Contacts of the strand formed by residues 16 - 21 (chain A) in PDB entry 2UZC
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 PHE 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.8 0.4 - - + -
14A TRP* 3.6 30.7 - + + -
15A GLY* 1.3 79.4 - - - +
17A ARG* 1.3 80.9 + - - +
18A LEU* 3.9 24.2 - - + -
30A ILE* 3.9 18.6 - - + -
32A SER 3.3 15.7 - - - +
33A LEU* 3.9 12.1 - - + +
39A ALA* 3.8 14.1 - - + -
70A ILE* 3.9 25.8 - - + -
77A LEU* 3.8 13.2 - - + -
79A MET* 3.9 21.1 - - + -
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Residues in contact with ARG 17 (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* 1.3 83.5 - - - +
18A LEU* 1.3 68.1 + - - +
30A ILE* 3.6 6.9 - - - -
31A SER* 2.9 32.2 + - - +
32A SER* 3.1 29.6 + - - +
67A GLN* 5.9 2.8 - - - +
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Residues in contact with LEU 18 (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 20.9 - - + -
17A ARG* 1.3 79.7 + - - +
19A GLN* 1.3 65.1 + - - +
28A LEU* 4.5 10.5 - - + -
29A THR 3.3 23.6 - - - +
30A ILE* 4.0 11.2 - - + -
31A SER* 3.2 9.5 + - - -
50A VAL* 4.0 14.1 - - + -
53A ILE* 5.8 0.2 - - + -
63A HIS* 3.1 28.3 + - + +
66A ALA* 4.3 18.8 - - + -
67A GLN* 4.8 14.8 - - + +
70A ILE* 3.7 26.7 - - + -
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Residues in contact with GLN 19 (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 LEU* 1.3 75.4 - - - +
20A GLY* 1.3 65.2 + - - +
26A MET* 3.8 19.4 - - + +
27A PRO 3.5 0.2 - - - +
28A LEU* 3.5 3.8 - - - +
29A THR* 2.9 33.1 + - - +
31A SER* 3.4 23.0 + - - +
63A HIS* 3.7 5.8 - - - -
64B LEU* 3.5 23.3 - - + +
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Residues in contact with GLY 20 (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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19A GLN* 1.3 77.9 - - - +
21A GLY* 1.3 59.6 + - - -
24A PHE* 3.7 18.5 - - - -
26A MET* 3.6 20.0 - - - +
27A PRO 3.5 9.6 - - - -
28A LEU* 3.5 4.9 - - - +
63A HIS* 2.7 36.0 + - - +
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Residues in contact with GLY 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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20A GLY* 1.3 72.8 - - - -
22A LYS* 1.3 66.8 + - - -
23A ASP* 3.3 7.2 - - - -
24A PHE 3.1 10.4 + - - -
25A ASN 3.2 5.2 + - - -
26A MET 2.8 23.7 + - - +
27A PRO 3.8 1.6 + - - -
28A LEU* 3.7 16.4 - - - +
59A GLN 6.0 0.7 - - - -
61A MET 3.7 9.9 - - - -
63A HIS 4.2 0.9 - - - -
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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