Contacts of the strand formed by residues 43 - 49 (chain A) in PDB entry 3IU3
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 LEU 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ILE* 4.0 13.9 - - + -
36A LYS 3.5 1.3 - - - -
37A GLN* 3.5 35.9 - - + +
42A GLY* 1.3 72.9 - - - -
44A GLU* 1.3 63.2 + - - +
93A TYR* 4.9 4.5 - - + -
105A TRP* 5.0 0.4 - - + -
35B TYR* 5.5 0.9 - - + -
37B GLN* 4.4 0.4 - - - +
43B PRO* 3.8 31.2 - - + -
86B TYR* 3.7 39.6 - - + -
95B PHE* 3.6 54.0 + - + +
96B GLY 4.5 3.6 + - - +
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Residues in contact with GLU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ILE* 3.2 7.6 - - - +
36A LYS* 2.7 72.0 + - + +
38A ARG* 4.0 15.6 + - - +
41A GLN* 6.1 0.9 - - - +
42A GLY 4.7 5.1 - - - +
43A LEU* 1.3 80.2 - - - +
45A TRP* 1.3 65.7 + - - +
59A ASN* 5.9 1.1 - - - +
61A LYS* 5.7 2.4 - - - +
62A PHE* 3.6 22.5 - - + -
95B PHE* 4.4 0.9 - - - +
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Residues in contact with TRP 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A HIS* 2.9 30.1 - + + -
34A TRP 4.0 8.1 - - - -
35A ILE* 4.6 7.0 - - + +
44A GLU* 1.3 70.9 - - - +
46A ILE* 1.3 61.2 + - - +
47A GLY* 3.5 29.7 + - - -
48A ALA* 3.7 11.7 - - + -
57A SER* 3.8 22.9 - - - -
58A TYR 3.7 3.6 - - - -
59A ASN* 3.0 70.7 + - + +
62A PHE* 3.8 5.2 - - - -
102A PHE* 4.9 3.6 - + - -
92B SER 3.7 18.6 - - - -
93B TYR* 3.1 49.1 - + + +
94B THR* 4.7 3.1 - - + +
95B PHE* 4.1 11.0 - + + +
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Residues in contact with ILE 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A TRP* 2.8 21.7 + - + +
35A ILE 4.4 2.5 - - - -
36A LYS* 3.9 20.4 - - + +
45A TRP* 1.3 76.0 - - - +
47A GLY* 1.3 57.9 + - - +
58A TYR* 3.8 7.6 - - + +
59A ASN* 3.0 24.2 + - - +
62A PHE* 4.0 24.2 - - + +
66A ALA* 3.8 26.9 - - + -
68A LEU* 4.2 9.2 - - + -
79A MET* 3.8 20.6 - - - -
81A LEU* 5.1 3.6 - - + -
92A TYR* 3.5 38.8 - - + -
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Residues in contact with GLY 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A HIS* 3.5 3.5 - - - -
34A TRP 3.0 24.4 + - - -
45A TRP* 3.5 22.0 + - - -
46A ILE* 1.3 84.2 - - - +
48A ALA* 1.3 60.3 + - - -
57A SER 3.1 13.7 - - - -
58A TYR* 4.1 1.8 - - - -
68A LEU* 3.8 10.0 - - - +
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A TRP* 3.9 15.5 - - + -
32A MET 3.2 10.1 - - - +
33A HIS* 3.6 32.1 - - + +
45A TRP* 3.7 7.3 - - + -
47A GLY* 1.3 74.2 - - - +
49A ILE* 1.3 61.6 + - - +
56A THR* 3.3 2.9 - - - -
57A SER* 2.9 33.9 + - - +
68A LEU* 3.6 8.7 - - - +
93B TYR* 6.4 0.2 - - + -
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Residues in contact with ILE 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A TRP* 3.3 5.9 - - - -
32A MET* 3.0 48.1 + - + +
34A TRP* 4.8 4.5 - - - +
48A ALA* 1.3 77.0 - - - +
50A TYR* 1.3 72.3 + - - +
51A PRO* 3.4 7.8 - - + +
54A SER* 4.3 12.1 - - - +
55A ASP 3.5 6.3 - - - +
56A THR* 3.7 17.5 - - + -
68A LEU* 3.8 23.1 - - + +
69A THR* 3.6 39.5 - - - +
70A ALA* 3.8 11.0 - - + +
77A ALA* 5.0 4.5 - - + -
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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