 2.8 35.6 + - - +
42B TYR* 1.3 83.1 - - - +
44B HIS* 1.3 67.3 + - - +
46B ARG* 3.2 9.8 + - - +
47B GLY* 3.1 20.8 + - - -
57B ASP* 3.5 26.2 - - - +
166B GLY 5.1 0.7 - - - +
168B PRO* 5.9 0.2 - - - +
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Residues in contact with HIS 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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40B ASN 2.9 17.7 + - - +
41B LEU* 3.4 10.8 - - + +
43B ASP* 1.3 76.2 - - - +
45B ALA* 1.3 66.2 + - + +
47B GLY* 3.1 14.3 + - - -
54B ARG* 3.5 45.9 - - + +
55B HIS 4.3 0.2 + - - -
56B ASP* 3.0 35.9 + - - +
57B ASP* 3.7 3.0 - - + +
59B TYR* 3.2 45.3 + + + +
61B SER* 3.9 6.0 + - - -
97B VAL* 5.4 0.7 - - + -
114B SER* 2.8 29.2 + - - -
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Residues in contact with ALA 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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41B LEU* 2.8 20.2 + - + +
42B TYR 3.8 2.2 - - - +
44B HIS* 1.3 79.6 - - + +
46B ARG* 1.3 58.0 + - - +
47B GLY 3.3 0.4 - - - -
54B ARG* 3.4 22.9 + - - +
97B VAL* 4.0 13.9 - - + -
101B LEU* 3.6 25.8 - - + -
106B PRO* 3.4 22.1 - - + +
107B HIS* 3.7 6.6 - - - -
112B GLU* 5.0 4.3 - - - +
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Residues in contact with ARG 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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42B TYR* 3.1 58.9 + - + +
43B ASP* 3.2 9.4 + - - +
45B ALA* 1.3 75.1 - - - +
47B GLY* 1.3 68.0 + - - +
48B THR* 3.6 3.8 + - - +
54B ARG* 5.1 0.4 - - - -
106B PRO* 4.0 22.9 - - + -
107B HIS* 5.1 5.6 + - - -
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Residues in contact with GLY 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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43B ASP 3.1 11.3 + - - -
44B HIS* 3.1 12.2 + - - -
45B ALA 3.3 0.2 - - - -
46B ARG* 1.3 83.1 - - - +
48B THR* 1.3 63.3 + - - -
54B ARG* 3.1 28.8 + - - -
56B ASP* 5.6 9.9 - - - -
57B ASP* 6.0 0.4 - - - -
107B HIS* 5.1 0.2 + - - -
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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