Contacts of the strand formed by residues 38 - 47 (chain B) in PDB entry 1SMN
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 PHE 38 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ASN* 3.9 3.8 - - - -
33B ASN* 3.1 23.4 + - - +
36B THR* 3.3 21.7 + - - -
37B LYS* 1.3 83.5 - - - +
39B ALA* 1.3 68.0 + - - +
71B LEU* 3.7 32.3 - - + -
76B TYR* 3.7 7.6 - - - -
108B LEU 5.3 1.1 - - - -
109B SER* 5.3 1.6 - - - +
111B ILE 3.5 18.8 - - - -
112B THR* 3.9 18.2 - - + -
113B PRO* 3.6 27.4 - - + -
148B PRO* 5.1 0.4 - - + -
150B TYR* 3.5 17.5 + - - +
157B LEU* 4.7 2.2 - - + -
164B HIS* 4.5 5.8 - + + -
165B THR 3.2 33.4 - - - -
166B ILE* 4.2 1.8 - - - -
167B PRO* 4.1 11.4 - - + -
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Residues in contact with ALA 39 (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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30B LEU* 3.7 21.1 - - + -
31B ASN 3.3 12.6 - - - +
32B ASN* 4.0 7.4 + - - +
38B PHE* 1.3 75.9 - - - +
40B ASN* 1.3 64.3 + - - +
41B TRP 3.3 1.6 - - - +
42B VAL* 4.0 10.3 - - + -
90B GLN* 3.4 16.9 + - - +
109B SER 3.6 21.9 + - - +
112B THR* 5.5 0.2 - - - +
148B PRO* 3.2 21.8 - - - +
150B TYR* 5.3 0.2 - - - -
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Residues in contact with ASN 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLY* 4.3 3.6 - - - -
18B SER* 2.8 35.0 + - - +
31B ASN* 2.7 35.9 + - - +
32B ASN 3.3 9.7 + - - -
33B ASN* 2.9 27.4 + - - +
38B PHE 3.5 0.4 + - - -
39B ALA* 1.3 72.6 - - - +
41B TRP* 1.3 71.9 + - + +
147B GLY* 3.8 3.6 - - - -
148B PRO* 3.6 18.6 - - - +
150B TYR* 5.5 4.8 - - - -
171B TRP* 4.0 6.8 - - - -
216B LEU* 4.1 9.7 - - + +
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Residues in contact with TRP 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B CYS* 3.6 20.9 - - + -
14B PRO* 3.6 47.7 + - + +
17B GLY* 4.3 7.2 - - - -
22B SER* 3.7 20.6 - - - -
29B THR* 3.6 35.0 - - + -
30B LEU* 3.6 1.5 - - - -
31B ASN* 3.1 45.2 + - + +
39B ALA* 3.3 1.3 - - - +
40B ASN* 1.3 84.7 - - + +
42B VAL* 1.3 72.6 + - - +
43B ALA* 3.9 15.3 - - + -
145B VAL* 4.2 4.9 - - + -
146B THR 3.2 11.9 - - - +
147B GLY* 4.4 1.1 - - - -
171B TRP* 4.1 14.4 - - + -
216B LEU* 3.8 26.0 - - + +
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Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B TYR* 3.7 31.9 - - + -
29B THR 3.4 6.1 - - - +
30B LEU* 4.1 10.1 - - + -
39B ALA* 4.0 17.7 - - + -
41B TRP* 1.3 82.0 - - - +
43B ALA* 1.3 62.9 + - - +
44B TYR* 4.2 1.8 + - + -
90B GLN* 3.6 26.5 - - + -
91B ALA* 3.8 20.2 - - + -
109B SER 5.1 0.2 - - - +
110B ASN* 3.9 2.9 - - - +
144B THR 3.9 0.5 - - - +
145B VAL* 3.3 1.6 - - - -
146B THR* 2.9 43.5 + - + +
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Residues in contact with ALA 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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8B ASN* 3.7 9.0 - - - +
9B CYS* 3.5 32.8 - - - -
14B PRO* 5.0 0.4 - - + -
28B TYR* 3.3 5.6 - - - +
29B THR* 2.8 33.7 + - - +
41B TRP* 3.9 14.8 - - + -
42B VAL* 1.3 74.0 - - - +
44B TYR* 1.3 61.2 + - - +
144B THR 3.3 8.5 - - - +
145B VAL* 4.2 9.9 - - + +
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Residues in contact with TYR 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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8B ASN* 3.8 9.8 + - - +
27B ALA 3.7 9.9 - - - +
28B TYR* 4.1 1.8 - - + +
42B VAL* 4.3 5.4 - - + -
43B ALA* 1.3 78.6 - - - +
45B HIS* 1.3 62.7 - - - +
46B ILE* 3.9 22.7 - - + -
91B ALA* 3.8 18.4 - - + -
92B PRO* 3.2 25.7 - - + +
96B LEU* 3.7 27.4 - - + -
130B GLU* 2.6 37.1 + - - -
143B TYR* 3.5 3.3 - - - -
144B THR* 2.9 54.5 + - + +
146B THR* 4.0 13.7 - - + -
172B LYS* 3.3 15.9 - - - -
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Residues in contact with HIS 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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7B ASP 4.3 7.7 + - - -
8B ASN* 4.0 18.9 + - - +
26B HIS 5.6 2.0 + - - +
27B ALA 5.1 0.8 + - - -
44B TYR* 1.3 76.3 - - - +
46B ILE* 1.3 72.8 + - - +
47B THR* 3.5 19.4 + - + +
50B THR* 4.0 8.1 - - - +
96B LEU* 3.7 12.9 - - - +
141B SER* 2.7 28.9 + - - -
142B VAL 3.3 5.2 - - - -
143B TYR* 3.3 41.9 + + + -
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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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44B TYR* 3.9 29.6 - - + -
45B HIS* 1.3 73.9 - - - +
47B THR* 1.3 71.2 + - - +
50B THR* 3.5 12.1 - - - +
51B PRO* 4.5 6.5 - - + -
95B SER* 3.8 32.3 - - - +
96B LEU* 4.3 4.7 - - + -
130B GLU* 4.0 28.3 - - + +
131B ARG* 4.7 4.7 - - - +
134B ILE* 3.9 19.4 - - + +
141B SER* 3.4 6.2 - - - -
142B VAL* 2.8 46.8 + - + +
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Residues in contact with THR 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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45B HIS* 3.5 33.7 - - + +
46B ILE* 1.3 80.2 - - - +
48B LYS* 1.3 66.0 + - - +
49B ASP* 3.0 22.0 + - - +
50B THR* 3.1 17.7 + - + +
51B PRO* 3.0 20.1 - - - +
134B ILE* 3.5 14.1 - - - -
140B SER 4.1 9.9 - - - +
141B SER* 4.5 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