Contacts of the strand formed by residues 124 - 130 (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 ASN 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A LYS* 3.5 5.6 - - - -
21A MET 2.7 29.6 + - - +
66A TYR* 3.9 27.5 + - - +
68A TRP* 3.2 44.4 - - + +
118A LEU* 3.8 7.7 - - - +
122A GLN* 3.3 24.6 + - - +
123A LYS* 1.3 78.0 + - - +
125A PRO* 1.3 80.9 - - + +
126A PHE* 3.8 2.3 - - - -
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Residues in contact with PRO 125 (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* 3.9 15.7 - - + -
17A PHE 3.1 16.4 - - - +
18A GLN* 3.3 22.0 - - - +
19A GLN 3.9 1.8 - - - +
20A LYS* 3.8 12.5 - - + +
60A ILE* 4.9 1.8 - - + -
64A ASP* 3.7 21.3 - - + +
66A TYR 3.3 24.2 - - - +
67A ALA* 4.3 2.9 - - + -
68A TRP* 3.3 17.3 + - - -
124A ASN* 1.3 91.7 - - + +
126A PHE* 1.3 69.8 + - + +
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Residues in contact with PHE 126 (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* 3.1 8.7 - - - -
17A PHE* 2.7 72.3 + + + -
19A GLN* 3.0 30.5 - - - -
21A MET* 3.4 27.8 - - + -
26A ALA* 3.5 22.2 - - + -
29A PHE* 3.9 10.1 - + - -
30A CYS* 4.3 2.0 - - - -
39A LEU* 4.2 4.0 - - + -
67A ALA* 4.5 4.3 - - - -
68A TRP* 4.0 24.5 - - + +
124A ASN 3.8 2.7 - - - -
125A PRO* 1.3 84.6 - - + +
127A VAL* 1.3 65.8 + - - +
128A CYS* 3.6 20.6 - - - -
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Residues in contact with VAL 127 (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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14A TYR* 4.4 6.1 - - + -
15A LYS 3.1 19.5 - - - +
16A PHE* 4.2 7.0 - - + -
30A CYS* 4.3 0.9 - - - -
39A LEU* 3.5 9.5 - - - +
40A VAL* 2.9 49.7 + - + +
52A VAL* 4.1 13.5 - - + -
55A LEU* 5.0 4.9 - - + -
56A VAL* 3.3 34.1 - - + -
67A ALA* 5.2 3.1 - - + -
68A TRP 3.9 6.5 + - - +
69A ILE* 6.2 0.2 - - + -
106A LEU* 5.5 1.3 - - + -
126A PHE* 1.3 83.4 - - - +
128A CYS* 1.3 70.2 + - - +
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Residues in contact with CYS 128 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A TRP* 3.5 23.9 - - + -
14A TYR* 3.3 5.9 - - - -
15A LYS 2.9 27.3 + - - -
17A PHE* 3.5 24.5 - - + -
29A PHE* 4.4 2.0 - - - -
30A CYS* 2.0 51.8 - - + -
33A GLN* 4.9 0.4 - - - -
38A HIS 3.3 4.0 - - - -
40A VAL 4.1 0.2 - - - -
126A PHE* 3.6 13.0 - - - -
127A VAL* 1.3 77.5 - - - +
129A LYS* 1.3 61.6 + - - +
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Residues in contact with LYS 129 (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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6A TRP* 4.3 1.3 - - - -
12A ASN* 4.3 19.9 - - + +
13A CYS 3.5 5.2 - - - +
14A TYR* 3.2 39.8 + - + -
36A GLY 3.9 0.2 - - - +
37A GLY* 2.8 25.3 - - - -
38A HIS* 2.7 17.4 + - - +
39A LEU 4.6 0.9 - - - +
40A VAL* 3.5 15.3 - - - +
41A SER* 2.9 36.3 + - - +
43A LYS* 6.1 0.8 - - - +
48A GLU* 3.0 19.2 + - - -
128A CYS* 1.3 76.4 - - - +
130A SER* 1.3 66.6 + - - +
281B ASP* 4.4 8.0 + - + +
283B MET* 5.4 2.6 - - - -
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Residues in contact with SER 130 (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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6A TRP* 3.6 14.0 - - - -
12A ASN* 4.5 4.5 - - - -
13A CYS* 2.8 32.0 + - - +
34A ALA* 3.6 24.8 - - - +
35A LYS 4.3 0.9 - - - -
36A GLY 3.4 14.8 - - - -
37A GLY* 3.5 8.1 - - - -
129A LYS* 1.3 83.1 - - - +
131A PRO* 1.3 74.2 + - - +
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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