Contacts of the strand formed by residues 36 - 41 (chain H) in PDB entry 1U3H
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 GLU 36 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143G TYR* 3.6 29.2 + - + -
29H ARG* 2.9 31.3 + - + +
30H TYR 3.3 7.2 - - - +
31H ILE* 3.8 7.5 - - + +
34H ARG 4.1 1.8 + - - -
35H GLU* 1.3 72.8 - - - +
37H TYR* 1.3 58.3 + - - +
38H LEU 3.8 13.7 - - - +
39H ARG* 2.5 50.6 + - - +
50H VAL* 3.3 27.0 - - + +
51H THR* 3.5 10.7 - - - +
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Residues in contact with TYR 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G ASN* 4.7 5.9 - - - +
73G LEU* 3.4 45.9 - - + +
9H VAL* 5.7 0.9 - - + +
30H TYR* 2.7 34.7 + + + +
31H ILE 3.6 21.1 - - - -
32H TYR* 3.5 22.2 - - + -
35H GLU* 3.3 4.4 + - - +
36H GLU* 1.3 75.3 - - - +
38H LEU* 1.3 88.2 + - + -
50H VAL* 2.9 22.0 + - - -
51H THR* 3.5 17.9 + - - +
53H LEU* 4.0 8.7 - - + -
54H GLY* 3.3 32.5 - - - +
57H ASP* 4.0 15.7 + - - -
61H TYR* 5.0 2.0 + - - -
4I TYR* 4.6 7.4 + - - -
7I SER* 5.4 0.2 + - - -
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Residues in contact with LEU 38 (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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30H TYR* 3.0 36.9 + - + +
36H GLU* 3.8 5.4 - - - +
37H TYR* 1.3 98.2 - - + +
39H ARG* 1.3 68.0 + - - +
47H TYR* 4.4 11.0 - - + -
48H ARG 3.5 24.2 - - - +
49H ALA* 4.1 0.2 - - - -
50H VAL* 3.9 1.3 - - - -
54H GLY* 4.0 18.6 - - - +
57H ASP* 3.8 14.6 - - + -
58H ALA* 4.1 15.7 - - - +
61H TYR* 3.6 40.6 - - + +
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Residues in contact with ARG 39 (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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27H VAL* 4.1 14.8 - - + -
28H THR 3.2 15.9 - - - +
29H ARG* 3.5 11.1 - - - +
30H TYR* 4.8 1.1 - - - -
36H GLU* 2.5 42.6 + - - +
38H LEU* 1.3 82.4 - - - +
40H PHE* 1.3 68.2 + - - +
41H ASP* 4.2 16.5 + - - +
46H GLU 3.7 1.9 - - - +
47H TYR* 3.3 5.5 - - - -
48H ARG* 2.9 39.2 + - + +
50H VAL* 3.6 24.5 - - + +
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Residues in contact with PHE 40 (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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26H TYR* 3.8 22.2 - + - -
27H VAL* 3.3 8.7 - - - +
28H THR* 2.9 39.0 + - - -
39H ARG* 1.3 75.8 - - - +
41H ASP* 1.3 58.7 + - - +
42H SER* 3.4 32.5 - - - -
45H GLY* 3.8 6.3 - - - -
46H GLU* 3.5 36.6 - - - -
47H TYR* 3.4 32.3 - + + -
68H LEU* 4.1 10.1 - - + -
71H THR* 3.5 27.8 - - + -
72H ARG* 4.0 23.6 - - + -
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Residues in contact with ASP 41 (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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1G ILE* 5.4 0.3 - - - +
25H ARG* 2.7 36.0 + - - +
26H TYR 3.7 2.9 - - - -
27H VAL* 3.9 12.5 - - + +
39H ARG* 4.2 17.1 + - - +
40H PHE* 1.3 80.6 - - - +
42H SER* 1.3 55.3 + - - +
43H ASP* 2.7 38.2 + - - +
44H VAL* 2.8 22.8 + - + +
45H GLY* 2.6 34.1 + - - -
46H GLU 4.0 4.8 + - - +
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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