Contacts of the helix formed by residues 22 - 33 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C ILE* 4.5 4.0 + - - +
21C LYS* 1.3 78.6 - - - +
23C SER* 1.3 66.4 + - - +
24C TYR 3.5 2.2 - - - -
25C ILE* 3.9 8.0 - - - +
26C MET* 3.3 44.6 + - + +
43C VAL* 3.6 14.6 - - + -
49C GLN 4.7 0.2 + - - -
52C ARG* 3.4 32.7 - - - +
53C ALA* 3.9 9.5 + - - +
56C LEU* 3.8 16.6 - - + -
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Residues in contact with SER 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C LYS* 4.0 0.6 - - - +
22C THR* 1.3 77.9 - - - +
24C TYR* 1.3 75.0 + - - +
26C MET* 3.3 7.8 - - - +
27C ASP* 2.7 35.2 + - - +
40C GLU* 4.2 8.6 - - - +
44C ARG* 6.2 2.5 - - - -
52C ARG* 6.4 0.2 - - - -
413C ASP* 6.1 1.6 - - - -
416C GLN* 3.8 21.0 + - - +
433C PHE* 4.5 8.0 - - - -
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Residues in contact with TYR 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C THR 3.5 0.2 - - - -
23C SER* 1.3 82.4 + - - +
25C ILE* 1.3 65.6 + - - +
26C MET 3.2 0.9 - - - -
27C ASP* 3.1 20.4 + - + +
28C HIS* 3.0 30.9 + + + +
78C GLU* 3.3 22.9 - - + +
124C VAL* 6.2 1.3 - - + -
416C GLN* 2.5 40.4 + - - -
419C VAL* 3.8 14.2 - - + +
426C CYS* 3.5 21.1 - - + +
428C ARG* 3.5 49.1 - - + +
433C PHE* 3.7 26.0 - + - -
435C TYR* 4.7 2.9 + - - -
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Residues in contact with ILE 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ILE* 3.9 12.3 - - + -
21C LYS 3.4 25.4 - - - +
22C THR* 3.9 7.2 - - - +
24C TYR* 1.3 74.2 - - - +
26C MET* 1.3 66.0 + - - +
28C HIS* 2.9 24.1 + - - +
29C MET* 3.1 19.4 + - - +
56C LEU* 4.4 8.3 - - + -
71C PHE* 3.9 22.7 - - + -
74C ALA* 3.8 23.8 - - + +
75C LEU* 3.7 25.1 - - + +
78C GLU* 3.9 17.3 - - + +
80C TYR* 4.0 7.6 - - + -
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Residues in contact with MET 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C THR* 3.3 34.3 + - + +
23C SER* 3.3 12.3 - - - +
24C TYR 3.2 0.6 - - - -
25C ILE* 1.3 82.6 - - - +
27C ASP* 1.3 55.9 + - - +
29C MET* 3.6 2.0 + - - +
30C ILE* 2.9 37.9 + - + +
35C LEU* 2.6 40.6 - - + +
39C GLU 4.6 0.4 - - - -
40C GLU* 3.5 45.1 - - + +
43C VAL* 3.8 26.2 - - + -
56C LEU* 4.1 10.3 - - + -
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Residues in contact with ASP 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C SER* 2.7 24.0 - - - +
24C TYR* 3.1 30.2 + - + +
26C MET* 1.3 72.4 - - - +
28C HIS* 1.3 59.4 + - + +
30C ILE* 3.1 10.8 + - - +
31C SER* 2.7 36.7 + - - -
40C GLU* 3.8 12.0 - - - +
416C GLN* 4.6 7.1 + - - -
420C ASN* 4.8 3.3 - - - +
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Residues in contact with HIS 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C TYR* 3.0 23.0 + + + -
25C ILE* 2.9 15.7 + - - +
27C ASP* 1.3 75.4 - - + +
29C MET* 1.3 58.5 + - - +
31C SER* 3.3 7.7 + - - -
32C ASP* 2.8 40.5 + - - +
74C ALA* 3.9 30.7 - - + +
77C HIS* 3.1 43.2 + + + -
78C GLU* 2.5 26.6 + - + -
428C ARG* 4.4 5.8 - - - -
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Residues in contact with MET 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ILE* 3.1 18.2 + - - +
26C MET* 4.1 2.2 - - - +
28C HIS* 1.3 73.7 - - - +
30C ILE* 1.3 56.5 + - - +
32C ASP* 3.1 1.1 + - - -
33C GLY 2.7 30.3 + - - -
34C PHE* 3.0 30.0 + - + +
35C LEU* 4.0 22.7 - - + +
56C LEU* 5.2 2.5 - - - -
60C ILE* 3.8 31.9 - - + -
63C LYS* 5.3 0.2 - - - -
67C SER* 3.7 25.8 - - - +
70C SER* 3.6 21.1 - - - +
71C PHE* 3.9 20.0 - - + -
74C ALA* 4.2 10.3 - - + -
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Residues in contact with ILE 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C MET* 2.9 43.2 + - + +
27C ASP* 3.4 8.7 - - - +
29C MET* 1.3 75.9 - - - +
31C SER* 1.3 61.5 + - - +
33C GLY* 3.4 11.4 + - - -
35C LEU* 4.0 31.4 - - + +
36C THR* 4.1 14.1 - - - +
37C ILE* 4.1 26.5 - - + -
40C GLU* 4.3 9.9 - - - +
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Residues in contact with SER 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ASP 2.7 16.0 + - - -
28C HIS* 3.4 10.5 + - - -
30C ILE* 1.3 76.0 - - - +
32C ASP* 1.3 71.4 + - - +
33C GLY* 3.1 2.8 + - - -
100C LYS* 4.8 13.2 + - - -
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Residues in contact with ASP 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C HIS* 2.8 28.8 + - - +
29C MET 3.5 5.6 - - - +
31C SER* 1.3 78.6 + - - +
33C GLY* 1.3 59.6 + - - +
34C PHE* 3.6 30.1 - - + -
70C SER* 3.0 28.7 + - - +
73C ASN* 5.8 1.4 - - - +
100C LYS* 4.7 19.6 - - - +
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Residues in contact with GLY 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C MET 2.7 11.4 + - - -
30C ILE 3.4 9.4 + - - -
31C SER 3.1 5.8 - - - -
32C ASP* 1.3 76.6 - - - +
34C PHE* 1.3 62.9 + - - -
35C LEU 3.6 5.6 - - - -
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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