Contacts of the strand formed by residues 43 - 50 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35H ILE* 3.8 18.4 - - + -
36H LYS 3.3 1.8 - - - -
37H GLN* 3.4 39.9 - - + +
42H GLY* 1.3 72.7 - - - -
44H GLU* 1.3 62.7 + - - +
93H TYR* 5.1 2.7 - - + -
35L TYR* 5.6 0.9 - - + -
43L PRO* 3.8 32.1 - - + -
86L TYR* 3.7 38.7 - - + -
95L PHE* 3.2 50.7 - - + +
96L GLY 4.6 2.5 + - - +
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Residues in contact with GLU 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H ILE* 3.3 6.7 - - - +
36H LYS* 2.7 75.8 + - + +
38H ARG* 4.8 12.0 + - - +
42H GLY 5.1 3.8 - - - +
43H LEU* 1.3 77.0 - - - +
45H TRP* 1.3 66.6 + - - +
59H ASN* 5.4 2.2 - - - +
61H LYS* 5.0 9.4 + - - +
62H PHE* 3.4 24.2 - - + -
95L PHE* 4.3 0.4 - - - +
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Residues in contact with TRP 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H HIS* 2.8 37.3 - + + -
34H TRP 4.0 9.0 - - - -
35H ILE* 4.6 7.2 - - + -
44H GLU* 1.3 73.2 - - - +
46H ILE* 1.3 61.9 + - - +
47H GLY* 3.4 29.5 + - - -
48H ALA* 4.0 6.7 - - + -
57H SER* 3.9 24.2 - - - -
58H TYR 3.8 4.5 - - - -
59H ASN* 2.9 68.0 + - + +
62H PHE* 4.1 5.0 - - - -
102H PHE* 5.0 1.8 - + - -
39I SER* 6.2 3.1 - - - -
42I LEU* 6.2 1.1 - - + -
92L SER 3.5 19.7 - - - -
93L TYR* 3.2 43.9 - + + +
94L THR* 4.6 4.2 - - - +
95L PHE* 4.0 13.9 - + + +
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Residues in contact with ILE 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H TRP* 2.8 27.5 + - + +
35H ILE 3.9 0.7 - - - +
36H LYS* 3.8 22.4 - - + +
45H TRP* 1.3 76.2 - - - +
47H GLY* 1.3 60.2 + - - +
58H TYR* 3.7 4.9 - - + +
59H ASN* 2.9 28.6 + - - +
62H PHE* 4.1 26.0 - - + +
66H ALA* 3.9 28.0 - - + -
68H LEU* 4.6 7.9 - - + -
79H MET* 3.9 17.0 - - + -
81H LEU* 5.8 0.7 - - + -
92H TYR* 3.6 35.7 - - + -
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Residues in contact with GLY 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H HIS* 3.4 3.8 - - - -
34H TRP* 3.0 24.0 + - - +
45H TRP* 3.4 18.5 + - - -
46H ILE* 1.3 84.0 - - - +
48H ALA* 1.3 62.5 + - - +
57H SER 3.1 14.4 - - - -
58H TYR* 4.2 2.7 - - - -
68H LEU* 4.0 10.3 - - - +
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Residues in contact with ALA 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H TRP* 3.8 20.6 - - + -
32H MET 3.3 9.2 - - - +
33H HIS* 3.7 26.9 - - + +
45H TRP* 4.2 5.8 - - + -
47H GLY* 1.3 75.5 - - - +
49H ILE* 1.3 62.3 + - - +
55H ASP 3.8 0.3 - - - +
56H THR* 3.3 8.0 - - - -
57H SER* 2.9 32.7 + - - +
68H LEU* 3.7 6.6 - - - +
42I LEU* 5.5 3.1 - - + -
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Residues in contact with ILE 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H TRP* 3.7 4.2 - - - -
32H MET* 3.0 51.5 + - + +
34H TRP* 4.6 4.5 - - - +
48H ALA* 1.3 76.9 - - - +
50H TYR* 1.3 71.0 + - - +
51H PRO* 3.5 8.7 - - + +
54H SER* 4.1 12.8 - - - +
55H ASP 3.5 4.3 - - - +
56H THR* 3.8 13.2 - - + -
68H LEU* 3.3 40.6 - - + +
69H THR* 3.6 23.1 - - - +
70H ALA* 3.9 12.1 - - + +
77H ALA* 4.8 9.9 - - + -
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Residues in contact with TYR 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H THR 3.2 20.9 + - - -
29H ARG* 3.5 33.5 + - - -
30H TYR 3.8 7.0 - - - -
31H TRP* 3.4 46.9 - + + -
49H ILE* 1.3 74.6 - - - +
51H PRO* 1.3 61.9 - - - +
52H GLY* 3.6 13.7 - - - -
53H ASN* 2.9 54.1 - - - +
54H SER* 3.5 1.7 - - - -
55H ASP* 3.0 16.3 + - + +
27I ASN* 3.6 23.5 + - - -
29I GLU* 4.9 0.7 - - - -
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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