Contacts of the helix formed by residues 23 - 32 (chain C) 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 ARG 23 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C THR* 1.3 91.3 - - + +
24C TYR* 1.3 108.4 + - + +
26C THR* 3.1 7.4 + - - -
27C LEU* 3.0 32.1 + - - +
81C MET* 5.2 6.5 - - - +
85C LYS* 5.0 7.1 - - - +
88C GLU* 5.7 2.8 - - - +
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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
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22C THR 4.5 2.2 - - - +
23C ARG* 1.3 129.9 + - + +
25C GLU* 1.3 61.1 + - + +
27C LEU* 3.9 4.0 - - + -
28C PHE* 2.9 31.9 + - - +
77C PHE* 3.9 5.1 - - + -
80C PHE* 3.6 10.0 - - + -
81C MET* 3.9 48.0 - - + -
84C LEU* 3.3 44.9 + - + -
85C LYS* 3.4 29.1 - - + +
88C GLU* 4.1 13.9 - - + +
152C LEU* 6.0 1.6 - - + -
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Residues in contact with GLU 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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22C THR* 3.9 27.9 + - - +
23C ARG 3.1 0.2 - - - -
24C TYR* 1.3 76.3 - - - +
26C THR* 1.3 59.4 + - - +
28C PHE* 4.0 1.5 - - - +
29C GLN* 2.9 34.4 + - - +
77C PHE* 3.5 32.1 - - + -
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Residues in contact with THR 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C THR* 2.4 32.0 + - - +
23C ARG* 3.5 4.5 - - - -
25C GLU* 1.3 75.9 - - - +
27C LEU* 1.3 63.6 + - + +
29C GLN* 3.3 11.4 + - - +
30C ALA* 2.9 22.8 + - + +
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Residues in contact with LEU 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 ARG 3.0 19.8 + - - +
24C TYR* 4.0 2.2 - - + +
26C THR* 1.3 78.3 - - + +
28C PHE* 1.3 57.3 + - - +
30C ALA* 3.1 7.9 + - + +
31C LEU* 2.9 33.4 + - + +
51C LEU* 4.2 21.3 - - + -
53C ILE* 4.8 2.5 - - + -
80C PHE* 3.6 17.7 - - + -
84C LEU* 3.9 18.2 - - + -
152C LEU* 4.4 12.6 - - + -
153C PHE* 3.5 39.0 - - + -
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Residues in contact with PHE 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 2.9 20.7 + - - +
25C GLU* 4.0 2.9 - - - +
27C LEU* 1.3 76.9 - - - +
29C GLN* 1.3 60.4 + - - +
31C LEU* 3.1 3.4 + - - +
32C ASP* 2.9 40.0 + - + +
37C GLY* 3.2 34.1 - - - -
38C VAL* 4.0 2.5 - - - -
39C VAL* 3.7 17.0 - - + -
75C LEU 3.4 21.3 - - - -
76C ASP 3.5 11.7 - - - -
77C PHE* 3.5 26.7 - + + -
80C PHE* 3.6 32.0 - + + -
1007C GOL 4.0 7.0 - - - -
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Residues in contact with GLN 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 GLU* 2.9 20.9 + - - +
26C THR* 3.6 10.6 - - - +
28C PHE* 1.3 81.1 - - - +
30C ALA* 1.3 62.2 + - - +
32C ASP* 4.0 13.6 - - - +
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Residues in contact with ALA 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 THR* 2.9 14.1 + - + +
27C LEU* 3.1 11.6 + - + +
29C GLN* 1.3 79.3 - - - +
31C LEU* 1.3 62.5 + - - +
32C ASP 3.7 2.1 + - - -
33C ARG* 4.8 3.6 + - - +
47C GLY* 5.3 3.5 - - - -
51C LEU* 3.8 36.4 - - + +
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Residues in contact with LEU 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 LEU* 2.9 17.8 + - + +
28C PHE 3.1 2.4 + - - +
30C ALA* 1.3 75.6 - - - +
32C ASP* 1.3 60.0 + - - +
33C ARG* 2.9 12.1 + - - +
39C VAL* 3.8 20.0 - - + -
43C GLU* 3.7 24.4 - - - +
44C LEU* 3.7 22.7 - - + +
47C GLY* 3.8 25.9 - - - -
48C LEU* 3.9 11.7 - - + +
51C LEU* 3.8 24.5 - - + -
80C PHE* 3.5 36.3 - - + -
153C PHE* 5.4 2.5 - - + -
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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 PHE* 2.9 28.3 + - + +
29C GLN* 4.0 11.8 + - - +
30C ALA 3.6 0.8 - - - -
31C LEU* 1.3 68.2 - - - +
33C ARG* 1.3 63.1 + - - +
34C ASN* 2.8 10.0 - - - +
35C GLY* 3.2 18.4 + - - -
36C ASP* 2.9 0.8 - - - +
37C GLY* 2.9 28.5 + - - -
38C VAL 2.8 10.3 - - - +
39C VAL* 3.8 14.1 - - + -
43C GLU* 4.4 0.2 - - - -
1001C CA 2.4 30.5 - - - -
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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