Contacts of the helix formed by residues 24 - 34 (chain A) in PDB entry 3CBG
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 SER 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ASP 3.8 1.4 + - - -
23A ASP* 1.3 80.1 - - - +
25A PHE* 1.3 68.7 + - - +
26A TYR* 4.8 1.2 + - - -
27A LEU* 3.4 12.1 + - - +
28A ALA* 3.0 14.7 + - - +
80A LEU* 3.5 27.6 - - - +
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Residues in contact with PHE 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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24A SER* 1.3 74.9 - - - +
26A TYR* 1.3 93.9 + + + +
28A ALA* 3.3 5.4 + - + +
29A GLN* 2.8 56.2 + - - +
32A ARG* 4.9 12.6 + - - -
107A LYS* 4.9 0.9 - - - -
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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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24A SER* 3.6 1.8 + - - -
25A PHE* 1.3 97.1 - + + +
27A LEU* 1.3 60.5 + - - +
29A GLN* 3.7 18.7 - - - +
30A LEU* 2.9 30.0 + - - +
76A LEU* 3.7 8.1 - - + +
80A LEU* 5.6 7.2 - - + -
104A TYR* 4.6 5.8 - + + +
107A LYS* 3.4 43.4 + - + -
108A ALA* 3.7 37.0 - - + -
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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 ASP* 3.7 27.6 - - + +
24A SER* 3.4 19.5 + - - +
25A PHE 3.3 0.6 - - - -
26A TYR* 1.3 75.0 - - - +
28A ALA* 1.3 64.0 + - - +
30A LEU* 3.4 1.4 + - - +
31A ARG* 3.1 19.1 + - - +
49A ALA* 4.8 4.0 - - + +
50A GLN* 6.0 4.0 - - - +
73A TYR* 3.4 57.8 - - + +
76A LEU* 3.9 10.0 - - + +
77A ALA* 3.7 31.0 - - + +
80A LEU* 3.9 17.0 - - + +
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Residues in contact with ALA 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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23A ASP* 3.6 23.9 - - + +
24A SER 3.0 17.8 + - - +
25A PHE* 3.6 4.5 - - - +
27A LEU* 1.3 76.4 - - - +
29A GLN* 1.3 54.2 + - - +
31A ARG* 3.7 4.1 - - - +
32A ARG* 2.7 48.5 + - - +
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Residues in contact with GLN 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 PHE* 2.8 43.7 + - + +
26A TYR* 3.8 12.0 - - - +
27A LEU 3.2 0.2 - - - -
28A ALA* 1.3 75.5 - - - +
30A LEU* 1.3 55.4 + - - +
32A ARG* 3.6 22.1 - - - +
33A GLU* 2.8 65.5 + - - +
104A TYR* 4.1 4.7 - - - -
107A LYS* 2.7 45.8 + - - +
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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 17.2 + - - +
27A LEU 3.7 4.3 - - - +
28A ALA 3.4 0.2 - - - -
29A GLN* 1.3 75.4 - - - +
31A ARG* 1.3 58.0 + - - +
34A THR* 2.8 40.4 + - + +
43A GLN* 4.0 12.8 - - - +
71A ARG* 3.7 21.5 - - + +
72A GLY 4.0 2.9 - - - -
73A TYR* 3.8 36.1 - - + +
76A LEU* 3.7 19.7 - - + -
104A TYR* 3.5 47.5 - - + -
105A TRP* 5.2 0.9 - - - +
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Residues in contact with ARG 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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3A LYS* 5.9 2.4 - - - +
23A ASP* 5.0 3.6 - - - +
27A LEU 3.1 14.8 + - - +
28A ALA* 3.7 6.3 - - - +
30A LEU* 1.3 85.1 - - - +
32A ARG* 1.3 64.5 + - - +
34A THR* 3.9 2.7 + - - -
35A ALA* 3.3 25.8 + - + +
40A ALA* 3.9 9.5 + - - +
43A GLN* 3.3 34.9 + - - +
44A ILE 2.4 28.1 + - - -
45A SER* 3.3 18.8 - - - +
46A PRO* 3.3 18.7 - - + +
73A TYR* 3.5 24.9 + - + +
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Residues in contact with ARG 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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25A PHE* 4.9 11.9 + - - -
28A ALA* 2.7 45.0 + - - +
29A GLN* 3.2 32.1 + - - +
31A ARG* 1.3 74.5 - - + +
33A GLU* 1.3 70.3 + - + +
34A THR 3.4 0.3 + - - -
35A ALA* 3.6 15.7 + - - +
36A HIS* 5.2 0.3 + - - -
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Residues in contact with GLU 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 GLN* 2.8 42.9 + - + +
32A ARG* 1.3 81.7 + - + +
34A THR* 1.3 58.4 + - - +
35A ALA 3.5 0.2 - - - -
36A HIS* 3.0 23.8 + - - -
103A LYS* 4.4 5.7 + - - -
104A TYR* 2.5 44.6 + - - +
107A LYS* 5.1 1.4 - - - -
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Residues in contact with THR 34 (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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30A LEU* 2.8 30.7 + - + +
31A ARG* 3.9 4.3 + - - -
33A GLU* 1.3 78.0 - - - +
35A ALA* 1.3 65.7 + - - +
36A HIS* 3.0 9.6 + - - -
37A LEU* 3.1 28.5 + - + +
40A ALA* 4.0 7.0 - - - +
43A GLN* 4.4 5.5 + - - -
71A ARG* 3.8 29.4 + - - -
100A ILE* 4.3 15.7 - - + -
104A TYR* 4.1 15.0 - - + +
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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