Contacts of the strand formed by residues 121 - 127 (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 ASN 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A VAL* 3.4 4.8 - - - -
23A GLY 3.2 23.1 + - - +
64A TYR* 4.0 10.5 - - - -
65A ASP* 2.9 49.7 + - - +
67A TRP* 3.6 22.5 - - + +
115A LEU* 4.7 0.8 - - - +
119A GLU* 2.9 50.5 + - - +
120A LYS* 1.3 76.5 + - - +
122A PRO* 1.3 68.6 - - - +
123A PHE* 3.9 2.1 + - - -
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Residues in contact with PRO 122 (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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18A VAL* 5.2 0.2 - - + -
19A PHE 3.1 22.2 - - - +
20A LYS* 3.7 13.5 - - + +
21A LYS 3.7 8.5 - - - +
22A VAL* 4.2 3.5 - - + -
59A LEU* 3.7 33.4 - - + -
64A TYR* 3.7 26.7 - - + -
65A ASP 3.1 16.4 - - - +
66A ALA* 3.2 6.0 - - - -
67A TRP 2.9 20.1 + - - -
121A ASN* 1.3 90.0 - - + +
123A PHE* 1.3 57.2 + - - +
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Residues in contact with PHE 123 (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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17A LYS 4.0 0.2 - - - +
18A VAL* 3.5 7.0 - - - +
19A PHE* 3.1 44.9 + + + -
21A LYS* 3.5 22.4 - - + -
22A VAL 4.8 6.5 - - - -
23A GLY* 5.0 2.0 - - - -
28A ALA* 3.4 42.4 - - + -
31A PHE* 3.5 25.6 - + + -
32A CYS* 3.9 2.0 - - - -
39A LEU* 3.7 4.7 - - + -
66A ALA* 4.5 0.4 - - - -
67A TRP* 3.6 24.7 - - + +
121A ASN 4.1 4.7 - - - -
122A PRO* 1.3 80.0 - - - +
124A ILE* 1.3 65.3 + - - +
125A CYS* 3.5 26.5 - - - -
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Residues in contact with ILE 124 (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 TYR* 4.6 7.2 - - + -
17A LYS 3.6 13.9 - - - +
18A VAL* 4.0 16.4 - - + -
32A CYS* 4.2 0.2 - - - -
39A LEU* 3.3 11.1 - - - +
40A ALA* 2.8 39.3 + - + -
51A VAL* 3.4 30.7 - - + -
54A LEU* 4.9 1.3 - - + -
55A ALA* 4.4 7.4 - - + -
66A ALA* 4.0 14.8 - - + -
67A TRP 3.3 12.9 + - - +
68A ILE* 4.4 4.3 - - + -
103A LEU* 3.6 21.3 - - + -
123A PHE* 1.3 83.8 - - - +
125A CYS* 1.3 69.0 + - - +
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Residues in contact with CYS 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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8A TRP* 3.7 24.5 - - + -
16A TYR* 3.1 27.7 - - - +
17A LYS 3.3 9.4 + - - -
19A PHE* 3.6 12.6 - - + -
31A PHE* 3.9 3.6 - - - -
32A CYS* 2.0 57.2 - - + +
35A ASN* 5.6 0.2 - - - -
37A GLY* 6.4 0.2 - - - -
38A HIS 3.4 0.2 - - - -
40A ALA 4.2 0.4 - - - -
123A PHE* 3.5 20.4 - - - -
124A ILE* 1.3 76.1 - - - +
126A LYS* 1.3 61.8 + - - +
127A SER* 5.8 0.2 - - - +
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Residues in contact with LYS 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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8A TRP* 4.7 0.2 - - - -
12A LYS* 5.5 0.2 - - - +
14A HIS* 3.3 44.2 + - + +
15A CYS 3.1 5.4 - - - +
16A TYR* 3.9 22.0 - - + -
37A GLY* 3.2 2.8 - - - -
38A HIS* 2.7 35.3 + - + +
39A LEU 4.6 0.9 - - - +
40A ALA* 3.8 13.5 - - - -
41A SER* 2.9 36.8 + - - +
43A ASP* 4.0 8.7 + - - -
47A GLU* 3.2 17.4 + - - +
125A CYS* 1.3 77.0 - - - +
127A SER* 1.3 70.1 + - - +
83B ASP* 3.5 12.8 + - + +
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Residues in contact with SER 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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8A TRP* 4.1 12.2 - - - -
13A GLY 4.1 2.8 - - - +
14A HIS* 3.2 26.4 + - - -
15A CYS* 2.9 40.1 + - - -
32A CYS 4.9 0.2 + - - -
35A ASN* 3.1 15.4 + - - +
36A SER* 3.0 28.1 + - - -
37A GLY* 3.6 2.3 - - - -
125A CYS* 5.8 0.2 - - - +
126A LYS* 1.3 76.4 + - - +
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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