Contacts of the helix formed by residues 22 - 30 (chain B) in PDB entry 1ZTG
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 GLY 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B HIS* 1.3 70.4 - - - +
23B LYS* 1.3 57.5 + - - +
25B VAL* 2.8 24.9 + - - +
26B GLY 3.1 10.0 + - - -
54B CYS 4.1 13.5 - - - -
55B PRO* 3.1 14.8 + - - +
57B ARG* 4.6 6.7 - - - -
4Z C 3.9 12.5 + - - -
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Residues in contact with LYS 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B HIS* 4.4 5.1 - - + +
22B GLY* 1.3 72.2 - - - +
24B GLU* 1.3 68.6 + - + +
25B VAL 3.3 0.7 + - - -
26B GLY* 3.4 2.9 + - - +
27B SER* 3.4 16.5 + - - -
82B ASP 5.7 2.0 - - - -
84B ASN* 4.5 19.8 + - - +
3Z C 5.4 0.9 - - - +
4Z C 5.8 0.2 - - - +
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU 4.5 1.2 - - - +
20B MET* 3.3 35.4 - - + +
21B HIS* 3.0 53.9 + - + +
22B GLY 3.2 0.2 - - - -
23B LYS* 1.3 80.7 - - + +
25B VAL* 1.3 58.6 + - - +
27B SER* 3.0 25.8 - - - -
28B ILE* 3.6 4.0 + - - +
79B LEU* 3.6 30.0 - - + +
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Residues in contact with VAL 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B MET* 3.7 16.4 - - + -
21B HIS 3.4 12.6 - - - +
22B GLY 2.8 16.1 + - - +
24B GLU* 1.3 69.4 - - - +
26B GLY* 1.3 66.9 + - - +
27B SER 3.0 2.0 - - - -
28B ILE* 2.8 18.5 + - + +
29B ILE* 3.0 35.0 + - + +
49B ILE* 3.9 16.4 - - + -
57B ARG* 3.6 39.7 - - + +
59B ILE* 3.8 13.5 - - + -
4Z C 4.3 0.9 - - - +
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Residues in contact with GLY 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B GLY 3.1 9.7 + - - -
23B LYS* 3.4 4.8 + - - -
25B VAL* 1.3 76.2 - - - +
27B SER* 1.3 62.2 + - - +
29B ILE* 4.1 1.7 - - - -
30B GLY 3.0 19.9 + - - -
3Z C 3.2 29.6 - - - +
4Z C 3.8 25.9 - - - +
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Residues in contact with SER 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LYS 3.4 9.1 + - - -
24B GLU* 3.0 18.3 + - - -
25B VAL 3.0 0.2 - - - -
26B GLY* 1.3 79.3 - - - +
28B ILE* 1.3 59.2 + - - +
30B GLY* 3.5 5.5 + - - -
35B SER* 3.8 1.6 + - - -
78B LYS* 3.5 38.0 + - - +
79B LEU* 4.4 8.5 - - - +
82B ASP* 2.9 34.1 + - - +
3Z C 3.5 13.0 + - - +
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Residues in contact with ILE 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B MET* 3.5 31.0 - - + -
24B GLU 4.0 7.6 - - - +
25B VAL* 2.8 14.3 + - + +
27B SER* 1.3 68.9 - - - +
29B ILE* 1.3 57.4 + - + +
35B SER* 2.6 27.6 - - - -
36B VAL* 3.2 17.6 + - + -
39B ILE* 4.3 17.9 - - + +
47B ILE* 6.1 1.1 - - + -
49B ILE* 4.7 9.9 - - + -
59B ILE* 3.7 18.8 - - + -
75B ILE* 3.6 32.1 - - + +
78B LYS* 4.8 9.4 - - + -
79B LEU* 4.0 10.5 - - + -
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Residues in contact with ILE 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B VAL* 3.0 31.8 + - + +
26B GLY* 4.3 3.4 - - - +
28B ILE* 1.3 74.6 - - - +
30B GLY* 1.3 71.5 + - - +
33B GLY* 3.3 20.1 - - - +
35B SER* 2.8 23.9 + - - -
36B VAL* 3.3 17.9 + - + -
49B ILE* 3.7 19.1 - - + -
57B ARG* 4.4 0.9 - - - +
3Z C 5.1 0.4 - - + -
4Z C 3.3 53.6 - - + +
5Z C 3.9 19.7 - - + +
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Residues in contact with GLY 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLY 3.0 11.9 + - - -
27B SER 3.9 5.2 - - - -
28B ILE 3.4 1.2 - - - -
29B ILE* 1.3 86.8 - - - +
31B LYS* 1.3 70.7 + - - +
32B LYS 3.2 0.3 + - - -
33B GLY 2.9 8.3 + - - -
34B GLU* 3.9 11.7 - - - -
35B SER* 3.9 1.1 - - - -
3Z C 3.4 29.0 - - - +
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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