Contacts of the strand formed by residues 53 - 60 (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 GLU 53 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47I TYR* 3.4 6.6 - - - -
48I ASP* 2.7 37.1 + - + +
51I THR* 3.3 38.8 + - - +
52I ASP* 1.3 80.5 - - - +
54I ASN* 1.3 61.5 + - - +
55I VAL* 3.6 4.9 + - + +
72I ILE* 3.2 20.1 - - + +
73I GLN 3.3 9.4 - - - +
74I ASP* 4.0 11.2 - - + +
80I LYS* 2.6 34.1 + - - -
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Residues in contact with ASN 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168E PRO* 4.2 10.4 - - - +
172E ASN* 5.7 1.4 + - - +
271E PRO* 3.6 30.1 - - + +
45I THR* 4.6 3.1 - - + -
46I ALA 3.8 3.3 - - - +
47I TYR* 3.2 30.0 - - - +
52I ASP 4.4 0.6 + - - -
53I GLU* 1.3 70.7 - - - +
55I VAL* 1.3 61.6 + - - +
56I MET* 3.7 19.9 - - + +
71I VAL 3.6 1.7 - - - +
72I ILE* 3.5 3.3 - - - -
73I GLN* 2.9 47.3 + - + +
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Residues in contact with VAL 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I ILE* 4.1 20.1 - - + +
12I THR* 4.4 7.2 - - + -
16I LEU* 3.3 35.4 - - + -
44I HIS 3.7 0.7 - - - +
45I THR* 3.5 1.9 - - - -
46I ALA* 2.9 35.0 + - + +
48I ASP* 4.4 7.0 - - + +
53I GLU* 4.0 15.3 - - + +
54I ASN* 1.3 75.1 - - - +
56I MET* 1.3 61.6 + - - +
57I LEU 4.2 0.4 + - - -
70I LEU* 4.2 11.0 - - + -
71I VAL 3.7 2.7 - - - -
72I ILE* 3.4 27.6 - - + -
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Residues in contact with MET 56 (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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270E SER* 4.9 0.2 - - - -
271E PRO* 3.7 23.3 - - + -
272E LEU* 3.6 40.8 - - + +
43I VAL* 3.9 7.0 - - + -
44I HIS 3.1 6.3 - - - +
45I THR* 3.5 24.2 - - + +
54I ASN* 3.7 22.7 - - + +
55I VAL* 1.3 77.5 - - - +
57I LEU* 1.3 60.4 + - - +
58I LEU* 3.5 16.5 - - + +
70I LEU* 3.5 6.5 - - - -
71I VAL* 2.8 46.2 + - + +
73I GLN* 3.9 15.3 - - + +
79I ASN* 4.3 8.1 - - - +
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Residues in contact with LEU 57 (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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4I LEU* 3.2 47.8 - - + +
7I ILE* 3.8 17.3 - - + -
8I ILE* 3.5 27.5 - - + +
44I HIS* 2.8 46.9 + - + +
55I VAL 4.2 0.8 - - - -
56I MET* 1.3 71.6 - - - +
58I LEU* 1.3 62.3 + - - +
59I THR* 4.0 17.7 - - + -
67I PRO* 4.7 2.9 - - + -
69I ALA 3.9 9.2 - - - +
70I LEU* 4.1 8.7 - - + +
84I LEU* 4.1 20.9 - - + -
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Residues in contact with LEU 58 (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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272E LEU* 4.3 11.4 - - + -
29I VAL* 4.6 0.9 - - + -
33I ILE* 4.0 22.0 - - + -
41I ILE* 3.5 19.5 - - + -
42I LEU 3.4 4.0 - - - -
43I VAL* 3.9 14.8 - - + -
56I MET* 3.5 31.2 - - + +
57I LEU* 1.3 74.3 - - - +
59I THR* 1.3 63.2 + - - +
67I PRO* 3.9 0.5 - - - +
68I TRP* 3.0 57.0 + - + +
69I ALA* 2.9 18.9 + - + +
71I VAL* 4.0 14.6 - - + -
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Residues in contact with THR 59 (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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4I LEU* 3.8 17.7 - - + -
41I ILE* 3.1 16.4 - - - +
42I LEU 3.0 24.6 + - - -
44I HIS* 2.9 32.3 - - + +
57I LEU* 4.0 15.5 - - + -
58I LEU* 1.3 79.6 - - - +
60I SER* 1.3 70.4 + - - +
65I TYR* 3.7 26.6 - - - +
66I LYS 3.5 7.6 - - - -
67I PRO* 4.3 6.1 - - + -
68I TRP* 4.3 0.4 - - - +
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Residues in contact with SER 60 (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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39I SER* 4.9 12.3 - - - -
40I ASP 3.6 7.2 - - - -
41I ILE* 4.5 4.5 - - - -
42I LEU* 3.7 3.9 - - - +
59I THR* 1.3 90.9 + - - +
61I ASP* 1.3 67.2 + - - +
64I GLU* 2.9 27.6 + - - +
65I TYR* 3.5 7.3 - - - -
66I LYS* 2.7 44.2 + - - +
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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