Contacts of the helix formed by residues 21 - 38 (chain B) in PDB entry 2Z9A
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 ASN 21 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLU* 3.7 18.8 + - - +
17B LYS 5.4 0.2 - - - +
18B LEU* 2.7 27.5 + - - +
19B ILE* 3.1 6.1 + - - +
20B ASP* 1.3 76.9 + - - +
22B ASN* 1.3 62.2 + - - +
23B LYS* 3.0 23.3 + - - +
24B THR* 3.3 14.8 + - - -
25B GLU* 3.2 22.7 + - - +
59B LEU* 4.6 1.1 - - - +
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Residues in contact with ASN 22 (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 ASN* 1.3 72.7 - - - +
23B LYS* 1.3 66.1 + - + +
25B GLU* 4.6 10.3 - - - +
26B LYS* 3.1 37.1 + - - +
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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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27A GLU* 5.1 12.1 - - - +
21B ASN* 3.0 11.9 + - - +
22B ASN* 1.3 76.9 - - - +
24B THR* 1.3 63.8 + - - +
26B LYS* 3.5 4.9 + - - +
27B GLU* 3.1 26.4 + - - +
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Residues in contact with THR 24 (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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19A ILE* 3.8 31.9 - - + -
24A THR* 5.4 5.0 + - + +
27A GLU* 4.8 4.5 + - - -
19B ILE* 2.6 37.0 + - + +
21B ASN* 3.3 13.2 + - - -
23B LYS* 1.3 77.9 - - - +
25B GLU* 1.3 62.1 + - - +
27B GLU* 3.2 16.7 + - - +
28B ILE* 3.1 27.9 + - + +
59B LEU* 4.1 16.4 - - + -
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Residues in contact with GLU 25 (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 ASN 3.2 14.5 + - - +
22B ASN* 4.2 11.2 - - - +
24B THR* 1.3 73.4 - - - +
26B LYS* 1.3 55.4 + - - +
28B ILE* 3.2 13.4 + - - +
29B LEU* 2.8 65.7 + - + +
55B GLY 4.7 2.9 - - - +
56B SER* 3.3 29.3 + - - +
59B LEU* 4.1 27.3 + - + +
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Residues in contact with LYS 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 ASN* 3.1 29.1 + - - +
23B LYS* 3.6 5.6 - - - +
25B GLU* 1.3 77.6 - - - +
27B GLU* 1.3 56.6 + - - +
29B LEU* 3.3 18.5 + - + +
30B ASP* 2.9 59.2 + - - +
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Residues in contact with GLU 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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18A LEU* 3.8 23.1 - - + +
19A ILE* 4.7 4.0 - - + +
21A ASN* 3.0 30.4 + - - +
23A LYS* 5.1 7.7 - - - +
24A THR* 4.3 9.0 + - - -
23B LYS* 3.1 13.4 + - - +
24B THR* 3.2 30.4 + - - +
26B LYS* 1.3 78.5 - - - +
28B ILE* 1.3 60.9 + - + +
30B ASP* 3.6 9.1 + - - +
31B ALA* 3.3 23.4 + - - +
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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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15A VAL* 3.7 30.3 - - + -
18A LEU* 4.0 10.1 - - + -
19A ILE* 4.0 22.2 - - + -
24B THR* 3.1 15.6 + - + +
25B GLU* 3.4 15.7 - - - +
27B GLU* 1.3 73.9 - - - +
29B LEU* 1.3 66.3 + - + +
31B ALA* 3.1 12.5 + - - +
32B PHE* 3.4 42.5 + - + -
35B MET* 4.7 2.0 - - + +
55B GLY 4.8 2.2 - - - +
58B ILE* 5.9 2.2 - - + -
59B LEU* 3.5 35.9 - - + +
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Residues in contact with LEU 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 GLU* 2.8 57.6 + - + +
26B LYS* 3.3 19.5 + - + +
28B ILE* 1.3 74.2 - - + +
30B ASP* 1.3 64.4 + - - +
31B ALA 3.3 0.7 + - - -
32B PHE* 3.7 32.9 + - + +
33B ASP* 4.4 4.9 - - - +
55B GLY 4.6 3.1 - - - +
56B SER* 4.5 12.8 - - - +
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Residues in contact with ASP 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 LYS* 2.9 48.5 + - - +
27B GLU* 3.9 8.7 - - - +
29B LEU* 1.3 76.4 - - - +
31B ALA* 1.3 58.4 + - - +
32B PHE 3.5 0.6 + - - -
33B ASP* 4.0 11.6 + - - +
34B LYS* 5.4 1.4 + - - +
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Residues in contact with ALA 31 (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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18A LEU* 4.3 14.4 - - + -
27B GLU 3.3 15.9 + - - +
28B ILE 3.1 6.4 + - - +
30B ASP* 1.3 77.2 - - - +
32B PHE* 1.3 64.8 + - - +
33B ASP 3.2 3.7 + - - -
34B LYS* 3.4 11.7 + - + +
35B MET* 3.1 39.8 + - + +
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Residues in contact with PHE 32 (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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11A LEU* 4.2 10.1 - - + -
15A VAL* 4.1 20.4 - - + -
28B ILE* 3.4 32.4 + - + -
29B LEU* 3.7 20.6 + - + +
30B ASP 3.5 1.6 - - - -
31B ALA* 1.3 76.3 - - - +
33B ASP* 1.3 59.6 + - - +
35B MET* 3.3 18.7 + - - +
36B CYS* 3.0 34.1 + - - -
51B VAL* 3.7 38.1 - - + -
55B GLY* 3.4 42.2 - - - -
58B ILE* 4.1 13.2 - - + -
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Residues in contact with ASP 33 (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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29B LEU 4.4 6.1 - - - +
30B ASP* 4.0 14.1 - - - +
31B ALA 3.2 0.2 - - - -
32B PHE* 1.3 77.3 + - - +
34B LYS* 1.3 65.3 + - + +
36B CYS* 3.4 6.3 + - - +
37B SER* 3.2 25.1 + - - -
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Residues in contact with LYS 34 (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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30B ASP 5.4 1.1 + - - +
31B ALA* 3.4 13.4 + - + +
33B ASP* 1.3 78.1 - - + +
35B MET* 1.3 63.9 + - + +
37B SER* 3.5 8.1 + - - -
38B LYS* 3.4 28.9 + - - +
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Residues in contact with MET 35 (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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10A PHE* 3.5 14.6 - - - -
11A LEU* 3.9 16.6 - - + -
14A GLU* 3.5 36.6 - - + +
15A VAL* 4.0 30.5 - - + +
18A LEU* 4.2 12.1 - - + -
28B ILE* 4.7 3.6 - - - +
31B ALA* 3.1 32.7 + - + +
32B PHE* 3.5 31.9 - - + +
33B ASP 3.2 0.2 - - - -
34B LYS* 1.3 76.6 - - + +
36B CYS* 1.3 62.3 + - - +
38B LYS* 3.1 25.1 + - - +
39B LEU 4.0 0.2 + - - -
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Residues in contact with CYS 36 (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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11A LEU* 4.8 0.4 - - - -
32B PHE 3.0 19.8 + - - +
33B ASP* 3.4 6.5 + - - +
35B MET* 1.3 75.7 - - - +
37B SER* 1.3 56.8 + - - +
39B LEU* 3.2 24.7 + - - +
44B SER* 4.3 16.8 + - - +
47B CYS* 2.1 64.2 - - + -
48B GLN* 4.0 11.4 - - + -
51B VAL* 3.9 10.3 - - - -
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Residues in contact with SER 37 (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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33B ASP 3.2 17.0 + - - -
34B LYS* 3.7 10.1 - - - -
35B MET 3.1 0.8 - - - -
36B CYS* 1.3 74.3 - - - +
38B LYS* 1.3 55.9 + - - +
39B LEU 2.9 17.9 + - - +
41B LYS* 5.7 3.1 + - - -
44B SER* 5.8 0.7 - - - -
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Residues in contact with LYS 38 (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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10A PHE* 4.0 11.4 - - + -
14A GLU* 3.3 29.3 + - - +
17A LYS* 4.1 16.0 - - - +
34B LYS* 3.4 18.4 - - - +
35B MET* 3.1 11.0 + - - +
37B SER* 1.3 74.8 - - - +
39B LEU* 1.3 63.4 + - - +
40B PRO* 4.3 2.4 - - - +
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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