Contacts of the strand formed by residues 53 - 60 (chain A) in PDB entry 1UGI
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A LYS* 5.2 0.5 + - - -
47A TYR* 3.5 4.5 - - - -
48A ASP* 2.7 44.0 + - + +
51A THR* 3.1 38.7 + - - +
52A ASP* 1.3 77.3 - - - +
54A ASN* 1.3 64.0 + - - +
55A VAL* 4.9 1.6 - - + +
72A ILE* 3.6 26.1 - - + +
73A GLN 3.3 12.3 - - - +
74A ASP* 4.1 16.9 - - + +
80A LYS* 5.3 6.8 + - - -
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Residues in contact with ASN 54 (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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45A THR* 5.2 7.4 - - + +
46A ALA 4.2 3.1 - - - -
47A TYR* 4.0 17.7 - - - +
52A ASP 5.2 1.2 + - - +
53A GLU* 1.3 75.1 - - - +
55A VAL* 1.3 60.1 + - - +
56A MET* 4.0 12.2 - - + +
71A VAL 3.4 1.9 - - - +
72A ILE* 3.1 6.2 - - - -
73A GLN* 2.8 73.5 + - + +
74A ASP 3.9 6.9 - - - +
75A SER* 5.5 0.3 - - - -
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Residues in contact with VAL 55 (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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8A ILE* 4.4 15.8 - - + +
12A THR* 4.3 17.3 - - + -
16A LEU* 4.2 18.6 - - + -
44A HIS 3.7 1.7 - - - +
45A THR* 3.3 2.5 - - - +
46A ALA* 2.8 49.3 + - + +
48A ASP* 4.4 15.3 - - + +
53A GLU* 4.5 1.6 - - + +
54A ASN* 1.3 73.0 - - - +
56A MET* 1.3 63.3 + - - +
70A LEU* 3.5 25.8 - - + -
71A VAL 3.5 2.0 - - - -
72A ILE* 3.5 23.8 - - + -
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Residues in contact with MET 56 (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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43A VAL* 4.0 18.8 - - + -
44A HIS 3.7 3.8 - - - -
45A THR* 3.8 24.5 - - + +
54A ASN* 4.3 9.0 - - + +
55A VAL* 1.3 78.0 - - - +
57A LEU* 1.3 59.5 + - - +
58A LEU* 3.4 12.7 - - + +
70A LEU* 3.5 3.6 - - - -
71A VAL* 2.6 69.0 + - + +
73A GLN* 4.0 31.4 - - + +
79A ASN* 4.7 1.1 - - - +
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Residues in contact with LEU 57 (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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4A LEU* 3.8 50.5 - - + +
7A ILE* 4.1 15.3 - - + -
8A ILE* 4.1 21.1 - - + -
42A LEU 3.4 0.3 - - - +
43A VAL* 3.6 0.9 - - - -
44A HIS* 2.9 48.8 + - + +
55A VAL 4.0 1.2 - - - -
56A MET* 1.3 71.6 - - - +
58A LEU* 1.3 68.0 + - - +
59A THR* 4.0 11.4 - - + -
67A PRO* 4.7 2.9 - - + -
69A ALA 3.8 2.7 - - - +
70A LEU* 4.0 7.0 - - + -
84A LEU* 3.6 31.4 - - + -
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Residues in contact with LEU 58 (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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24A MET* 5.3 3.1 - - + -
29A VAL* 4.2 21.3 - - + -
32A VAL* 6.3 0.4 - - + -
33A ILE* 4.4 12.1 - - + -
41A ILE* 3.8 21.5 - - + -
42A LEU 3.4 4.5 - - - -
43A VAL* 4.3 15.3 - - + -
56A MET* 3.4 27.1 - - + +
57A LEU* 1.3 77.1 - - - +
59A THR* 1.3 61.3 + - - +
67A PRO* 3.9 0.7 - - - +
68A TRP* 2.8 36.3 + - + -
69A ALA* 2.8 32.0 + - + +
71A VAL* 4.0 12.8 - - + -
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Residues in contact with THR 59 (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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4A LEU* 4.4 9.0 - - + -
41A ILE* 3.3 11.7 - - - +
42A LEU* 2.6 38.6 + - - +
44A HIS* 3.0 33.6 + - + +
57A LEU* 4.0 17.0 - - + -
58A LEU* 1.3 77.1 - - - +
60A SER* 1.3 69.6 + - - +
65A TYR* 3.6 22.6 - - + +
66A LYS 3.1 12.6 - - - -
67A PRO* 4.1 8.5 - - + -
68A TRP 4.2 0.2 - - - +
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Residues in contact with SER 60 (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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39A SER* 5.9 4.9 - - - -
40A ASP 3.7 12.3 - - - -
41A ILE* 4.2 5.7 - - - +
42A LEU* 3.9 4.4 - - - +
59A THR* 1.3 90.6 + - - +
61A ASP* 1.3 70.4 + - - +
64A GLU* 4.0 6.6 + - - +
65A TYR* 3.4 7.6 + - - -
66A LYS* 2.9 38.3 + - - +
68A TRP* 5.1 0.6 - - - +
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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