Contacts of the strand formed by residues 17 - 23 (chain A) in PDB entry 1ZQ1
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 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A GLY 3.4 3.0 + - - -
16A ASP* 1.3 69.6 - - - +
18A VAL* 1.3 59.9 + - - +
32A GLU* 4.1 8.5 - - + -
33A GLY* 3.5 29.2 - - - -
34A TYR* 3.5 45.8 - + + -
52A GLU* 3.6 33.4 - - + -
70A LEU* 3.0 52.4 + - + -
71A GLU* 2.9 56.1 + - + +
72A ARG* 4.5 0.8 - - - +
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Residues in contact with VAL 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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12A ILE* 4.8 3.1 - - + -
16A ASP* 3.7 15.0 - - + +
17A PHE* 1.3 81.1 - - - +
19A ARG* 1.3 81.6 + - - +
20A ILE* 3.8 19.7 - - + -
32A GLU* 3.1 6.2 - - - +
33A GLY 2.6 37.8 + - - +
35A ILE* 4.1 23.8 - - + -
49A LEU* 4.8 2.7 - - + -
67A ILE* 4.1 8.3 - - + +
68A GLU 2.8 19.7 - - - +
69A VAL* 4.0 17.5 - - + -
70A LEU* 4.2 7.5 - - - +
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Residues in contact with ARG 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 VAL* 1.3 80.0 - - - +
20A ILE* 1.3 60.5 + - - +
21A THR* 4.6 5.9 + - - +
30A THR* 4.1 14.8 - - - +
31A TYR 3.3 15.9 - - - +
32A GLU* 3.1 29.4 + - + -
66A ARG* 3.8 2.6 - - - +
68A GLU* 3.0 56.9 + - + +
70A LEU* 4.0 27.3 - - + +
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Residues in contact with ILE 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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18A VAL* 3.8 19.0 - - + +
19A ARG* 1.3 71.9 - - - +
21A THR* 1.3 77.3 + - - +
22A LYS* 4.5 4.7 - - + +
29A VAL 4.5 0.2 - - - -
30A THR* 3.4 5.4 + - - -
31A TYR* 2.8 41.6 + - + +
35A ILE* 5.6 1.8 - - + -
47A LEU* 3.4 33.4 - - + -
49A LEU* 4.5 14.3 - - + +
59A ILE* 3.7 28.5 - - + -
64A ILE* 4.0 18.4 - - + -
66A ARG 3.3 5.4 - - - +
67A ILE* 4.1 11.7 - - + -
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Residues in contact with THR 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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19A ARG* 4.6 7.6 + - - +
20A ILE* 1.3 79.5 + - - +
22A LYS* 1.3 65.4 + - - +
28A GLU* 3.6 39.0 - - + +
29A VAL 3.4 9.6 - - - +
30A THR* 4.3 10.2 + - - +
65A ARG* 2.9 27.2 + - + -
66A ARG* 2.7 39.4 + - + +
68A GLU* 5.3 2.4 + - - -
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Residues in contact with LYS 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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20A ILE* 4.5 4.9 - - + -
21A THR* 1.3 78.8 - - - +
23A GLU* 1.3 59.8 - - - +
24A GLU* 2.9 34.8 - - - +
28A GLU* 3.4 5.0 - - - +
29A VAL* 2.8 45.1 + - + +
31A TYR* 3.7 31.2 - - + -
59A ILE* 3.4 24.7 - - + +
63A LYS* 2.9 33.7 - - + +
64A ILE* 4.0 2.7 - - - -
65A ARG* 4.2 2.9 - - - +
115C PRO 5.2 1.1 + - - -
117C ASP* 2.7 31.7 + - - +
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Residues in contact with GLU 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 LYS* 1.3 75.9 + - - +
24A GLU* 1.3 62.6 + - - +
25A ASP 4.3 0.4 - - - -
26A GLY* 4.2 17.6 + - - +
27A GLU 3.3 16.3 + - - +
28A GLU* 4.8 8.7 - - + -
63A LYS* 2.9 35.6 + - - +
65A ARG* 2.6 46.1 + - + +
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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