Contacts of the helix formed by residues 22 - 32 (chain A) in PDB entry 4BPU
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 PRO 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A TYR* 4.7 1.8 - - - +
20A LEU 3.1 8.9 - - - +
21A PHE* 1.3 87.8 - - + +
23A TYR* 1.3 63.9 + - - +
24A SER 3.1 4.0 + - - -
25A GLN* 3.2 27.3 - - + +
26A TYR* 3.0 20.5 + - + +
321A PHE* 4.1 46.0 - - + -
383A TYR* 5.0 9.2 - - + -
388A LEU* 4.9 3.4 - - + -
392A VAL* 4.4 13.7 - - + -
395A PHE* 5.3 0.7 - - + -
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Residues in contact with TYR 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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17A TYR* 2.5 37.3 + - - +
18A ARG 5.1 4.3 - - - -
21A PHE* 2.7 49.3 + + + -
22A PRO* 1.3 70.4 - - - +
24A SER* 1.3 57.2 + - - +
26A TYR* 3.4 7.7 - - - +
27A TYR* 2.9 31.5 + - - +
63A GLN* 3.7 6.3 + - + +
66A LEU* 4.2 14.9 - - + +
67A GLU* 3.5 53.6 - - + +
70A MET* 3.5 42.5 - - + +
71A GLN* 3.9 11.8 - - - +
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Residues in contact with SER 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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22A PRO 3.1 1.0 + - - -
23A TYR* 1.3 79.6 - - - +
25A GLN* 1.3 70.5 + - - +
27A TYR* 3.7 2.4 - - - +
28A ARG* 2.8 36.5 + - - +
63A GLN* 3.5 20.8 + - - +
380A THR* 6.1 0.3 - - - -
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Residues in contact with GLN 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 PRO* 3.2 26.8 - - + +
24A SER* 1.3 85.5 - - - +
26A TYR* 1.3 56.2 + - - +
28A ARG* 4.0 9.0 - - - +
29A TRP* 2.8 27.7 + - - +
383A TYR* 2.7 37.9 + - - -
392A VAL* 3.6 6.0 - - + +
395A PHE* 3.7 18.3 - - + -
396A GLU* 3.0 32.9 + - + +
399A LEU* 3.3 24.6 - - + +
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Residues in contact with TYR 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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21A PHE* 3.5 27.6 - + + -
22A PRO* 3.0 13.6 + - + +
23A TYR* 3.4 13.7 - - - +
25A GLN* 1.3 77.4 - - - +
27A TYR* 1.3 57.9 + - - +
29A TRP* 3.2 18.5 + + - +
30A LEU* 2.9 53.3 + - + +
40A PHE* 5.6 0.2 - + - -
45A PHE* 3.3 23.7 - + - -
66A LEU* 3.8 25.4 - - + -
70A MET* 5.4 2.0 - - - -
78A ILE* 4.2 4.9 - - + +
80A ILE* 3.3 17.5 - - + +
319A SER* 2.7 32.1 + - - -
320A PRO* 4.2 6.1 - - + -
321A PHE* 5.2 6.1 - + - -
395A PHE* 4.0 10.4 - + + -
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Residues in contact with TYR 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 TYR 2.9 17.6 + - - +
24A SER 3.8 1.1 - - - +
26A TYR* 1.3 73.6 - - - +
28A ARG* 1.3 63.4 + - + +
30A LEU 4.4 0.2 - - - +
31A ASN* 2.8 71.7 + - + +
40A PHE* 3.7 43.1 - + + -
41A GLN* 4.1 11.6 + - - -
62A ASN* 4.0 7.7 - - + +
63A GLN* 3.6 53.6 - - + +
66A LEU* 5.6 2.7 - - + -
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Residues in contact with ARG 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 SER* 2.8 22.4 + - - +
25A GLN* 3.4 15.8 - - - +
26A TYR 3.3 0.2 - - - -
27A TYR* 1.3 78.9 - - + +
29A TRP* 1.3 65.5 + - - +
31A ASN* 4.5 1.5 - - - +
32A TYR* 3.3 14.9 + - - -
33A GLY 4.3 3.3 + - - -
396A GLU* 4.0 26.7 + - - +
399A LEU* 3.5 37.3 - - + +
400A GLU* 4.2 12.5 + - - +
403A ASP* 3.5 24.0 + - - -
406A ARG* 5.0 4.9 + - - -
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Residues in contact with TRP 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 GLN 2.8 13.4 + - - +
26A TYR* 3.3 18.2 - + - +
28A ARG* 1.3 81.3 - - - +
30A LEU* 1.3 81.1 + - + +
32A TYR* 3.2 43.9 + + - -
80A ILE* 3.7 27.6 - - + -
105A GLU* 4.1 7.2 - - - -
156A LEU* 4.7 3.8 - - + -
168A TRP* 3.9 37.2 - + + -
170A CYS* 3.5 20.5 - - - -
320A PRO* 3.8 22.2 - - + -
395A PHE* 3.7 21.3 - + + -
398A PHE* 3.7 19.3 - + - -
399A LEU* 3.4 14.8 - - + +
402A LEU* 4.2 3.3 - - + +
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Residues in contact with LEU 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 TYR* 2.9 43.9 + - + +
29A TRP* 1.3 110.9 - - + +
31A ASN* 1.3 59.5 + - - +
32A TYR* 3.4 14.0 - - - -
39A TYR* 3.9 10.4 - - - -
40A PHE* 3.9 25.5 - - + +
43A ARG* 3.9 30.2 + - + +
45A PHE* 3.3 35.7 - - + -
80A ILE* 4.4 9.0 - - + -
105A GLU* 4.2 2.7 - - - +
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Residues in contact with ASN 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 TYR* 2.8 61.8 + - + +
28A ARG* 4.5 1.6 - - - +
30A LEU* 1.3 75.2 - - - +
32A TYR* 1.3 72.5 + - - +
33A GLY* 4.5 2.4 - - - +
34A GLY* 3.2 31.9 + - - +
36A ILE 4.9 3.8 + - - +
39A TYR* 4.8 8.8 + - - +
40A PHE* 3.7 18.2 + - + +
41A GLN* 4.8 4.5 + - - +
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Residues in contact with TYR 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 ARG 3.3 6.2 + - - -
29A TRP* 3.2 39.4 + - - -
30A LEU* 3.5 15.7 - - - -
31A ASN* 1.3 77.2 - - - +
33A GLY* 1.3 63.0 + - - +
34A GLY 3.2 1.0 + - - -
35A VAL* 3.5 21.9 - - + +
39A TYR* 3.5 26.0 - + + -
43A ARG* 3.9 6.1 - - - -
105A GLU* 2.8 27.8 + - - -
170A CYS* 3.4 12.2 - - - +
175A ARG* 3.1 44.2 + - - +
402A LEU* 3.9 23.1 - - + -
406A ARG* 3.4 29.5 - - - +
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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