Contacts of the helix formed by residues 23 - 35 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B CYS* 4.0 11.2 - - + +
21B PHE 3.1 0.4 + - - -
22B GLY* 1.3 70.5 - - - -
24B ARG* 1.3 65.6 + - - +
25B TYR 3.2 2.9 - - - -
26B ALA* 3.0 16.4 + - + -
27B LEU* 3.1 14.7 + - - +
343B PHE* 3.7 6.3 - - - -
377B TYR* 3.9 18.6 + - - +
380B ARG* 2.9 44.2 + - - -
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Residues in contact with ARG 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B PHE* 2.9 33.8 + - + +
22B GLY 3.3 0.6 - - - -
23B ASP* 1.3 78.7 + - - +
25B TYR* 1.3 64.7 + - - +
27B LEU* 3.1 6.1 + - - +
28B VAL* 2.9 34.9 + - + +
136B TRP 4.6 5.1 + - - -
140B TRP* 3.5 22.2 - - - -
338B GLY 2.9 30.5 + - - +
339B GLY 3.4 10.9 + - - -
340B GLY* 3.0 29.4 + - - -
343B PHE* 3.7 40.6 - - + +
346B THR* 4.1 10.4 - - + +
350B TRP* 3.7 24.6 - - - -
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Residues in contact with TYR 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL 3.0 24.0 + - - -
7B TYR* 3.2 16.5 - - + +
11B TYR* 3.4 17.8 - + - -
12B ARG* 3.7 37.7 - - + -
15B CYS* 3.8 26.2 + - + +
16B CYS* 4.0 7.4 - - - -
21B PHE 4.8 0.2 + - - -
22B GLY 4.8 0.6 + - - -
23B ASP 3.2 1.0 - - - -
24B ARG* 1.3 80.9 - - - +
26B ALA* 1.3 59.4 + - - +
28B VAL* 3.4 5.5 + - - +
29B MET* 2.9 55.9 + - + +
136B TRP* 4.0 13.0 - - + +
137B GLY* 3.8 33.4 - - - -
350B TRP* 6.4 0.2 - - - -
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Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ARG* 3.5 32.5 - - - +
16B CYS* 3.5 18.9 - - - -
23B ASP* 3.0 11.3 + - + +
25B TYR* 1.3 78.0 - - - +
27B LEU* 1.3 66.8 + - - +
30B ASP* 2.9 29.8 + - - +
377B TYR* 3.7 18.4 - - - +
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ASP* 3.1 25.1 + - - +
24B ARG* 3.6 7.6 - - - +
26B ALA* 1.3 76.0 - - - +
28B VAL* 1.3 64.3 + - - +
30B ASP* 4.1 0.3 - - - +
31B LEU* 2.9 28.1 + - - +
343B PHE* 4.2 16.2 - - + +
344B PRO* 4.3 11.0 - - + -
347B ALA* 4.0 6.1 - - + -
375B HIS* 5.2 0.3 + - - -
377B TYR* 3.6 33.2 - - + -
380B ARG* 3.5 57.4 - - + +
381B TYR* 3.7 17.9 + - - +
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Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ARG* 2.9 26.1 + - + +
25B TYR* 3.6 10.1 - - - +
27B LEU* 1.3 77.1 - - - +
29B MET* 1.3 64.1 + - - +
31B LEU* 3.3 2.4 + - - +
32B ILE* 3.1 27.8 + - + +
136B TRP* 3.6 39.3 - - + -
343B PHE 5.1 0.2 - - - +
346B THR* 4.5 0.2 - - + -
347B ALA* 3.8 28.3 - - + +
350B TRP* 3.7 33.0 - - + -
351B THR* 4.1 0.5 + - - -
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Residues in contact with MET 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 3.7 33.7 - - + -
6B VAL 4.7 0.7 - - - +
7B TYR* 3.8 33.4 - - + -
12B ARG* 4.5 12.6 - - - +
25B TYR* 2.9 54.8 + - + +
26B ALA 4.3 1.6 - - - +
28B VAL* 1.3 75.1 - - + +
30B ASP* 1.3 60.0 + - - +
32B ILE* 3.4 7.3 + - + +
33B ASN* 2.9 27.2 + - - +
38B ILE* 4.2 15.3 - - + +
136B TRP* 4.2 15.3 - - - -
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Residues in contact with ASP 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ARG* 2.8 40.8 + - - -
26B ALA 2.9 19.3 + - - +
27B LEU 4.1 0.9 - - - +
29B MET* 1.3 76.6 - - - +
31B LEU* 1.3 59.3 + - - +
33B ASN* 3.6 11.9 + - - +
34B ALA* 2.8 29.1 + - - +
375B HIS* 3.9 13.8 - - + +
376B SER* 4.5 6.4 + - - -
377B TYR* 3.3 25.0 - - + -
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LEU 2.9 19.3 + - - +
28B VAL 3.8 1.3 - - - +
30B ASP* 1.3 73.3 - - - +
32B ILE* 1.3 68.1 + - - +
34B ALA* 3.2 2.4 + - + +
35B TYR* 3.0 50.7 + - + -
347B ALA* 3.7 17.7 - - + +
348B ARG* 4.0 7.6 - - - +
351B THR* 3.5 22.4 - - - +
372B ILE* 4.0 22.0 - - + -
373B PRO* 4.2 2.9 - - + -
375B HIS* 3.8 25.0 + - + +
381B TYR* 3.7 26.0 - - + +
387B LEU* 4.5 2.7 - - + -
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Residues in contact with ILE 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ILE* 4.2 9.0 - - + -
28B VAL* 3.1 20.0 + - + +
29B MET* 3.6 11.2 - - - +
31B LEU* 1.3 77.6 - - - +
33B ASN* 1.3 60.4 + - - +
35B TYR 3.4 4.2 + - - -
37B LEU* 3.1 51.1 + - + +
38B ILE* 4.0 19.7 - - + -
41B LEU* 4.3 3.4 - - + -
136B TRP* 3.6 23.8 - - + +
350B TRP 4.5 1.3 - - - +
351B THR* 3.6 21.8 - - + +
354B THR* 3.5 29.4 - - + +
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Residues in contact with ASN 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B MET 2.9 17.6 + - - +
30B ASP* 3.6 13.0 + - - +
31B LEU 3.2 0.2 - - - -
32B ILE* 1.3 75.4 - - - +
34B ALA* 1.3 60.9 + - - +
36B LYS* 2.9 26.2 + - - +
37B LEU 4.8 0.4 - - - +
38B ILE* 3.6 29.9 - - + +
39B PRO* 5.6 0.9 - - - +
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Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ASP 2.8 20.9 + - - +
31B LEU* 3.2 8.4 + - - +
33B ASN* 1.3 76.1 - - - +
35B TYR* 1.3 57.5 + - - +
36B LYS* 3.1 16.8 + - - +
373B PRO* 3.7 30.2 - - + +
374B GLU 4.4 2.5 - - - +
375B HIS* 3.8 33.4 - - + +
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Residues in contact with TYR 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.0 41.1 + - + +
32B ILE 3.9 4.0 - - - +
33B ASN 3.1 0.4 - - - -
34B ALA* 1.3 75.5 - - - +
36B LYS* 1.3 71.5 + - - +
37B LEU* 3.3 24.0 + - + +
351B THR* 3.8 13.0 - - + -
368B ILE* 2.9 36.6 - - + -
369B SER* 2.9 29.2 + - - -
371B GLU 3.2 14.2 + - - -
372B ILE* 3.7 3.3 - - + +
373B PRO* 3.4 28.0 - - + -
387B LEU* 3.5 25.8 - - + +
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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