Contacts of the helix formed by residues 24 - 36 (chain A) in PDB entry 3J8B
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 LYS 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A PHE 4.2 0.2 + - - -
19A LEU* 4.7 11.4 - - + +
22A GLY* 3.2 10.1 + - - +
23A LYS* 1.3 74.1 - - - +
25A GLN* 1.3 58.8 + - - +
27A ALA* 3.1 10.1 + - - +
28A LEU* 2.9 27.4 + - - +
61A LEU* 6.1 4.5 - - + -
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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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23A LYS 3.3 0.6 - - - -
24A LYS* 1.3 78.4 - - - +
26A PRO* 1.3 58.3 - - - +
28A LEU* 3.2 7.5 + - - +
29A ASP* 2.9 32.2 + - - +
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Residues in contact with PRO 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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18A PHE* 5.1 4.0 - - + -
23A LYS* 3.2 25.5 - - + +
25A GLN* 1.3 78.4 - - - +
27A ALA* 1.3 58.6 + - - +
29A ASP* 3.5 5.8 + - + +
30A VAL* 2.9 29.5 + - - +
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Residues in contact with ALA 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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15A ALA* 3.6 36.4 - - + +
18A PHE* 3.6 16.5 - - + +
19A LEU* 4.4 5.4 - - + +
23A LYS 3.1 8.3 + - - +
24A LYS* 3.1 13.4 + - - +
26A PRO* 1.3 76.7 - - - +
28A LEU* 1.3 62.1 + - - +
30A VAL* 3.2 8.4 + - - +
31A LEU* 3.2 21.7 + - - +
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Residues in contact with LEU 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 LYS 2.9 12.6 + - - +
25A GLN* 3.6 9.9 - - - +
27A ALA* 1.3 75.7 - - - +
29A ASP* 1.3 63.3 + - - +
31A LEU* 3.2 8.7 + - - +
32A TYR* 3.1 21.0 + - - +
54A TYR* 5.4 4.2 - - - +
57A LEU* 5.2 15.5 - - + +
58A CYS* 5.2 10.5 - - + +
61A LEU* 5.9 6.5 - - + -
63A LYS* 6.3 2.9 - - + -
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Residues in contact with ASP 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 2.9 17.6 + - - +
26A PRO* 3.9 5.8 - - + +
28A LEU* 1.3 77.5 - - - +
30A VAL* 1.3 60.2 + - - +
32A TYR* 3.4 9.3 + - - +
33A ASP* 3.2 20.6 + - - +
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Residues in contact with VAL 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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14A ARG 6.5 0.4 - - - -
15A ALA* 6.0 3.6 - - + -
26A PRO 2.9 18.6 + - - +
27A ALA* 3.3 9.6 - - - +
28A LEU 3.1 0.2 - - - -
29A ASP* 1.3 78.9 - - - +
31A LEU* 1.3 61.3 + - - +
33A ASP* 3.2 17.7 + - - +
34A VAL* 3.3 11.1 + - - +
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Residues in contact with LEU 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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11A ALA* 6.1 5.2 - - + +
15A ALA* 5.4 8.5 - - + -
27A ALA 3.2 8.3 + - - +
28A LEU* 3.2 9.5 + - - +
30A VAL* 1.3 77.2 - - - +
32A TYR* 1.3 66.9 + - - +
34A VAL* 3.0 18.4 + - - +
35A MET* 3.0 16.1 + - - +
50A ILE 5.6 0.2 - - - +
54A TYR* 3.4 32.4 - - + +
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Residues in contact with TYR 32 (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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28A LEU 3.1 11.9 + - - +
29A ASP* 3.4 14.6 - - - +
30A VAL 3.3 0.2 - - - -
31A LEU* 1.3 76.8 - - - +
33A ASP* 1.3 62.5 + - - +
35A MET* 3.4 3.2 + - - +
36A LYS* 3.1 29.3 + - - +
54A TYR* 4.9 2.4 - - - +
66A LEU* 5.9 7.4 - - + +
70A GLY* 5.9 8.3 - - - -
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Residues in contact with ASP 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 ASP 3.2 9.4 + - - +
30A VAL* 3.3 13.2 - - - +
31A LEU 3.2 0.4 - - - -
32A TYR* 1.3 79.5 - - - +
34A VAL* 1.3 61.1 + - - +
36A LYS* 3.9 2.0 - - - -
37A SER* 3.3 22.5 + - - -
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Residues in contact with VAL 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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11A ALA* 4.6 20.0 - - + -
30A VAL 3.3 8.5 + - - +
31A LEU* 3.0 12.8 + - - +
33A ASP* 1.3 80.7 - - - +
35A MET* 1.3 62.6 + - + +
37A SER* 3.4 19.0 - - - -
40A HIS* 5.0 4.0 - - - +
50A ILE* 6.6 0.9 - - + -
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Residues in contact with MET 35 (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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31A LEU 3.0 13.6 + - - +
32A TYR* 4.5 2.9 - - - +
34A VAL* 1.3 77.4 - - - +
36A LYS* 1.3 58.4 + - - +
37A SER 3.3 1.7 + - - -
40A HIS* 4.1 15.2 - - - +
47A HIS* 6.4 2.0 - - + -
50A ILE 5.6 0.2 - - - -
51A MET* 3.8 34.5 - - + +
54A TYR* 5.7 2.5 - - + -
70A GLY* 5.8 1.8 - - - +
74A TYR* 4.1 22.6 - - + +
77A ILE* 5.4 0.7 - - - +
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Residues in contact with LYS 36 (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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32A TYR 3.1 18.6 + - - +
33A ASP* 3.9 3.8 - - - +
35A MET* 1.3 76.1 - - - +
37A SER* 1.3 64.4 + - - +
38A LYS 3.8 0.5 + - - -
70A GLY* 5.4 6.5 - - - +
73A GLN* 4.3 27.3 - - + +
74A TYR 5.2 2.2 - - - +
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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