Contacts of the strand formed by residues 41 - 48 (chain I) in PDB entry 1UGH
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 ILE 41 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I ILE 3.4 2.3 - - - +
23I LEU* 3.4 1.8 - - - -
24I MET* 2.7 40.2 + - - +
29I VAL* 3.7 17.3 - - + -
37I PRO* 3.7 37.0 - - + -
39I SER* 3.5 7.2 + - - +
40I ASP* 1.3 75.5 - - - +
42I LEU* 1.3 66.6 - - - +
43I VAL* 3.7 6.4 + - + -
58I LEU* 3.5 34.8 - - + -
59I THR 3.1 20.9 - - - +
60I SER* 4.5 3.4 - - - -
66I LYS* 5.8 0.4 - - - +
68I TRP* 4.0 21.8 - - + -
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Residues in contact with LEU 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E ASP* 6.1 0.4 - - - +
214E ALA* 4.3 22.2 - - + +
215E ASN* 4.4 10.5 - - + -
21I SER* 4.4 7.4 - - - +
22I ILE 3.6 2.9 - - - -
23I LEU* 4.0 28.3 - - + +
40I ASP 4.0 0.4 + - - -
41I ILE* 1.3 72.7 - - - +
43I VAL* 1.3 60.4 + - - +
44I HIS* 3.0 32.0 + - + +
57I LEU 3.4 0.9 - - - +
58I LEU* 3.4 1.4 - - - -
59I THR* 3.0 22.5 + - - +
60I SER 3.7 11.9 - - - +
61I ASP* 3.8 10.1 - - - +
62I ALA 3.7 10.5 - - - +
65I TYR* 3.6 33.0 - - + -
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Residues in contact with VAL 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270E SER* 4.3 4.0 - - - +
272E LEU* 4.1 19.7 - - + -
20I GLU 3.7 0.3 - - - +
21I SER* 3.3 2.9 + - - -
22I ILE* 2.8 44.0 + - + +
24I MET* 3.7 26.0 - - + -
29I VAL* 5.4 0.2 - - + -
41I ILE* 4.2 16.2 - - + +
42I LEU* 1.3 70.5 - - - +
44I HIS* 1.3 59.7 + - - +
45I THR* 3.4 19.1 + - - +
56I MET* 3.9 29.8 - - + -
57I LEU 4.1 1.8 - - - -
58I LEU* 3.9 10.1 - - + -
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Residues in contact with HIS 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E HIS* 5.0 1.6 - + - -
214E ALA* 4.6 4.7 - - + +
4I LEU* 3.3 26.9 - - + +
18I ILE* 3.7 25.7 - - + +
20I GLU 3.4 7.0 - - - -
21I SER* 3.0 25.0 + - - +
42I LEU* 3.0 35.2 + - + +
43I VAL* 1.3 69.8 - - - +
45I THR* 1.3 60.3 + - - +
55I VAL 3.7 0.9 - - - +
56I MET* 3.1 3.3 - - - -
57I LEU* 2.8 57.4 + - + +
59I THR* 2.9 32.1 + - + +
65I TYR* 4.6 3.8 - - - -
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Residues in contact with THR 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E PRO* 3.8 24.2 - - + -
270E SER* 4.4 4.7 + - - -
271E PRO* 4.4 9.9 - - + -
18I ILE* 3.6 2.9 - - - +
19I GLN* 2.8 25.8 + - - +
20I GLU* 2.8 35.1 + - - +
22I ILE* 5.5 0.2 - - - +
43I VAL* 3.4 16.5 + - - +
44I HIS* 1.3 73.8 - - - +
46I ALA* 1.3 66.4 + - - +
54I ASN* 4.5 4.7 - - + +
55I VAL 3.5 4.7 - - - +
56I MET* 3.5 27.6 - - + +
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Residues in contact with ALA 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E PRO* 4.9 1.1 - - - -
8I ILE* 5.1 2.0 - - + -
16I LEU* 3.7 25.8 - - + -
17I VAL 2.9 32.1 - - - +
18I ILE* 4.1 9.0 - - + -
19I GLN* 4.3 2.5 - - - +
44I HIS 4.3 0.2 + - - -
45I THR* 1.3 77.9 - - - +
47I TYR* 1.3 60.3 + - - +
48I ASP 4.2 0.2 - - - -
54I ASN* 3.8 3.1 - - - -
55I VAL* 2.9 33.8 + - + +
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Residues in contact with TYR 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E PRO* 4.6 11.4 - - + -
16I LEU* 3.9 9.9 - - - +
17I VAL 4.3 2.6 + - - -
19I GLN* 4.7 7.9 - - + +
46I ALA* 1.3 75.1 - - - +
48I ASP* 1.3 63.0 + - - +
49I GLU* 3.4 36.1 + - + +
52I ASP* 2.8 54.9 + - - -
53I GLU 3.4 8.3 - - - -
54I ASN* 3.2 28.9 - - - +
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Residues in contact with ASP 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I LYS* 2.8 41.3 + - - +
16I LEU* 4.0 21.6 - - + +
46I ALA 4.1 1.2 + - - -
47I TYR* 1.3 71.6 - - - +
49I GLU* 1.3 54.1 + - - +
50I SER* 3.1 12.1 + - - -
51I THR* 2.9 34.7 + - - +
52I ASP* 2.7 31.0 + - - -
53I GLU 2.7 23.2 + - - +
55I VAL* 4.4 5.1 - - + +
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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