Contacts of the strand formed by residues 20 - 26 (chain A) in PDB entry 1UG4
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 LEU 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A LEU* 3.4 8.6 - - - +
3A CYS* 3.8 1.9 - - - -
19A ASN* 1.3 88.1 - - - +
21A CYS* 1.3 62.9 + - - +
38A CYS* 3.4 5.4 - - - +
39A ILE* 2.9 39.4 + - + +
40A ASP 4.0 13.9 - - - +
41A VAL* 4.0 2.5 - - - -
42A CYS* 3.7 36.6 - - + +
53A CYS* 4.5 7.9 - - + -
54A CYS* 3.6 18.2 - - - +
55A ASN* 3.8 15.0 - - + +
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Residues in contact with CYS 21 (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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1A LEU* 3.9 9.6 - - - -
2A LYS 3.6 8.7 - - - -
3A CYS* 2.0 53.4 - - - -
20A LEU* 1.3 74.5 - - - +
22A TYR* 1.3 61.9 + - - +
37A GLY 3.3 1.6 - - - -
53A CYS* 3.2 6.4 - - - +
54A CYS 2.9 33.6 + - - +
56A THR 3.9 13.7 - - - -
59A CYS* 3.8 6.3 - - - -
60A ASN* 3.5 22.7 - - + +
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Residues in contact with TYR 22 (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 CYS* 1.3 76.9 - - - +
23A LYS* 1.3 74.8 + - - +
24A MET* 4.3 19.6 - - + +
35A LYS* 2.9 49.7 + - + +
36A ARG* 3.3 2.1 - - - -
37A GLY* 2.9 50.4 + - - -
38A CYS 3.5 18.8 - - - -
39A ILE* 3.7 31.4 - - + -
43A PRO* 5.2 0.2 - - + -
51A TYR* 4.2 14.4 - + - -
52A VAL 3.2 11.2 - - - +
53A CYS* 3.7 16.8 - - - +
60A ASN* 3.0 19.8 + - - -
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Residues in contact with LYS 23 (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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22A TYR* 1.3 82.7 - - - +
24A MET* 1.3 61.0 + - - +
25A PHE* 2.8 46.0 + - + -
33A PRO* 4.7 7.6 - - + +
35A LYS 3.4 7.6 - - - +
36A ARG* 4.3 9.8 - - + +
50A LYS 3.9 0.2 - - - +
51A TYR* 3.5 4.3 - - - -
52A VAL* 2.9 46.7 + - + +
54A CYS* 5.9 1.1 - - - -
59A CYS 5.1 2.0 - - - +
60A ASN* 2.9 42.6 - - + +
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Residues in contact with MET 24 (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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22A TYR* 4.3 11.0 - - + +
23A LYS* 1.3 75.2 - - - +
25A PHE* 1.3 64.6 + - - +
26A MET* 4.7 11.9 - - - -
33A PRO* 3.8 4.7 - - - +
34A VAL* 2.9 40.4 + - - +
35A LYS* 2.8 39.1 + - + +
49A VAL* 3.6 21.5 - - + -
50A LYS 3.4 2.9 - - - +
51A TYR* 3.4 39.9 - - + +
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Residues in contact with PHE 25 (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 LYS* 2.8 37.7 - - + -
24A MET* 1.3 79.4 - - - +
26A MET* 1.3 64.2 + - - +
30A PRO* 3.0 41.7 - - + -
31A LYS 5.0 1.3 - - - -
32A VAL 3.6 9.9 - - - -
33A PRO* 3.9 15.9 - - + -
34A VAL* 4.6 2.5 - - - -
49A VAL* 3.5 8.3 - - - +
50A LYS* 2.8 50.3 + - + +
52A VAL* 4.2 25.4 - - + -
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Residues in contact with MET 26 (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* 4.7 8.7 - - - +
25A PHE* 1.3 79.4 - - - +
27A VAL* 1.3 71.3 + - - +
29A ALA* 3.2 31.2 + - + -
30A PRO* 3.7 1.5 - - - +
34A VAL* 4.0 36.1 - - + +
48A LEU* 3.5 6.5 - - + +
49A VAL* 3.6 32.8 - - + -
50A LYS* 6.1 0.2 - - - -
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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