Contacts of the strand formed by residues 38 - 44 (chain B) in PDB entry 3I8E
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 ARG 38 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B LYS* 2.9 51.0 - - + +
12B PRO* 4.9 7.2 - - + -
34B ALA* 3.6 0.7 - - - -
35B LYS* 3.1 44.5 + - + -
36B ASN 3.5 1.2 - - - +
37B THR* 1.3 88.4 - - - +
39B LEU* 1.3 60.2 + - - +
40B GLU* 4.0 5.2 - - - +
54B GLU* 2.8 33.3 + - - +
55B VAL 3.2 7.0 - - - +
56B GLY* 3.0 23.7 - - - +
61B ILE* 3.5 11.2 - - - +
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 5.0 4.0 - - + -
33B ILE 3.8 3.8 - - - +
34B ALA* 4.7 0.2 - - + -
37B THR 4.3 0.4 + - - -
38B ARG* 1.3 75.1 - - - +
40B GLU* 1.3 64.0 + - - +
41B ILE* 3.9 23.3 - - + -
53B LYS 3.6 4.2 - - - +
54B GLU* 4.7 0.7 - - - -
55B VAL* 3.0 56.0 + - + +
56B GLY 5.3 0.2 - - - -
57B MET* 5.1 6.7 - - + -
61B ILE* 4.6 9.0 - - + -
64B MET* 3.6 31.0 - - - -
77B LEU* 3.9 27.1 - - + -
79B ILE* 4.1 13.0 - - + -
89B LEU* 5.6 2.0 - - + -
100B ILE* 4.1 6.3 - - + -
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Residues in contact with GLU 40 (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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11B LYS* 5.9 0.3 - - - +
31B LEU 3.7 0.3 - - - +
32B LEU* 3.4 7.1 - - - +
33B ILE* 2.8 39.9 + - + +
35B LYS* 2.3 43.7 + - - +
38B ARG* 4.0 4.4 - - - +
39B LEU* 1.3 74.3 - - - +
41B ILE* 1.3 63.1 + - - +
42B TYR* 3.4 39.6 + - + +
51B PRO* 6.5 0.2 - - + -
53B LYS 4.0 1.3 - - - -
54B GLU* 3.5 32.8 - - + +
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Residues in contact with ILE 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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23B PHE* 3.4 34.8 - - + -
24B THR* 4.2 9.6 - - - +
30B ASN* 4.7 0.2 - - - +
31B LEU 3.8 1.8 - - - -
32B LEU* 4.0 17.0 - - + -
39B LEU* 3.9 16.2 - - + -
40B GLU* 1.3 79.3 - - - +
42B TYR* 1.3 69.5 + - - +
51B PRO* 3.8 2.9 - - - +
52B VAL* 3.0 45.0 + - + -
53B LYS* 2.9 28.8 + - + +
91B TYR* 4.6 3.8 - - + -
100B ILE* 3.8 22.2 - - + -
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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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30B ASN* 3.0 30.3 - - - +
31B LEU* 2.8 25.0 + - + +
33B ILE* 3.6 28.3 - - + +
35B LYS* 5.1 0.2 + - - -
40B GLU* 3.4 44.5 + - + +
41B ILE* 1.3 78.1 - - - +
43B VAL* 1.3 64.4 + - - +
49B LEU* 3.6 42.2 - - + -
50B ARG 3.5 2.2 - - - -
51B PRO* 3.7 36.5 - - + +
353B PHE* 5.9 8.2 - + - -
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Residues in contact with VAL 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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24B THR* 3.8 10.5 - - + +
28B ASP* 4.2 24.5 - - - +
29B LEU 3.3 11.9 - - - +
30B ASN* 3.4 17.7 - - - +
42B TYR* 1.3 75.0 - - - +
44B VAL* 1.3 73.2 + - - +
45B THR* 5.6 2.0 - - + -
49B LEU* 3.5 2.4 - - - -
50B ARG* 2.6 54.1 + - + +
52B VAL* 3.8 23.6 - - + -
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Residues in contact with VAL 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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29B LEU* 3.0 47.7 + - + +
30B ASN 4.4 5.6 - - - +
31B LEU* 4.7 1.6 - - + +
43B VAL* 1.3 82.2 - - - +
45B THR* 1.3 79.1 + - - +
48B GLY* 3.6 9.0 - - - +
49B LEU* 4.4 13.2 - - + +
317B LEU* 4.1 26.5 - - + -
318B ASP* 4.4 20.9 - - + +
321B VAL* 5.9 3.4 - - + -
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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