Contacts of the helix formed by residues 24 - 36 (chain E) in PDB entry 3BBX
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 ASN 24 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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599B A 4.4 26.0 + - - +
600B G 5.8 2.7 + - - -
21E ARG* 5.2 9.3 - - - +
22E ASP* 5.1 1.0 - - - +
23E PHE* 1.3 96.2 + - - +
25E GLU* 1.3 66.8 + - - +
26E ALA* 3.3 4.6 - - + +
27E LEU* 2.9 28.2 + - - +
28E VAL 4.0 1.0 + - - -
104E ALA* 3.7 16.4 - - - +
18L ARG 3.1 1.9 - - - +
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Residues in contact with GLU 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1244B A 5.7 5.5 - - - +
23E PHE* 3.4 3.2 + - - -
24E ASN* 1.3 70.1 - - - +
26E ALA 1.3 48.1 - - - +
27E LEU 2.8 1.4 + - - -
28E VAL* 3.0 6.3 + - - -
29E HIS 2.9 2.9 + - - -
17L LYS* 1.7 70.7 + - + +
18L ARG* 1.3 60.6 + - - +
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Residues in contact with ALA 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B U 4.6 6.5 - - - +
599B A 5.4 5.4 - - - +
24E ASN* 3.3 4.7 - - + +
25E GLU* 1.3 64.1 - - - +
27E LEU 1.3 48.0 - - - +
18L ARG* 1.4 87.7 - - - +
19L LEU* 0.7 113.3 + - - +
20L GLY* 2.3 19.3 - - - +
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Residues in contact with LEU 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599B A 4.4 14.8 + - - +
600B G 6.3 0.2 - - - -
24E ASN* 2.9 25.1 + - - +
25E GLU 2.8 1.4 + - - -
26E ALA* 1.3 66.6 - - - +
28E VAL* 1.3 52.5 - - - +
31E VAL* 4.4 2.2 - - + -
100E MET* 3.4 55.6 - - + +
103E GLY* 3.1 37.5 - - - +
104E ALA* 4.3 4.5 - - + -
18L ARG 1.8 5.7 + - - -
19L LEU* 0.7 264.2 - - + +
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Residues in contact with VAL 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E PHE* 4.3 14.1 - - + +
24E ASN 4.1 3.1 - - - +
25E GLU* 3.0 22.6 + - - +
27E LEU* 1.3 73.5 - - + +
29E HIS* 1.3 49.5 + - - +
31E VAL* 3.1 6.1 + - + +
32E VAL* 2.7 53.3 + - + +
103E GLY 5.2 0.2 - - - -
104E ALA* 4.1 19.5 - - + +
105E LEU* 6.1 0.7 - - + -
177E PRO* 5.2 10.8 - - + -
16L GLY* 1.9 49.6 - - - +
17L LYS* 4.0 0.4 - - + -
18L ARG 3.4 0.9 - - - +
19L LEU* 2.0 13.0 - - - +
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Residues in contact with HIS 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1244B A 3.9 7.9 + - - -
1245B G 3.0 46.6 - - - -
28E VAL* 1.3 68.1 - - - +
30E GLN* 1.3 54.8 + - - -
32E VAL* 3.7 6.0 - - - +
33E VAL* 2.9 54.3 + - + +
17L LYS 2.2 21.7 + - - +
18L ARG* 1.3 104.7 - - + +
19L LEU* 2.7 2.0 - - - +
23L ILE* 3.8 20.0 - - + +
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Residues in contact with GLN 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659B G 4.0 10.3 + - - -
660B C 1.6 86.4 + - - +
661B A 5.8 0.4 - - - -
29E HIS* 1.3 66.2 - - - +
31E VAL* 1.3 52.5 + - + +
32E VAL 3.1 1.1 - - - -
33E VAL* 3.2 5.7 + - + +
34E ALA* 2.6 41.4 + - + +
96E VAL* 5.1 6.0 - - + +
100E MET* 4.4 5.1 - - - -
19L LEU* 2.0 76.0 - - + +
23L ILE* 6.0 4.5 - - + -
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Residues in contact with VAL 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E LEU* 3.8 14.8 - - + +
28E VAL* 3.7 8.1 - - + +
30E GLN* 1.3 71.6 - - - +
32E VAL* 1.3 54.3 + - + +
34E ALA* 3.2 8.1 + - - +
35E TYR* 2.6 34.2 + - + +
96E VAL* 3.6 24.2 - - + -
100E MET 3.2 26.9 - - - +
101E TYR* 3.8 33.0 - - + +
103E GLY 5.5 0.4 - - - +
105E LEU* 6.1 1.6 - - + -
176E ASP* 4.3 10.1 - - - +
177E PRO* 5.6 4.0 - - + -
19L LEU* 2.7 11.7 - - + +
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Residues in contact with VAL 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E VAL* 2.7 49.1 + - + +
29E HIS* 3.7 9.4 - - - +
31E VAL* 1.3 71.6 - - + +
33E VAL* 1.3 63.0 + - + +
35E TYR* 2.7 23.0 + - - +
36E ALA* 3.2 11.7 + - + +
176E ASP* 5.7 0.4 - - - +
177E PRO* 5.6 2.0 - - + -
178E VAL* 4.1 30.9 - - + +
181E ILE* 5.7 2.2 - - + -
15L ALA* 5.7 7.4 - - + -
16L GLY 4.7 8.3 - - - +
17L LYS 4.5 3.1 - - - +
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Residues in contact with VAL 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1245B G 4.6 15.3 - - - +
1246B A 5.2 3.8 - - - -
29E HIS* 2.9 53.1 + - + +
30E GLN* 3.7 5.4 - - + +
32E VAL* 1.3 83.2 - - + +
34E ALA* 1.3 60.7 + - - +
35E TYR 3.4 0.2 + - - -
36E ALA* 3.4 19.8 + - - +
37E ALA* 4.6 3.1 - - - +
23L ILE* 4.8 20.0 - - + -
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Residues in contact with ALA 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660B C 6.2 1.6 - - - -
30E GLN* 2.6 27.6 + - + +
31E VAL* 3.3 11.0 - - - +
33E VAL* 1.3 72.7 - - - +
35E TYR* 1.3 62.3 + - - +
36E ALA 3.3 0.2 - - - -
37E ALA* 3.7 21.8 + - - +
38E GLY* 5.0 0.7 - - - -
94E GLN* 4.2 25.6 - - + +
95E LYS 5.6 0.2 - - - -
96E VAL* 4.5 18.2 - - + +
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Residues in contact with TYR 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615B U 1.2 222.2 + + - +
31E VAL* 2.6 16.9 + - + +
32E VAL 2.7 11.0 + - - +
34E ALA* 1.3 72.6 - - - +
36E ALA* 1.3 53.0 + - - +
37E ALA 2.7 18.0 + - - -
38E GLY* 3.6 8.5 + - - +
101E TYR* 5.2 0.2 - + - -
170E ARG* 5.3 5.2 + - - -
176E ASP* 3.1 32.3 + - + +
178E VAL* 3.4 36.8 - - + -
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Residues in contact with ALA 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443B A 4.0 20.9 + - - +
32E VAL 3.2 8.0 + - - +
33E VAL* 3.4 13.1 + - - +
34E ALA 3.3 0.6 - - - -
35E TYR* 1.3 76.4 - - - +
37E ALA* 1.3 62.6 + - - +
178E VAL* 5.5 0.2 - - - +
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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