Contacts of the helix formed by residues 22 - 32 (chain A) in PDB entry 4ZCU
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ARG* 1.3 68.2 + - - +
24A TYR 3.5 0.7 - - - -
25A GLU* 3.2 35.2 - - - +
26A THR* 2.3 45.6 + - - -
1006A SO4 3.3 16.9 + - - +
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Residues in contact with ARG 23 (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 THR* 1.3 78.9 - - - +
24A TYR* 1.3 93.9 + - + +
26A THR* 3.1 5.0 + - - -
27A LEU* 3.0 30.0 + - + +
81A MET* 4.7 4.2 - - - +
148A ARG* 5.7 9.6 - - - +
1006A SO4 2.3 49.5 + - - -
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Residues in contact with TYR 24 (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 ARG* 1.3 108.4 + - + +
25A GLU* 1.3 60.2 + - - +
27A LEU* 3.8 8.7 - - + -
28A PHE* 2.9 31.0 + - - +
77A PHE* 4.1 2.8 - - + -
80A PHE* 3.6 7.6 - - + -
81A MET* 3.6 47.6 - - + -
84A LEU* 3.4 36.9 + - + -
85A LYS* 3.6 14.1 - - + -
88A GLU* 3.3 29.0 - - + +
148A ARG* 6.1 2.2 - - - -
152A LEU* 5.3 5.6 - - + -
1006A SO4 3.0 22.6 + - - +
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Residues in contact with GLU 25 (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 THR* 3.2 30.6 + - - +
23A ARG 3.2 0.4 - - - -
24A TYR* 1.3 76.4 - - - +
26A THR* 1.3 58.6 + - - +
28A PHE* 4.0 1.5 - - - +
29A GLN* 2.9 35.0 + - - +
77A PHE* 3.6 27.2 - - + -
1006A SO4 3.1 22.6 + - - +
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Residues in contact with THR 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 THR* 2.3 37.3 + - - -
23A ARG* 3.2 5.8 - - - -
25A GLU* 1.3 76.8 - - - +
27A LEU* 1.3 65.1 + - + +
29A GLN* 3.9 7.9 - - - +
30A ALA* 2.9 25.5 + - + +
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Residues in contact with LEU 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 ARG* 3.0 17.4 + - + +
24A TYR* 4.0 5.2 - - + +
25A GLU 3.4 0.2 - - - -
26A THR* 1.3 78.8 - - + +
28A PHE* 1.3 57.6 + - - +
30A ALA* 3.2 5.3 + - + +
31A LEU* 2.9 36.4 + - + +
51A LEU* 4.1 22.0 - - + -
53A ILE* 5.8 0.7 - - + -
80A PHE* 3.6 17.5 - - + -
84A LEU* 3.7 23.6 - - + -
152A LEU* 4.6 11.0 - - + -
153A PHE* 3.4 38.4 - - + -
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Residues in contact with PHE 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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24A TYR 2.9 19.7 + - - +
25A GLU 4.0 2.7 - - - +
27A LEU* 1.3 72.9 - - - +
29A GLN* 1.3 64.0 + - - +
31A LEU* 3.1 3.9 + - - +
32A ASP* 2.8 41.4 + - + +
37A GLY* 3.2 35.4 - - - -
38A VAL* 4.1 2.7 - - - -
39A VAL* 3.7 17.5 - - + -
75A LEU 3.6 19.3 - - - -
76A ASP 3.7 12.1 - - - -
77A PHE* 3.7 32.5 - + + -
80A PHE* 3.6 31.1 - + + -
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Residues in contact with GLN 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 GLU 2.9 20.4 + - - +
26A THR* 3.9 6.7 - - - +
28A PHE* 1.3 81.1 - - - +
30A ALA* 1.3 62.2 + - - +
32A ASP* 3.7 16.7 - - - +
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Residues in contact with ALA 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 THR* 2.9 17.4 + - + +
27A LEU* 3.3 11.2 - - + +
29A GLN* 1.3 79.4 - - - +
31A LEU* 1.3 64.1 + - - +
32A ASP 4.4 2.4 - - - -
33A ARG* 4.6 4.0 + - - +
47A GLY* 5.6 1.7 - - - -
51A LEU* 4.2 29.8 - - + -
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Residues in contact with LEU 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 LEU* 2.9 19.9 + - + +
28A PHE* 3.1 3.6 + - - +
30A ALA* 1.3 75.7 - - - +
32A ASP* 1.3 62.3 + - - +
33A ARG* 2.9 12.0 + - - +
39A VAL* 3.9 20.0 - - + -
43A GLU* 3.5 24.8 - - - +
44A LEU* 3.9 21.5 - - + +
47A GLY* 3.7 35.0 - - - -
48A LEU* 4.1 8.1 - - + +
51A LEU* 3.8 18.8 - - + -
80A PHE* 3.6 35.4 - - + -
153A PHE* 5.8 1.3 - - + -
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Residues in contact with ASP 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 PHE* 2.8 30.5 + - + +
29A GLN* 3.7 13.9 - - - +
30A ALA 3.4 0.6 - - - -
31A LEU* 1.3 68.3 - - - +
33A ARG* 1.3 61.3 + - - +
34A ASN* 2.9 9.9 - - - +
35A GLY* 3.1 18.0 + - - -
36A ASP* 3.1 1.5 - - - +
37A GLY* 3.0 26.8 + - - -
38A VAL 3.4 9.0 - - - -
39A VAL* 3.9 13.2 - - + +
43A GLU* 4.2 2.0 - - - -
1001A CA 2.3 29.8 - - - -
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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