Contacts of the strand formed by residues 66 - 72 (chain A) in PDB entry 1UEX
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 ALA 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ALA* 5.1 1.8 - - + -
59A LEU* 4.1 21.8 - - + -
64A TYR 4.0 1.0 + - - -
65A ASP* 1.3 72.3 - - - +
67A TRP* 1.3 65.6 + - - +
68A ILE* 3.5 1.2 + - - +
102A GLY* 3.2 2.4 - - - -
103A LEU* 2.8 44.1 + - + +
109A TYR* 4.1 3.9 - - + -
122A PRO 3.2 10.1 - - - +
123A PHE 4.9 0.4 - - - +
124A ILE* 4.0 27.1 - - + -
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Residues in contact with TRP 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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23A GLY 3.1 28.0 + - - -
25A TRP* 3.4 37.3 - + + +
28A ALA* 4.1 5.6 - - + -
39A LEU* 4.1 9.5 - - + +
65A ASP 4.0 0.8 + - - -
66A ALA* 1.3 73.1 - - - +
68A ILE* 1.3 62.3 + - - +
100A CYS* 3.2 37.2 - - + -
101A PHE 3.2 21.5 - - - -
102A GLY* 4.2 2.0 - - - -
115A LEU* 3.5 26.0 - - + -
116A PRO 3.4 22.7 - - - -
117A CYS* 4.4 0.2 - - - -
119A GLU* 3.2 23.1 + - + -
121A ASN* 3.6 28.8 - - + +
122A PRO 2.9 8.7 + - - -
123A PHE* 3.6 13.4 - - + +
124A ILE* 3.3 24.3 + - - +
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Residues in contact with ILE 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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25A TRP* 3.0 23.6 + - - -
39A LEU* 3.2 12.1 - - - +
40A ALA* 3.8 15.9 - - + +
42A ILE* 5.1 6.7 - - + -
51A VAL* 5.4 0.9 - - + -
66A ALA 4.0 0.4 - - - +
67A TRP* 1.3 78.8 - - - +
69A GLY* 1.3 59.5 + - - +
70A LEU* 3.2 12.4 + - + +
101A PHE* 3.2 24.4 + - + +
102A GLY* 3.6 17.3 - - - +
103A LEU* 3.8 26.9 - - + -
112A TRP* 4.0 36.1 - - + +
124A ILE* 4.4 8.7 - - + -
81B TRP* 4.5 6.3 - - + -
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Residues in contact with GLY 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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25A TRP* 4.3 5.2 - - - -
39A LEU* 3.3 25.2 - - - +
40A ALA 2.7 20.0 + - - -
68A ILE* 1.3 71.1 - - - +
70A LEU* 1.3 54.8 + - - +
80B ARG 3.7 0.3 - - - +
81B TRP* 2.9 36.7 - - - -
82B THR* 3.0 13.6 + - - +
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Residues in contact with LEU 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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25A TRP* 3.7 6.7 + - - -
68A ILE* 3.2 7.4 + - + +
69A GLY* 1.3 76.6 - - - +
71A ARG* 1.3 62.7 - - - +
101A PHE* 2.9 53.2 + - + +
112A TRP* 3.8 34.1 - - + -
79B LEU* 4.0 4.5 - - + -
80B ARG* 3.5 28.7 - - - +
81B TRP* 3.6 25.4 - - + +
87B LEU* 3.9 26.5 - - + -
92B LEU* 4.3 6.5 - - + -
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Residues in contact with ARG 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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25A TRP* 3.0 45.3 - - + -
26A GLU* 3.1 26.7 + - - -
70A LEU* 1.3 76.5 - - - +
72A ASP* 1.3 70.5 + - - +
73A GLU* 3.5 25.9 + - - +
99A LYS* 3.1 20.2 + - - +
100A CYS* 3.7 12.9 - - - -
101A PHE* 4.1 8.1 - - - -
117A CYS* 3.9 7.9 - - - +
79B LEU* 3.3 6.1 - - - +
80B ARG 3.2 33.3 + - - +
81B TRP 6.1 0.2 - - - +
82B THR* 5.3 1.8 - - + -
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Residues in contact with ASP 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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71A ARG* 1.3 82.4 + - - +
73A GLU* 1.3 65.1 + - - +
74A SER* 2.6 25.8 + - - -
79A CYS* 3.3 19.1 + - - +
98A THR 5.3 1.2 - - - +
99A LYS* 2.7 63.6 + - + +
101A PHE* 4.8 2.7 - - + -
74B TRP* 4.5 6.4 - - + -
77B CYS* 3.8 2.9 - - - +
78B PRO* 3.2 14.9 - - - +
79B LEU* 4.1 16.1 - - + +
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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