Contacts of the helix formed by residues 20 - 31 (chain A) in PDB entry 1B4V
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 TYR 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A GLY* 1.3 67.6 - - - +
21A GLY* 1.3 64.1 + - - +
23A ALA* 3.9 0.9 - - - +
24A VAL* 3.2 31.6 + - - +
116A SER* 3.1 27.3 - - - -
119A ASN* 2.9 23.7 + - - -
155A LEU* 3.9 8.3 - - + -
194A VAL* 5.4 2.9 - - - +
228A LEU* 3.6 27.8 - - + +
487A PHE* 3.3 43.4 - + + -
490A ILE* 3.9 13.9 - - + -
491A THR* 3.2 25.4 - - + +
494A ALA* 5.1 0.2 - - - -
510A FAD 3.0 44.2 + - - +
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Residues in contact with GLY 21 (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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20A TYR* 1.3 77.8 - - - +
22A ALA* 1.3 58.4 + - - +
24A VAL* 3.6 2.3 + - - +
25A SER* 2.8 31.7 + - - -
473A THR* 3.2 35.9 + - - -
474A ASP* 4.3 1.8 - - - -
490A ILE* 4.0 3.3 - - - +
494A ALA* 4.1 8.8 - - - +
510A FAD 3.2 10.3 + - - -
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Residues in contact with ALA 22 (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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15A VAL* 3.4 18.7 - - + +
17A GLY 3.1 36.1 - - - +
18A THR* 3.8 7.0 - - - -
19A GLY 3.5 5.3 + - - +
20A TYR 3.3 0.4 - - - -
21A GLY* 1.3 74.5 - - - +
23A ALA* 1.3 59.0 + - - +
25A SER* 3.3 3.1 + - - -
26A ALA* 2.9 32.4 + - - +
38A MET* 3.5 3.5 - - + +
288A GLY* 4.1 12.4 - - - -
473A THR* 3.6 5.7 + - - -
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Residues in contact with ALA 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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18A THR 4.6 0.2 - - - +
19A GLY 2.8 22.8 + - - +
20A TYR 3.9 2.9 - - - +
22A ALA* 1.3 69.3 - - - +
24A VAL* 1.3 66.7 + - - +
26A ALA* 4.0 1.4 - - - +
27A LEU* 3.2 24.4 + - - +
38A MET* 4.1 1.1 - - - +
228A LEU* 4.2 11.4 - - + -
232A TYR* 3.6 28.4 - - + +
233A LEU* 3.7 29.2 - - + -
236A ALA* 4.8 0.7 - - - +
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Residues in contact with VAL 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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20A TYR* 3.2 17.6 + - - +
23A ALA* 1.3 76.3 - - - +
25A SER* 1.3 64.3 + - - +
27A LEU* 3.4 1.9 + - - +
28A ARG* 3.2 23.7 + - - +
232A TYR* 3.8 20.4 - - + -
491A THR* 3.7 34.3 - - + +
494A ALA* 3.6 16.8 - - + +
495A GLU* 3.6 47.1 - - - +
498A VAL* 4.3 2.7 - - + -
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Residues in contact with SER 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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15A VAL* 4.8 3.1 - - - -
21A GLY 2.8 21.7 + - - -
22A ALA* 3.7 5.6 - - - -
24A VAL* 1.3 79.9 - - - +
26A ALA* 1.3 57.3 + - - +
28A ARG* 3.4 0.7 + - - -
29A LEU* 2.9 38.5 + - - +
286A PHE* 4.2 22.1 - - - -
473A THR* 3.3 21.0 - - - +
494A ALA* 5.0 2.8 + - - +
498A VAL* 4.0 20.7 - - - +
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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
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15A VAL* 4.4 6.4 - - + +
22A ALA 2.9 17.6 + - - +
23A ALA* 4.0 2.9 - - - +
25A SER* 1.3 75.5 - - - +
27A LEU* 1.3 57.3 + - - +
29A LEU* 3.8 9.7 - - - +
30A GLY 2.9 23.6 + - - -
36A THR* 4.5 3.1 - - + -
38A MET* 3.5 35.0 - - + -
236A ALA* 4.1 5.6 - - + -
242A VAL* 3.4 20.0 - - + +
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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
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23A ALA 3.2 18.1 + - - +
24A VAL 3.6 3.8 - - - +
26A ALA* 1.3 76.8 - - - +
28A ARG* 1.3 82.8 + - - +
30A GLY* 3.2 2.4 + - - -
31A GLU* 3.0 54.7 + - + +
154A MET* 4.2 14.6 - - + -
232A TYR* 3.6 26.5 - - + +
235A ALA* 3.6 19.7 - - + +
236A ALA* 3.6 32.6 - - + +
239A THR* 4.1 2.0 - - + +
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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 VAL* 3.2 15.5 + - - +
25A SER 4.0 0.9 - - - +
27A LEU* 1.3 87.1 - - - +
29A LEU* 1.3 64.9 + - - +
31A GLU* 2.8 35.4 + - - +
32A ALA* 3.0 24.1 + - - +
150A ARG* 3.8 15.6 - - - +
154A MET* 3.7 23.6 - - - +
495A GLU* 2.8 38.5 + - - +
498A VAL* 3.5 29.2 - - + -
499A GLU* 5.6 2.7 - - + +
502A ILE* 3.5 12.9 - - + +
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Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ALA* 4.3 3.4 - - + -
15A VAL* 4.1 12.6 - - + -
25A SER 2.9 29.9 + - - +
26A ALA 3.8 2.0 - - - +
28A ARG* 1.3 76.2 - - - +
30A GLY* 1.3 60.9 + - - +
32A ALA* 3.1 8.6 + - - +
34A VAL* 3.0 47.5 + - + +
36A THR* 3.5 22.0 - - + +
284A TYR* 5.8 0.9 - - + -
286A PHE* 3.6 46.7 - - + -
498A VAL* 4.5 1.6 - - + -
502A ILE* 3.9 22.7 - - + -
506A VAL* 4.8 6.7 - - + -
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Residues in contact with GLY 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 ALA 2.9 14.5 + - - -
27A LEU 3.7 3.6 - - - -
29A LEU* 1.3 78.2 - - - +
31A GLU* 1.3 57.0 + - - +
33A GLY* 3.0 19.1 + - - -
34A VAL 4.0 3.1 - - - -
239A THR* 3.7 23.4 - - - -
241A LYS* 3.7 22.9 - - - +
242A VAL* 4.0 4.2 - - - +
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Residues in contact with GLU 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 LEU* 3.0 29.1 + - + +
28A ARG* 2.8 44.7 + - - +
29A LEU 3.3 0.2 - - - -
30A GLY* 1.3 76.1 - - - +
32A ALA* 1.3 59.2 + - - +
33A GLY 3.1 1.1 + - - -
239A THR* 3.8 17.0 - - + +
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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