Contacts of the helix formed by residues 22 - 32 (chain D) in PDB entry 1Z6T
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 THR 22 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D ILE* 4.2 8.3 - - + +
21D LYS* 1.3 76.4 - - - +
23D SER* 1.3 59.5 + - - +
24D TYR 3.5 0.9 - - - -
25D ILE* 3.3 7.7 + - - +
26D MET* 2.8 51.8 + - - +
43D VAL* 3.9 4.7 - - - +
52D ARG* 3.6 29.2 + - + +
53D ALA* 3.7 35.4 - - + +
56D LEU* 4.0 17.9 - - + -
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Residues in contact with SER 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LYS* 3.5 2.4 - - - +
22D THR* 1.3 81.3 + - - +
24D TYR* 1.3 87.1 + - - +
26D MET* 3.9 12.2 - - - +
27D ASP* 3.2 26.8 + - - +
40D GLU* 4.9 1.4 - - - +
52D ARG* 6.0 3.8 - - - -
412D GLU* 6.2 0.2 - - - +
413D ASP* 5.6 5.8 - - - -
416D GLN* 3.8 15.3 - - - -
433D PHE* 4.2 9.0 - - - -
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Residues in contact with TYR 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LYS 4.9 1.0 + - - -
23D SER* 1.3 98.5 + - - +
25D ILE* 1.3 68.0 + - - +
26D MET 3.2 0.6 + - - -
27D ASP* 3.3 13.1 + - + +
28D HIS* 3.2 29.9 + + + +
78D GLU* 3.4 22.2 - - - +
412D GLU 5.4 0.3 + - - -
416D GLN* 3.5 37.2 + - + +
419D VAL* 3.9 16.5 - - + +
426D CYS* 3.5 23.7 - - + +
428D ARG* 3.5 36.8 - - + +
433D PHE* 3.4 36.3 - + + -
435D TYR* 4.4 5.5 + - - -
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Residues in contact with ILE 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D ILE* 4.1 16.6 - - + -
21D LYS 3.6 19.7 + - - +
22D THR* 3.3 8.8 + - - +
24D TYR* 1.3 80.6 - - - +
26D MET* 1.3 62.0 + - - +
28D HIS* 3.4 6.1 - - - +
29D MET* 3.2 22.5 + - - +
56D LEU* 4.2 11.9 - - + -
71D PHE* 3.8 22.7 - - + -
74D ALA* 3.7 25.5 - - + +
75D LEU* 3.7 27.8 - - + -
78D GLU* 4.1 16.7 - - + +
80D TYR* 3.9 12.3 - - + -
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Residues in contact with MET 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D THR* 2.8 34.9 + - - +
23D SER* 3.9 9.6 - - - +
25D ILE* 1.3 70.9 - - - +
27D ASP* 1.3 56.8 + - - +
29D MET* 3.1 4.1 + - - +
30D ILE* 2.8 41.0 + - - +
35D LEU* 3.6 27.1 - - + -
40D GLU* 3.8 31.2 - - + +
43D VAL* 3.5 46.7 - - + -
44D ARG* 4.9 8.1 - - + +
56D LEU* 3.9 19.3 - - + -
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Residues in contact with ASP 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D SER 3.2 16.7 + - - +
24D TYR* 3.5 21.8 - - + +
26D MET* 1.3 76.4 - - - +
28D HIS* 1.3 61.6 + - + +
30D ILE* 3.1 9.1 + - - +
31D SER* 2.9 30.9 + - - -
40D GLU* 3.7 14.0 - - - +
416D GLN* 3.6 17.9 + - - +
420D ASN* 5.1 3.0 - - - +
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Residues in contact with HIS 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D TYR* 3.2 16.2 + - + -
25D ILE 3.4 6.1 - - - +
27D ASP* 1.3 81.0 - - + +
29D MET* 1.3 57.0 + - - +
31D SER* 3.4 5.4 + - - -
32D ASP* 2.9 38.8 + - - +
74D ALA* 3.7 27.4 - - + -
77D HIS* 3.0 40.2 + + + -
78D GLU* 2.3 41.7 + - + -
428D ARG* 4.4 7.0 - - - -
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Residues in contact with MET 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ILE* 3.2 17.9 + - - +
26D MET* 3.1 9.6 + - - +
28D HIS* 1.3 73.7 - - - +
30D ILE* 1.3 62.0 + - - +
32D ASP* 3.6 2.0 + - - +
33D GLY 3.1 2.6 + - - -
34D PHE* 2.9 43.4 + - + +
35D LEU* 3.4 16.9 + - + -
56D LEU* 4.8 9.2 - - - -
60D ILE* 3.8 35.0 - - + -
63D LYS* 5.6 0.2 - - + -
67D SER* 3.7 27.8 - - - +
70D SER* 3.6 28.5 - - - +
71D PHE* 3.9 15.0 - - + +
74D ALA* 4.3 2.9 - - + -
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Residues in contact with ILE 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D MET 2.8 28.0 + - - +
27D ASP* 3.5 8.1 - - - +
29D MET* 1.3 71.2 - - - +
31D SER* 1.3 61.9 + - - +
33D GLY* 2.8 20.4 + - - -
35D LEU* 3.4 31.9 - - + +
36D THR 4.6 2.9 - - - +
37D ILE* 4.4 22.4 - - + +
40D GLU* 3.1 44.0 - - + +
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Residues in contact with SER 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ASP 2.9 16.8 + - - -
28D HIS* 3.5 7.4 - - - -
30D ILE* 1.3 78.9 - - - +
32D ASP* 1.3 65.5 + - - +
33D GLY* 3.2 1.2 + - - -
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Residues in contact with ASP 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D HIS* 2.9 21.2 + - - +
29D MET 3.8 1.8 - - - +
30D ILE 3.3 0.2 - - - -
31D SER* 1.3 79.8 + - - +
33D GLY* 1.3 60.3 + - - +
34D PHE* 3.4 34.6 - - + -
70D SER* 2.8 30.3 + - - +
73D ASN* 5.3 4.0 + - - +
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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