Contacts of the helix formed by residues 23 - 35 (chain C) in PDB entry 4BZ5
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 ASP 23 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C CYS* 4.0 11.9 - - + -
21C PHE 3.2 0.2 + - - -
22C GLY* 1.3 70.5 - - - -
24C ARG* 1.3 65.1 + - - +
25C TYR 3.3 2.7 - - - -
26C ALA* 3.0 16.0 + - + +
27C LEU* 3.1 15.1 + - - +
343C PHE* 3.7 7.1 - - - -
377C TYR* 3.9 18.7 + - - +
380C ARG* 2.9 44.3 + - - -
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Residues in contact with ARG 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C PHE* 2.9 35.2 + - + +
22C GLY 3.3 0.6 - - - -
23C ASP* 1.3 77.0 + - - +
25C TYR* 1.3 64.5 + - - +
27C LEU* 3.1 5.8 + - - +
28C VAL* 3.0 34.3 + - + +
136C TRP 4.6 5.7 + - - -
140C TRP* 3.5 22.2 - - - -
338C GLY 2.9 30.3 + - - +
339C GLY 3.4 11.5 + - - -
340C GLY* 3.0 29.4 + - - -
343C PHE* 3.7 39.7 - - + +
346C THR* 4.1 10.6 - - + +
350C TRP* 3.7 24.5 - - - -
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Residues in contact with TYR 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C VAL 2.9 25.1 + - - -
7C TYR* 3.2 16.3 - - + +
11C TYR* 3.4 18.8 - + - -
12C ARG* 3.7 35.9 - - + -
15C CYS* 3.8 27.6 + - + +
16C CYS* 4.1 6.7 - - - -
22C GLY 4.9 0.6 + - - -
23C ASP 3.3 0.6 - - - -
24C ARG* 1.3 81.4 - - - +
26C ALA* 1.3 58.7 + - - +
28C VAL* 3.3 6.8 + - - +
29C MET* 2.9 52.1 + - + +
136C TRP* 3.9 14.4 - - + +
137C GLY* 3.8 31.9 - - - -
350C TRP* 6.4 0.2 - - - -
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Residues in contact with ALA 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ARG* 3.6 31.4 - - - +
16C CYS* 3.5 19.8 - - - -
23C ASP* 3.0 12.2 + - + +
25C TYR* 1.3 77.6 - - - +
27C LEU* 1.3 59.9 + - - +
30C ASP* 2.9 34.8 + - - +
377C TYR* 3.7 19.5 - - + +
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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
----------------------------------------------------------
23C ASP* 3.1 28.1 + - - +
24C ARG* 3.1 9.0 + - - +
26C ALA* 1.3 76.4 - - - +
28C VAL* 1.3 63.5 + - - +
30C ASP* 3.8 0.5 - - - +
31C LEU* 2.9 27.4 + - - +
343C PHE* 4.3 15.9 - - + +
344C PRO* 4.3 9.9 - - + -
347C ALA* 4.0 7.0 - - + -
375C HIS* 5.2 0.5 + - - -
377C TYR* 3.7 29.4 - - + -
380C ARG* 3.6 56.8 - - + +
381C TYR* 3.7 17.7 + - - +
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Residues in contact with VAL 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ARG* 3.0 27.0 + - + +
25C TYR* 3.5 10.5 - - - +
27C LEU* 1.3 77.6 - - - +
29C MET* 1.3 65.7 + - - +
31C LEU* 3.8 1.9 - - - +
32C ILE* 3.1 27.7 + - + +
136C TRP* 3.5 41.3 - - + +
347C ALA* 3.8 27.1 - - + +
350C TRP* 3.7 32.8 - - + -
351C THR* 4.2 0.7 + - - -
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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
----------------------------------------------------------
5C ILE* 3.8 33.0 - - + -
6C VAL 4.7 0.4 - - - +
7C TYR* 3.9 31.6 - - + -
12C ARG* 4.5 12.3 - - - +
25C TYR* 2.9 56.9 + - + +
26C ALA 4.3 1.8 - - - +
28C VAL* 1.3 76.9 - - - +
30C ASP* 1.3 58.5 + - - +
32C ILE* 3.4 7.5 + - + +
33C ASN* 2.9 28.3 + - - +
38C ILE* 4.2 15.9 - - + +
136C TRP* 4.2 15.3 - - - -
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Residues in contact with ASP 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ARG* 2.8 40.5 + - - -
26C ALA 2.9 18.2 + - - +
27C LEU 4.0 1.8 - - - +
29C MET* 1.3 78.4 - - - +
31C LEU* 1.3 58.8 + - - +
33C ASN* 3.7 11.9 + - - +
34C ALA* 2.8 28.6 + - - +
375C HIS* 3.9 12.8 - - + +
376C SER* 4.4 6.6 + - - -
377C TYR* 3.3 25.9 - - + -
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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
----------------------------------------------------------
27C LEU 2.9 18.5 + - - +
28C VAL 3.8 1.6 - - - +
30C ASP* 1.3 74.3 - - - +
32C ILE* 1.3 66.0 + - - +
34C ALA* 3.2 2.4 + - + +
35C TYR* 3.1 49.6 + - + -
347C ALA* 3.7 18.6 - - + +
348C ARG* 3.9 7.4 - - - +
351C THR* 3.4 21.5 - - - +
372C ILE* 4.0 20.6 - - + -
373C PRO* 4.3 2.7 - - + -
375C HIS* 3.8 25.2 + - + +
381C TYR* 3.7 24.9 - - + +
387C LEU* 4.4 3.6 - - + -
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Residues in contact with ILE 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ILE* 4.2 8.5 - - + -
28C VAL* 3.1 19.9 + - + +
29C MET* 3.6 11.0 - - + +
31C LEU* 1.3 78.1 - - - +
33C ASN* 1.3 60.6 + - - +
35C TYR 3.4 3.5 + - - -
37C LEU* 3.1 46.3 + - + +
38C ILE* 4.0 19.5 - - + -
41C LEU* 4.3 4.0 - - + -
136C TRP* 3.5 25.4 - - + +
350C TRP 4.4 2.0 - - - +
351C THR* 3.6 26.5 - - + +
354C THR* 3.5 29.4 - - + +
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Residues in contact with ASN 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C MET 2.9 18.0 + - - +
30C ASP* 3.7 13.6 + - - +
32C ILE* 1.3 75.4 - - - +
34C ALA* 1.3 61.8 + - - +
36C LYS* 2.9 22.1 + - - +
38C ILE* 3.5 29.5 - - + +
39C PRO* 5.6 1.2 - - - +
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Residues in contact with ALA 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ASP 2.8 21.9 + - - +
31C LEU* 3.2 8.0 + - - +
33C ASN* 1.3 75.9 - - - +
35C TYR* 1.3 56.6 + - - +
36C LYS* 3.1 15.0 + - - +
373C PRO* 3.7 29.4 - - + +
374C GLU 4.4 2.9 - - - +
375C HIS* 3.9 32.8 - - + +
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Residues in contact with TYR 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 3.1 41.6 + - + +
32C ILE 3.4 4.9 + - - +
33C ASN 3.1 0.8 - - - -
34C ALA* 1.3 74.9 - - - +
36C LYS* 1.3 71.6 + - - +
37C LEU* 3.2 21.8 + - + +
351C THR* 3.8 11.9 - - + -
368C ILE* 2.7 42.9 - - + +
369C SER* 2.9 31.4 + - - -
371C GLU 3.3 13.7 + - - -
372C ILE* 3.7 2.4 - - + +
373C PRO* 3.4 28.5 - - + +
387C LEU* 3.5 25.6 - - + +
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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