Contacts of the helix formed by residues 23 - 35 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A CYS* 4.0 11.4 - - + +
21A PHE 3.2 0.4 + - - -
22A GLY* 1.3 70.5 - - - -
24A ARG* 1.3 66.1 + - - +
25A TYR 3.2 2.9 - - - -
26A ALA* 2.9 22.6 + - + +
27A LEU* 3.2 16.3 + - - +
343A PHE* 3.7 6.8 - - - -
377A TYR* 3.9 11.6 + - - +
380A ARG* 2.9 43.7 + - - -
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Residues in contact with ARG 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 2.9 37.6 + - + +
22A GLY 3.3 0.6 - - - -
23A ASP* 1.3 77.9 + - - +
25A TYR* 1.3 64.7 + - - +
27A LEU* 3.1 6.1 + - - +
28A VAL* 3.0 30.7 + - + +
136A TRP 4.6 5.1 + - - -
140A TRP* 3.5 22.2 - - - -
338A GLY 2.9 30.5 + - - +
339A GLY 3.3 11.5 + - - -
340A GLY* 2.9 29.6 + - - -
343A PHE* 3.7 37.4 - - + +
346A THR* 4.1 10.8 - - + +
350A TRP* 3.7 24.0 - - - -
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Residues in contact with TYR 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL 3.0 23.9 + - - -
7A TYR* 3.5 12.4 - - + +
11A TYR* 3.4 19.6 - + - -
12A ARG* 3.8 37.0 - - + -
15A CYS* 3.8 28.2 + - + +
16A CYS* 4.0 5.6 - - - -
22A GLY 4.8 0.6 + - - -
23A ASP 3.1 1.0 + - - -
24A ARG* 1.3 80.1 - - - +
26A ALA* 1.3 58.7 + - - +
28A VAL* 3.7 6.3 - - - +
29A MET* 3.0 53.7 + - + +
136A TRP* 4.0 12.8 - - + +
137A GLY* 3.8 36.1 - - - -
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Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 3.5 31.2 - - - +
16A CYS* 3.5 19.5 - - - -
23A ASP* 2.9 12.4 + - + +
25A TYR* 1.3 77.6 - - - +
27A LEU* 1.3 59.5 + - - +
30A ASP* 2.9 36.0 + - - +
377A TYR* 3.7 18.8 - - - +
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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
----------------------------------------------------------
23A ASP* 3.2 32.0 + - - +
24A ARG* 3.1 9.2 + - - +
26A ALA* 1.3 75.5 - - - +
28A VAL* 1.3 67.7 + - - +
30A ASP* 4.1 0.2 - - - +
31A LEU* 2.9 27.4 + - - +
343A PHE* 4.1 17.5 - - + +
344A PRO* 4.1 10.8 - - + -
347A ALA* 4.0 5.8 - - + -
375A HIS* 5.2 0.5 + - - -
377A TYR* 3.6 42.4 - - + -
380A ARG* 3.8 36.3 - - + +
381A TYR* 3.7 16.4 + - - +
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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
----------------------------------------------------------
24A ARG* 3.0 27.6 + - + +
25A TYR* 3.7 10.5 - - - +
27A LEU* 1.3 75.9 - - - +
29A MET* 1.3 64.9 + - - +
31A LEU* 3.3 2.3 + - - +
32A ILE* 3.1 27.5 + - + +
136A TRP* 3.6 39.7 - - + -
347A ALA* 3.8 27.4 - - + +
350A TRP* 3.7 33.4 - - + -
351A THR* 4.2 0.7 + - - -
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Residues in contact with MET 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 3.7 33.0 - - + -
6A VAL 4.6 0.7 - - - +
7A TYR* 4.0 29.8 - - + -
12A ARG* 4.4 12.8 - - - +
25A TYR* 3.0 56.1 + - + +
26A ALA 4.3 1.6 - - - +
28A VAL* 1.3 77.6 - - + +
30A ASP* 1.3 59.1 + - - +
32A ILE* 3.4 7.7 + - + +
33A ASN* 2.9 27.7 + - - +
38A ILE* 4.2 16.8 - - + +
136A TRP* 4.2 14.8 - - - -
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Residues in contact with ASP 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 2.9 38.9 + - - -
26A ALA 2.9 19.3 + - - +
27A LEU 4.1 2.0 - - - +
29A MET* 1.3 74.6 - - - +
31A LEU* 1.3 60.8 + - - +
33A ASN* 3.6 11.3 + - - +
34A ALA* 2.8 29.1 + - - +
375A HIS* 3.7 8.9 - - + +
376A SER* 2.7 32.5 + - - +
377A TYR* 3.4 8.6 - - + -
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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
----------------------------------------------------------
27A LEU 2.9 18.7 + - - +
28A VAL 3.3 1.3 + - - +
30A ASP* 1.3 73.6 - - - +
32A ILE* 1.3 65.9 + - - +
34A ALA* 3.2 5.8 + - + +
35A TYR* 3.1 50.2 + - + -
347A ALA* 3.6 20.6 - - + +
348A ARG* 3.9 10.1 - - - +
351A THR* 3.4 22.2 - - - +
372A ILE* 4.1 20.6 - - + -
373A PRO* 4.8 0.2 - - + -
375A HIS* 3.9 23.7 + - + +
381A TYR* 3.8 21.8 - - + +
387A LEU* 4.5 3.8 - - + -
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Residues in contact with ILE 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 4.1 10.1 - - + -
28A VAL* 3.1 20.0 + - + +
29A MET* 3.6 11.7 - - + +
31A LEU* 1.3 77.1 - - - +
33A ASN* 1.3 61.3 + - - +
35A TYR* 3.3 6.8 + - - -
37A LEU* 3.3 43.3 + - + +
38A ILE* 3.8 22.9 - - + -
41A LEU* 4.3 8.7 - - + -
136A TRP* 3.5 37.2 - - + +
350A TRP 4.5 1.3 - - - +
351A THR* 3.7 21.5 - - + +
354A THR* 3.5 12.8 - - + +
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Residues in contact with ASN 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 MET 2.9 18.3 + - - +
30A ASP* 3.6 13.2 + - - +
32A ILE* 1.3 75.4 - - - +
34A ALA* 1.3 62.0 + - - +
36A LYS* 2.9 30.7 + - - +
37A LEU 4.9 0.2 - - - +
38A ILE* 3.7 28.7 - - + +
39A PRO* 5.7 0.5 - - - +
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Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASP 2.8 20.5 + - - +
31A LEU* 3.2 10.0 + - + +
33A ASN* 1.3 76.9 - - - +
35A TYR* 1.3 58.4 + - - +
36A LYS* 3.2 18.2 + - - +
373A PRO* 3.8 27.2 - - + +
374A GLU 5.0 0.7 - - - +
375A HIS* 3.8 34.5 - - + +
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Residues in contact with TYR 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 LEU* 3.1 47.3 + - + +
32A ILE 3.8 4.3 - - - +
33A ASN 3.1 1.0 - - - -
34A ALA* 1.3 76.3 - - - +
36A LYS* 1.3 71.0 + - - +
37A LEU* 3.2 18.5 + - + +
351A THR* 3.7 11.0 - - + -
368A ILE* 2.8 51.6 - - + +
369A SER* 2.8 30.0 + - - -
371A GLU 3.2 12.8 + - - -
372A ILE* 3.8 2.7 - - + +
373A PRO* 3.6 21.8 - - + +
387A LEU* 3.6 24.3 - - + +
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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