Contacts of the helix formed by residues 26 - 42 (chain D) in PDB entry 4F9K
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 GLY 26 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D VAL 3.0 11.5 + - - -
23D GLN 3.8 6.1 - - - -
24D LEU 3.1 6.2 + - - -
25D HIS* 1.3 77.2 - - - +
27D ILE* 1.3 64.4 + - - +
28D GLN* 3.2 3.9 + - - -
29D GLN* 3.4 10.1 + - - +
30D VAL* 3.1 20.5 + - - +
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Residues in contact with ILE 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ILE* 5.2 4.3 - - + -
38C LEU* 3.9 26.5 - - + -
46C PRO* 4.0 12.1 - - + -
47C MSE 3.7 22.4 - - + -
50C LEU* 5.5 1.8 - - + -
21D TYR* 4.3 5.8 - - + +
22D VAL* 3.1 33.6 + - + -
25D HIS* 3.6 30.3 - - + +
26D GLY* 1.3 76.8 - - - +
28D GLN* 1.3 58.2 + - - +
30D VAL* 3.0 22.0 + - + +
31D LEU* 3.1 34.9 + - + +
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Residues in contact with GLN 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D VAL* 3.6 22.6 - - + +
26D GLY 3.2 1.4 - - - -
27D ILE* 1.3 76.6 - - - +
29D GLN* 1.3 59.1 + - - +
31D LEU* 3.6 9.6 + - + +
32D LYS* 3.4 24.4 + - + +
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Residues in contact with GLN 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D GLY* 3.4 9.0 + - - +
28D GLN* 1.3 72.4 - - - +
30D VAL* 1.3 65.6 + - - +
31D LEU 3.1 2.8 + - - -
32D LYS* 3.8 23.8 - - - +
33D ASP* 3.0 47.5 + - - +
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Residues in contact with VAL 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C MSE 3.7 33.4 - - + -
50C LEU* 5.1 2.7 - - + -
25D HIS 4.5 2.0 - - - +
26D GLY 3.1 17.3 + - - +
27D ILE* 3.0 19.2 + - + +
29D GLN* 1.3 76.6 - - - +
31D LEU* 1.3 66.6 + - + +
33D ASP* 3.7 6.2 - - - +
34D CYS* 3.2 21.7 + - - -
53D HIS* 4.9 2.9 + - - +
54D PHE* 3.8 29.8 - - + -
57D LEU* 6.1 2.0 - - + -
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Residues in contact with LEU 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C LEU* 4.9 21.0 - - + +
34C CYS* 4.5 21.1 - - - -
35C ILE* 3.6 30.1 - - + -
50C LEU* 5.6 2.5 - - + -
27D ILE* 3.1 36.2 + - + +
28D GLN* 3.6 7.6 + - + +
29D GLN 3.1 0.2 - - - -
30D VAL* 1.3 86.2 - - + +
32D LYS* 1.3 56.3 + - - +
33D ASP 3.1 1.3 - - - -
34D CYS* 2.9 8.4 + - + +
35D ILE* 2.8 40.8 + - + +
54D PHE* 5.2 8.5 - - + -
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Residues in contact with LYS 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D GLN* 3.4 16.6 + - + +
29D GLN* 3.8 23.6 - - - +
31D LEU* 1.3 74.5 - - - +
33D ASP* 1.3 52.1 + - - +
35D ILE* 3.2 31.3 - - + +
36D VAL* 2.8 72.1 + - + +
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Residues in contact with ASP 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D GLN* 3.0 39.6 + - - +
30D VAL* 3.7 7.1 - - - +
31D LEU 3.1 0.6 - - - -
32D LYS* 1.3 76.6 - - - +
34D CYS* 1.3 60.5 + - - +
36D VAL* 4.1 9.3 - - - +
37D HIS* 3.4 21.8 + - - +
53D HIS* 4.0 10.1 - - + +
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Residues in contact with CYS 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C LEU* 5.0 13.5 - - + -
30D VAL 3.2 11.9 + - - +
31D LEU* 2.9 17.8 + - + +
33D ASP* 1.3 74.2 - - - +
35D ILE* 1.3 67.3 + - - +
36D VAL 3.1 1.7 + - - -
37D HIS* 3.2 1.6 + - - +
38D LEU* 2.9 31.2 + - + +
49D PHE* 5.1 1.0 - - - -
50D LEU* 4.4 14.6 - - + -
53D HIS* 3.6 21.5 - - - -
54D PHE* 3.3 37.9 - - - -
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Residues in contact with ILE 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LYS* 5.0 13.7 - - + +
27C ILE* 6.1 2.9 - - + -
31C LEU* 4.4 18.3 - - + +
31D LEU* 2.8 23.5 + - + +
32D LYS* 3.2 41.5 - - + +
34D CYS* 1.3 71.4 - - - +
36D VAL* 1.3 60.7 + - + +
38D LEU* 3.6 7.3 - - - +
39D CYS* 3.0 44.9 + - - -
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Residues in contact with VAL 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D LYS* 2.8 43.2 + - - +
33D ASP* 4.4 9.2 - - - +
35D ILE* 1.3 76.4 - - + +
37D HIS* 1.3 67.8 + - - +
39D CYS* 3.0 10.5 + - + +
40D ILE* 3.0 35.4 + - + +
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Residues in contact with HIS 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ASP 3.4 18.8 + - - +
34D CYS 3.2 3.8 + - - +
36D VAL* 1.3 78.8 - - - +
38D LEU* 1.3 62.4 + - - +
40D ILE* 3.4 17.7 - - + +
41D SER* 3.0 32.2 + - - -
49D PHE* 3.2 24.9 - + + -
53D HIS* 3.3 23.6 + - + +
56D LYS* 3.1 30.7 - - + -
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Residues in contact with LEU 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C CYS* 4.8 0.7 - - - -
21C TYR* 4.1 19.0 - - + +
27C ILE* 4.2 28.7 - - + -
31C LEU* 5.7 2.5 - - + -
34D CYS* 2.9 19.8 + - + +
35D ILE* 3.6 6.1 - - - +
37D HIS* 1.3 76.4 - - - +
39D CYS* 1.3 55.9 + - - +
42D LYS* 2.6 37.8 + - - +
43D PRO* 3.6 21.3 - - + -
46D PRO* 4.5 5.8 - - + -
49D PHE* 3.3 31.7 - - + -
50D LEU* 3.9 28.5 - - + -
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Residues in contact with CYS 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LYS* 4.6 7.6 - - - -
17C GLY 4.9 0.9 - - - +
18C CYS* 2.0 51.6 - - + -
22C VAL* 5.5 2.2 - - - -
35D ILE* 3.0 35.1 + - - +
36D VAL* 3.0 14.3 + - + +
38D LEU* 1.3 74.7 - - - +
40D ILE* 1.3 60.8 + - + +
42D LYS* 3.1 30.4 + - - +
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Residues in contact with ILE 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D VAL* 3.0 24.4 + - + +
37D HIS* 3.4 28.5 - - + +
39D CYS* 1.3 74.3 - - + +
41D SER* 1.3 73.1 + - - +
42D LYS* 4.5 2.1 - - - +
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Residues in contact with SER 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D HIS* 3.0 26.2 + - - -
40D ILE* 1.3 80.6 - - - +
42D LYS* 1.3 72.6 + - - +
43D PRO* 3.3 3.6 - - - +
49D PHE* 3.4 28.8 - - - -
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Residues in contact with LYS 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B GLU* 3.7 21.3 + - - +
17C GLY 3.5 25.1 + - - -
18C CYS* 4.0 12.1 - - - +
21C TYR* 3.6 38.6 - - + -
38D LEU 2.6 18.0 + - - +
39D CYS 3.1 24.7 + - - +
40D ILE 4.5 2.2 - - - +
41D SER* 1.3 73.8 - - - +
43D PRO* 1.3 72.7 - - - +
44D GLU 3.7 0.5 + - - -
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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