Contacts of the helix formed by residues 21 - 27 (chain A) in PDB entry 1Z29
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 ILE 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A PRO* 5.9 0.2 - - + -
12A LEU* 4.3 8.0 - - + +
20A LEU* 1.3 74.0 - - - +
22A LYS* 1.3 69.0 + - - +
23A TYR* 3.8 22.0 - - + +
24A PHE* 2.9 56.8 + - + +
25A ALA* 2.9 19.4 + - - +
148A VAL* 3.7 35.9 - - + +
149A TYR* 4.1 27.1 - - + +
168A SER* 3.8 15.5 + - - +
169A TYR* 5.2 0.2 - - + -
721A ACY 4.6 4.0 - - + +
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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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10A PRO* 4.2 29.0 + - + +
11A PRO* 4.1 18.1 + - + +
13A GLU* 4.4 17.7 - - + -
20A LEU 3.2 5.8 + - - -
21A ILE* 1.3 71.3 - - - +
23A TYR* 1.3 76.2 + - + +
25A ALA* 3.1 16.0 + - - +
26A GLU* 3.0 42.8 + - + +
148A VAL 5.4 0.2 + - - -
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Residues in contact with TYR 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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8A SER 4.7 8.2 + - - -
10A PRO* 4.3 21.7 - - + +
21A ILE* 4.0 13.5 - - + -
22A LYS* 1.3 91.0 - - + +
24A PHE* 1.3 58.8 + + + +
26A GLU* 3.0 26.2 + - - +
27A ALA* 2.8 27.7 + - - +
85A LYS* 3.1 33.2 - - + +
86A VAL* 4.5 0.9 - - - -
87A PRO* 3.5 42.7 - - + +
148A VAL* 4.3 23.1 - - + -
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Residues in contact with PHE 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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20A LEU* 4.7 9.8 - - + +
21A ILE* 2.9 52.8 + - + +
23A TYR* 1.3 75.9 - + - +
25A ALA* 1.3 60.7 + - - +
27A ALA* 3.5 8.6 + - - +
28A LEU* 3.5 19.1 + - - +
81A PHE* 3.7 21.5 - + - -
83A GLU* 3.6 27.2 - - + +
84A PHE* 4.0 20.9 - + - -
85A LYS 3.4 30.1 - - - -
86A VAL* 5.6 0.7 - - + -
109A LEU* 6.5 0.2 - - + -
148A VAL* 5.5 4.5 - - + -
169A TYR* 3.2 29.4 - + + +
721A ACY 4.1 7.4 - - - -
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Residues in contact with ALA 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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13A GLU* 3.7 26.9 - - + +
15A VAL* 4.2 14.9 - - + +
20A LEU* 4.5 6.3 - - + +
21A ILE 2.9 10.6 + - - +
22A LYS 3.1 13.2 - - - +
23A TYR 3.0 0.2 - - - -
24A PHE* 1.3 76.6 - - - +
26A GLU* 1.3 63.2 + - + +
28A LEU* 3.3 28.2 + - - +
29A GLY 4.5 0.5 + - - -
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Residues in contact with GLU 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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13A GLU* 6.5 0.2 - - + -
22A LYS* 3.0 42.9 - - + +
23A TYR* 3.2 31.3 - - - +
25A ALA* 1.3 76.5 - - + +
27A ALA* 1.3 58.1 - - - +
28A LEU 3.1 4.7 + - - -
29A GLY* 3.5 3.8 + - - -
30A PRO* 3.3 16.3 - - - +
85A LYS* 5.2 5.6 - - + +
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Residues in contact with ALA 27 (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 TYR 2.8 14.8 + - - +
24A PHE 3.7 4.3 - - - +
25A ALA 3.2 0.4 - - - -
26A GLU* 1.3 75.8 - - - +
28A LEU* 1.3 59.9 + - - +
29A GLY 3.4 0.7 - - - -
30A PRO* 3.5 12.5 - - - +
31A LEU* 3.3 23.0 + - - +
82A LEU 5.7 0.7 - - - +
83A GLU* 3.4 28.7 - - - +
84A PHE 4.1 4.0 - - - +
85A LYS* 3.6 20.8 - - + +
91A SER* 6.3 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