Contacts of the helix formed by residues 25 - 39 (chain A) in PDB entry 1ZGA
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 TYR 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A TYR* 2.9 51.5 + + + +
22A LYS* 3.8 3.1 - - - +
24A VAL* 1.3 89.0 - - + +
26A ASN* 1.3 63.9 + - - +
27A PHE* 3.2 22.4 - + - -
28A VAL* 3.1 29.8 + - + +
29A SER* 4.2 1.7 + - - -
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Residues in contact with ASN 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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22A LYS* 3.1 22.6 + - - +
23A HIS* 3.9 33.6 + - - +
24A VAL 3.3 1.8 - - - -
25A TYR* 1.3 76.3 - - - +
27A PHE* 1.3 65.3 + - - +
29A SER* 2.8 28.9 + - - -
30A SER* 3.7 4.5 + - - -
313A GLU* 4.6 8.5 + - - -
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Residues in contact with PHE 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 HIS 5.0 0.2 + - - -
24A VAL* 3.1 29.1 + - + -
25A TYR* 3.2 18.1 - + - -
26A ASN* 1.3 78.2 - - - +
28A VAL* 1.3 88.1 + - + +
30A SER* 3.1 13.5 + - - -
31A MET* 3.0 37.7 + - + +
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Residues in contact with VAL 28 (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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25A TYR* 3.3 24.0 - - + +
26A ASN 2.8 0.8 + - - -
27A PHE* 1.3 110.1 - - + +
29A SER* 1.3 56.9 + - - +
31A MET* 3.2 6.9 + - + +
32A ALA* 2.9 28.1 + - + +
77A LEU* 4.1 19.1 - - + -
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Residues in contact with SER 29 (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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25A TYR 4.2 1.4 + - - -
26A ASN* 2.8 21.2 + - - -
28A VAL* 1.3 74.4 - - - +
30A SER* 1.3 62.2 + - - +
32A ALA* 3.5 7.0 + - - +
33A LEU* 3.1 22.5 + - - +
77A LEU* 4.5 11.1 - - - +
78A LEU* 4.9 2.3 - - - +
81A ASN* 3.2 26.7 + - - +
83A PHE* 6.1 0.3 - - - -
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Residues in contact with SER 30 (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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26A ASN 3.7 5.3 + - - -
27A PHE* 3.1 14.0 + - - -
29A SER* 1.3 77.4 - - - +
31A MET* 1.3 72.4 + - - +
33A LEU* 3.1 8.2 + - - +
34A LYS 2.9 24.6 + - - -
127A LEU* 3.4 24.7 - - - +
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Residues in contact with MET 31 (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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27A PHE* 3.0 34.0 + - + +
28A VAL* 3.2 9.1 + - + +
30A SER* 1.3 90.9 - - - +
32A ALA* 1.3 57.2 + - - +
34A LYS* 3.3 23.0 + - - +
35A SER* 3.0 32.4 + - - -
74A PHE* 5.0 2.2 - - + -
127A LEU* 4.0 16.8 - - + -
132A LEU* 4.0 27.1 - - + -
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Residues in contact with ALA 32 (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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28A VAL* 2.9 17.5 + - + +
29A SER* 3.7 4.9 - - - +
30A SER 3.2 0.2 - - - -
31A MET* 1.3 74.0 - - - +
33A LEU* 1.3 65.3 + - - +
35A SER* 3.3 2.6 + - - -
36A ALA 3.1 17.3 + - - -
74A PHE* 4.1 24.9 - - + +
77A LEU* 4.0 20.4 - - + -
78A LEU* 3.5 27.3 - - + +
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Residues in contact with LEU 33 (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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29A SER 3.1 13.7 + - - +
30A SER* 3.1 11.7 + - - +
32A ALA* 1.3 76.3 - - - +
34A LYS* 1.3 65.0 + - - +
36A ALA* 3.2 6.6 + - + +
37A MET* 3.1 20.6 + - - +
78A LEU* 3.9 8.5 - - + +
83A PHE* 3.5 47.1 - - + -
111A LEU* 4.1 20.2 - - + -
123A VAL* 4.4 23.6 - - + -
127A LEU* 5.3 3.6 - - + -
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Residues in contact with LYS 34 (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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30A SER 2.9 13.2 + - - +
31A MET* 3.3 32.1 - - - +
33A LEU* 1.3 77.7 - - - +
35A SER* 1.3 58.4 + - - +
37A MET* 3.3 20.2 - - + +
38A GLU* 3.0 63.5 + - - +
123A VAL* 4.4 3.8 - - + +
124A LYS* 5.5 1.3 - - - +
127A LEU* 3.6 40.4 - - + +
132A LEU* 5.7 0.4 - - - -
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Residues in contact with SER 35 (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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31A MET* 3.0 14.5 + - - +
32A ALA 3.6 8.1 - - - -
33A LEU 3.2 0.2 - - - -
34A LYS* 1.3 76.8 + - - +
36A ALA* 1.3 60.9 + - - +
38A GLU* 3.2 18.5 + - - +
39A LEU* 2.9 45.4 + - - +
74A PHE* 3.3 29.7 - - - -
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Residues in contact with ALA 36 (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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32A ALA 3.1 5.5 + - - -
33A LEU* 3.2 14.3 + - + +
35A SER* 1.3 76.1 - - - +
37A MET* 1.3 61.8 + - - +
39A LEU 3.6 0.2 + - - -
40A GLY 3.3 2.3 + - - -
41A ILE* 3.2 44.9 + - + +
42A ALA* 4.6 2.1 + - - +
78A LEU* 3.5 30.2 - - + +
83A PHE* 6.4 0.2 - - + -
84A PHE* 4.5 11.0 - - + -
111A LEU* 5.1 7.8 - - + +
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Residues in contact with MET 37 (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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33A LEU 3.1 10.1 + - - +
34A LYS* 3.3 15.5 - - + +
36A ALA* 1.3 75.7 - - - +
38A GLU* 1.3 88.4 - - + +
40A GLY* 3.2 12.8 + - - -
42A ALA* 6.5 0.2 - - - -
111A LEU* 3.9 32.1 - - + +
120A SER* 4.3 19.7 + - - +
123A VAL* 3.8 20.2 - - + -
124A LYS* 3.4 46.4 - - + +
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Residues in contact with GLU 38 (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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34A LYS* 3.0 54.0 + - - +
35A SER* 3.2 27.6 + - - +
37A MET* 1.3 92.2 - - + +
39A LEU* 1.3 67.1 + - + +
40A GLY 3.5 0.2 + - - -
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Residues in contact with LEU 39 (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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35A SER* 2.9 32.9 + - - +
38A GLU* 1.3 86.3 - - + +
40A GLY* 1.3 63.6 + - - +
41A ILE* 4.0 25.4 - - + -
61A LEU* 3.1 32.0 - - + +
63A LEU* 5.2 15.0 - - + -
71A LEU* 5.2 9.0 - - + -
74A PHE* 6.1 4.5 - - + -
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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