Contacts of the helix formed by residues 24 - 41 (chain C) in PDB entry 6X0A
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C ILE 3.0 12.0 + - - +
21C ALA* 3.6 3.5 - - - -
23C ASP* 1.3 89.3 - - - +
25C PRO* 1.3 69.0 - - - +
26C ARG* 3.2 18.9 + - - +
27C ALA* 3.3 26.0 + - - +
28C ALA 3.3 6.1 + - - -
66F ASN* 4.0 15.7 + - - -
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Residues in contact with PRO 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C TRP* 3.9 20.1 - - + -
21C ALA* 3.5 24.2 - - + +
23C ASP 4.6 1.6 - - - +
24C SER* 1.3 83.8 - - - +
26C ARG* 1.3 63.1 + - + +
28C ALA* 3.2 4.9 + - - +
29C ASP* 3.2 24.4 + - - -
85F HIS* 5.8 0.9 - - + +
88F ARG* 4.8 9.2 - - - +
91F SER 5.6 5.6 - - - +
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Residues in contact with ARG 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C SER* 3.1 9.8 + - - +
25C PRO* 1.3 82.0 - - + +
27C ALA* 1.3 65.6 + - - +
29C ASP* 2.9 22.8 + - + +
30C HIS* 3.1 41.8 + - + -
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Residues in contact with ALA 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ILE* 3.9 15.6 - - + +
23C ASP* 5.2 4.3 - - - +
24C SER* 3.3 22.5 + - - +
26C ARG* 1.3 80.1 - - - +
28C ALA* 1.3 62.5 + - - +
30C HIS* 3.2 11.9 + - - +
31C PHE* 3.0 23.6 + - - +
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Residues in contact with ALA 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C TRP* 3.2 57.6 - - + +
20C ILE* 3.6 13.8 - - + +
21C ALA* 3.8 12.1 - - - +
24C SER 3.3 3.5 + - - +
25C PRO 3.2 8.0 + - - +
26C ARG 3.1 0.6 - - - -
27C ALA* 1.3 79.6 - - - +
29C ASP* 1.3 60.9 + - - +
31C PHE* 3.3 1.9 + - - +
32C LEU* 3.2 19.2 + - - +
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Residues in contact with ASP 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C TRP* 3.0 23.8 + - - +
25C PRO 3.2 11.9 + - - +
26C ARG* 2.9 14.6 + - - +
28C ALA* 1.3 77.6 - - - +
30C HIS* 1.3 65.2 + - + +
32C LEU* 3.6 2.7 + - - +
33C ASP* 3.1 33.6 + - - +
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Residues in contact with HIS 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ARG* 3.1 58.5 + - + -
27C ALA* 3.2 12.1 + - - +
29C ASP* 1.3 78.9 - - + +
31C PHE* 1.3 59.1 + - - +
33C ASP* 3.4 10.6 + - - +
34C ALA* 2.9 26.9 + - - +
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Residues in contact with PHE 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ILE* 3.6 16.2 - - + -
20C ILE* 3.5 33.7 - - + -
27C ALA 3.0 11.5 + - - +
28C ALA 4.0 2.0 - - - +
29C ASP 3.3 0.2 - - - -
30C HIS* 1.3 77.0 - - - +
32C LEU* 1.3 57.5 + - - +
34C ALA* 2.9 13.9 + - + +
35C ILE* 2.7 56.5 + - + +
64C ILE* 4.2 28.7 - - + -
65C GLY* 5.2 5.6 - - - -
67C TYR* 4.2 28.9 - + - -
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Residues in contact with LEU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU* 3.6 51.8 - - + +
14C VAL* 5.7 0.4 - - - -
16C ILE* 4.8 4.7 - - + -
17C TRP* 3.1 42.0 - - + -
28C ALA 3.2 12.3 + - - +
29C ASP* 4.1 3.4 - - - +
31C PHE* 1.3 78.2 - - + +
33C ASP* 1.3 53.1 + - - +
35C ILE* 3.1 14.0 + - + +
36C ALA* 2.7 36.1 + - - +
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Residues in contact with ASP 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ASP* 3.1 20.7 + - - +
30C HIS* 3.4 13.2 - - - +
32C LEU* 1.3 76.3 - - - +
34C ALA* 1.3 52.0 + - - +
36C ALA* 3.1 7.5 + - - +
37C GLU* 2.6 38.9 + - - +
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Residues in contact with ALA 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C HIS 2.9 12.8 + - - +
31C PHE* 2.9 20.7 + - + +
33C ASP* 1.3 75.2 - - - +
35C ILE* 1.3 60.7 + - - +
37C GLU* 3.5 11.3 + - - +
38C ARG* 3.0 23.0 + - - +
64C ILE* 3.9 19.1 - - + +
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Residues in contact with ILE 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU* 3.9 23.1 - - + -
16C ILE* 4.3 8.7 - - + -
31C PHE* 2.7 58.4 + - + +
32C LEU* 3.4 28.5 - - + +
34C ALA* 1.3 69.9 - - - +
36C ALA* 1.3 59.5 + - - +
38C ARG* 3.1 4.8 + - - +
39C ILE* 2.8 46.2 + - + +
64C ILE* 4.2 15.9 - - + -
69C ILE* 4.1 13.0 - - + -
83C ILE* 4.9 4.7 - - + -
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Residues in contact with ALA 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU 2.7 16.5 + - - +
33C ASP* 3.4 11.9 - - - +
35C ILE* 1.3 71.3 - - - +
37C GLU* 1.3 59.1 + - - +
39C ILE* 2.6 30.1 + - - +
40C LEU* 2.7 32.1 + - + +
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Residues in contact with GLU 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ASP 2.6 21.1 + - - +
34C ALA* 3.8 10.8 - - - +
36C ALA* 1.3 72.1 - - - +
38C ARG* 1.3 68.8 + - - +
40C LEU* 4.0 8.3 - - - +
41C GLN* 2.9 46.3 + - - +
64C ILE* 5.7 1.2 - - - +
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Residues in contact with ARG 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ALA 3.0 13.8 + - - +
35C ILE 3.4 9.0 - - - +
36C ALA 2.7 4.0 + - - -
37C GLU* 1.3 80.6 + - - +
39C ILE* 1.3 63.3 + - - +
41C GLN* 3.2 36.6 + - - +
42C LEU 4.1 0.5 + - - -
48C SER* 5.7 0.7 - - - -
62C LEU* 3.3 49.9 - - + +
63C THR* 3.1 34.8 + - - +
64C ILE* 4.2 13.0 - - + -
69C ILE* 4.1 13.2 - - + -
37D GLU* 2.5 44.6 + - - -
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Residues in contact with ILE 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C ILE* 4.1 19.5 - - + +
13C LEU* 5.2 7.0 - - + -
35C ILE* 2.8 33.7 + - + +
36C ALA* 2.6 16.7 + - - +
38C ARG* 1.3 72.2 - - - +
40C LEU* 1.3 61.0 + - + +
42C LEU* 2.9 32.6 + - + +
69C ILE* 3.4 32.1 - - + -
80C ILE* 3.8 37.2 - - + -
83C ILE* 5.0 5.4 - - + -
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Residues in contact with LEU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C ILE* 4.3 13.2 - - + -
36C ALA* 2.7 56.3 + - + +
37C GLU* 4.2 7.2 - - - +
39C ILE* 1.3 77.7 - - + +
41C GLN* 1.3 62.2 + - - +
42C LEU 3.2 0.7 + - - -
43C ALA* 3.3 18.1 + - - +
44C ALA* 4.4 1.0 + - - +
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Residues in contact with GLN 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C GLU* 2.9 38.9 + - - +
38C ARG* 3.2 39.2 + - - +
39C ILE 3.2 0.6 - - - -
40C LEU* 1.3 77.8 - - - +
42C LEU* 1.3 58.5 + - - +
43C ALA 3.2 0.2 - - - -
44C ALA* 3.2 8.6 + - - +
45C PHE* 2.9 39.0 + - + +
48C SER* 5.4 6.4 + - - +
62C LEU* 5.3 2.3 - - + +
41D GLN* 5.5 4.2 + - - -
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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