Contacts of the helix formed by residues 22 - 34 (chain X) in PDB entry 3JW0
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 THR 22 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20X SER 4.5 6.3 - - - +
21X ASP* 1.3 72.9 - - - +
23X ILE* 1.3 52.7 + - - +
24X GLU* 2.9 12.6 + - - +
25X ASN* 2.5 68.2 + - - +
26X VAL* 3.6 3.4 + - - +
52X ASP 3.9 11.2 - - - +
53X GLY* 5.7 1.6 - - - -
54X ARG 2.9 17.5 - - - +
55X THR* 4.5 5.4 - - + -
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Residues in contact with ILE 23 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X ASP 3.7 2.2 + - - -
22X THR* 1.3 69.6 - - - +
24X GLU* 1.3 60.4 + - - +
25X ASN 3.0 1.4 + - - -
26X VAL* 3.0 21.8 + - + +
27X LYS* 3.5 27.4 + - - +
43X LEU* 4.5 10.3 - - + -
50X LEU* 3.9 41.5 - - + +
51X GLU 2.9 33.7 - - - +
52X ASP* 4.2 0.8 + - - -
54X ARG* 3.2 15.6 + - + +
55X THR 4.7 4.7 - - - +
56X LEU* 3.7 27.8 - - + -
59X TYR* 4.8 1.3 - - + -
61X ILE* 4.0 4.7 - - + -
67X LEU* 4.7 3.1 - - + -
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Residues in contact with GLU 24 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22X THR* 2.7 14.4 + - - +
23X ILE* 1.3 75.3 - - - +
25X ASN* 1.3 67.3 + - - +
27X LYS* 3.9 8.7 - - - +
28X ALA* 3.8 13.2 + - - +
38X PRO* 5.0 8.3 - - + +
52X ASP* 3.4 42.3 - - + +
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Residues in contact with ASN 25 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X ASP* 5.0 11.6 + - + +
22X THR* 2.5 51.2 + - - +
24X GLU* 1.3 81.0 + - - +
26X VAL* 1.3 60.3 + - - +
27X LYS 2.9 6.3 + - - -
28X ALA* 3.1 22.6 + - + +
29X LYS* 3.3 13.2 + - - +
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Residues in contact with VAL 26 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3X ILE* 4.2 23.3 - - + -
5X VAL* 4.7 2.7 - - + -
15X LEU* 3.9 14.6 - - + +
17X VAL* 5.1 9.0 - - + -
21X ASP* 5.4 3.8 - - + +
22X THR 4.1 3.1 - - - +
23X ILE* 3.0 31.8 + - + +
25X ASN* 1.3 77.5 - - + +
27X LYS* 1.3 56.5 + - - +
29X LYS* 3.7 2.9 + - - +
30X ILE* 3.0 36.0 + - + +
43X LEU* 3.8 22.2 - - + -
56X LEU* 3.9 24.9 - - + -
67X LEU* 4.8 2.7 - - + -
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Residues in contact with LYS 27 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23X ILE* 3.6 23.1 - - - +
24X GLU 3.9 8.1 - - - +
25X ASN 2.9 0.2 - - - -
26X VAL* 1.3 76.9 - - - +
28X ALA* 1.3 54.9 + - - +
29X LYS 3.0 2.0 - - - -
30X ILE* 4.3 0.7 - - - +
31X GLN* 2.7 37.4 + - - +
38X PRO* 3.9 32.3 + - + +
41X GLN* 3.3 59.6 + - + +
42X ARG* 4.3 7.3 - - - +
43X LEU* 4.5 16.6 - - + +
50X LEU 5.3 3.2 + - - -
52X ASP* 2.7 33.8 + - - +
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Residues in contact with ALA 28 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24X GLU 3.8 5.8 + - - +
25X ASN* 3.1 24.9 + - - +
27X LYS* 1.3 77.3 - - - +
29X LYS* 1.3 50.8 + - - +
31X GLN* 3.1 27.1 - - - +
32X ASP* 2.7 25.6 - - - +
38X PRO* 4.4 6.2 - - + +
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Residues in contact with LYS 29 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15X LEU* 3.7 36.3 - - + -
16X GLU* 2.4 40.1 + - - +
17X VAL* 4.4 6.6 - - + +
25X ASN 3.3 11.0 + - - +
26X VAL* 4.0 5.2 - - - +
27X LYS 3.0 0.6 - - - -
28X ALA* 1.3 75.4 - - - +
30X ILE* 1.3 61.9 + - - +
31X GLN 2.9 6.1 + - - -
32X ASP* 3.1 18.7 + - + +
33X LYS* 3.4 12.6 + - + +
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Residues in contact with ILE 30 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5X VAL* 3.4 37.9 - - + -
13X ILE* 3.7 24.5 - - + -
15X LEU* 3.4 18.6 - - + -
26X VAL* 3.0 23.6 + - + +
27X LYS 3.2 4.4 + - - +
29X LYS* 1.3 75.5 - - - +
31X GLN* 1.3 56.7 + - - +
32X ASP 3.2 0.7 - - - -
33X LYS* 4.0 6.3 - - - +
34X GLU* 2.9 31.2 + - + +
36X ILE* 4.4 1.4 + - + -
41X GLN* 3.7 26.2 - - - +
43X LEU* 4.2 15.5 - - + -
69X LEU* 3.9 10.3 - - + -
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Residues in contact with GLN 31 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27X LYS 2.7 18.7 + - - +
28X ALA* 3.1 16.2 - - - +
29X LYS 2.9 0.6 - - - -
30X ILE* 1.3 78.0 - - - +
32X ASP* 1.3 66.8 + - - +
35X GLY* 3.2 17.2 - - - -
36X ILE 3.6 28.0 - - - +
37X PRO* 3.7 9.2 - - + +
38X PRO* 3.0 30.6 - - + +
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Residues in contact with ASP 32 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28X ALA 2.7 22.5 - - - +
29X LYS* 3.1 10.4 + - + +
31X GLN* 1.3 88.2 - - - +
33X LYS* 1.3 66.1 - - + +
34X GLU 3.3 1.5 - - - -
35X GLY* 4.2 2.9 + - - +
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Residues in contact with LYS 33 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11X LYS* 5.0 0.5 + - - -
13X ILE* 3.5 30.7 - - + +
14X THR* 2.7 35.4 + - - +
15X LEU* 4.1 9.0 - - + +
29X LYS* 3.4 11.7 + - + +
30X ILE 4.3 2.0 - - - +
32X ASP* 1.3 81.8 - - - +
34X GLU* 1.3 69.3 + - + +
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Residues in contact with GLU 34 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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940C LYS* 5.4 0.7 + - - +
943C MET* 3.8 25.2 - - - +
7X THR* 3.8 12.5 - - - +
11X LYS* 2.8 35.8 + - - +
13X ILE* 3.3 35.9 - - + +
30X ILE* 2.9 17.6 + - + +
32X ASP 5.0 0.2 - - - -
33X LYS* 1.3 93.6 - - + +
35X GLY* 1.3 61.1 + - - +
36X ILE* 3.8 25.1 - - + +
69X LEU* 4.9 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