Contacts of the strand formed by residues 66 - 73 (chain A) in PDB entry 1U0O
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 TYR 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ASP* 4.7 2.6 - - - +
65A LEU* 1.3 109.8 - - + +
67A ALA* 1.3 62.0 + - - +
105A ALA* 3.8 2.9 - - + -
106A LEU 3.3 10.1 - - - +
107A GLU* 4.4 7.6 - - + -
112A PHE* 4.2 4.8 - - - -
116A ILE* 3.7 30.3 - - + +
118A LEU* 3.5 49.1 - - + +
122A GLN* 4.5 6.3 - - - -
124A ASN* 3.9 20.1 + - - +
125A PRO* 3.3 27.7 - - - +
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Residues in contact with ALA 67 (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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16A PHE* 5.2 0.9 - - + -
56A VAL* 4.5 20.4 - - + -
66A TYR* 1.3 77.3 - - - +
68A TRP* 1.3 63.6 + - - +
105A ALA* 3.8 2.5 - - - -
106A LEU* 2.6 42.9 + - + +
112A PHE* 4.3 16.4 - - + -
124A ASN* 4.8 0.2 - - - -
125A PRO* 3.7 14.4 - - + +
126A PHE* 4.5 10.3 - - - -
127A VAL* 5.2 1.1 - - + -
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Residues in contact with TRP 68 (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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21A MET 3.1 20.3 + - - -
22A ASN 3.7 12.1 - - - -
23A TRP* 3.8 20.2 - + + -
26A ALA* 4.4 5.6 - - + -
39A LEU* 4.1 17.2 - - + +
40A VAL* 4.4 0.7 - - - +
66A TYR 4.4 0.2 - - - -
67A ALA* 1.3 74.9 - - - +
69A ILE* 1.3 64.9 + - - +
103A CYS* 3.1 34.5 - - + -
104A PHE 3.5 17.3 - - - -
105A ALA* 3.6 5.4 - - + -
118A LEU* 3.8 16.4 - - + -
119A TYR 3.2 21.5 - - - -
120A CYS* 4.0 6.1 - - - -
122A GLN* 3.6 17.7 - - + -
124A ASN* 3.2 48.2 - - + +
125A PRO 3.3 12.1 + - - +
126A PHE* 4.0 2.0 - - + +
127A VAL* 3.9 21.0 + - - +
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Residues in contact with ILE 69 (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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23A TRP* 2.8 23.9 + - - -
39A LEU* 3.4 8.7 - - - -
40A VAL* 3.4 27.1 - - + +
42A ILE* 3.9 13.7 - - + -
67A ALA 4.0 0.4 - - - +
68A TRP* 1.3 78.9 - - - +
70A GLY* 1.3 59.2 + - - +
71A LEU* 3.0 5.2 + - + +
104A PHE* 3.1 36.4 + - + +
105A ALA* 4.3 1.3 - - - +
106A LEU* 3.6 29.2 - - + -
115A TRP* 4.2 17.9 - - + +
127A VAL* 5.8 0.4 - - + -
279B TRP* 3.6 28.3 - - + -
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Residues in contact with GLY 70 (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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23A TRP* 4.0 6.2 - - - -
39A LEU* 3.1 25.9 - - - +
40A VAL 2.7 20.7 + - - -
69A ILE* 1.3 69.3 - - - +
71A LEU* 1.3 48.0 + - - +
278B GLU 3.8 0.3 - - - +
279B TRP* 2.7 41.8 - - - +
280B THR* 2.8 14.6 + - - +
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Residues in contact with LEU 71 (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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23A TRP* 4.1 2.5 + - - -
69A ILE 3.0 7.7 + - - +
70A GLY* 1.3 76.1 - - - +
72A ARG* 1.3 62.3 + - - +
104A PHE* 3.1 56.1 + - + +
115A TRP* 4.0 19.1 - - + -
277B PHE* 3.5 28.7 - - + -
278B GLU 3.4 23.6 - - - +
279B TRP* 3.4 46.2 - - + +
285B PHE* 4.6 1.8 - - + -
290B TYR* 4.4 8.3 - - + -
293B ILE* 5.1 1.3 - - + -
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Residues in contact with ARG 72 (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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23A TRP* 3.7 43.0 - - + -
24A ALA* 5.7 3.8 - - - +
70A GLY 4.3 0.2 - - - -
71A LEU* 1.3 75.2 - - - +
73A VAL* 1.3 78.5 + - - +
74A GLU* 3.3 4.3 + - - +
102A LYS* 3.0 31.6 - - - +
103A CYS* 4.4 10.0 - - - -
104A PHE* 4.1 1.3 - - - -
120A CYS* 3.9 20.0 - - - +
277B PHE* 3.4 8.9 - - - +
278B GLU* 3.3 34.5 + - + +
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Residues in contact with VAL 73 (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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72A ARG* 1.3 88.8 + - - +
74A GLU* 1.3 62.8 + - - +
75A ASN* 3.5 25.5 - - + +
80A CYS* 3.8 1.1 - - - -
101A LYS 4.4 4.0 - - - +
102A LYS* 2.9 47.7 + - + +
104A PHE* 4.2 4.7 - - + -
117A ASN* 5.4 0.9 - - - +
272B TRP* 4.4 4.5 - - + +
275B CYS* 3.4 42.2 - - + -
276B ARG 3.9 3.1 - - - -
277B PHE* 4.0 18.4 - - + -
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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