Contacts of the helix formed by residues 22 - 46 (chain D) in PDB entry 2KAD
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 22 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D SER* 1.4 66.2 + - - +
24D ASP* 3.2 2.2 - - - -
25D PRO* 3.9 30.3 - - - +
26D LEU* 3.1 39.4 + - - +
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Residues in contact with SER 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D SER* 1.4 75.3 - - - +
24D ASP* 1.4 58.3 + - - +
26D LEU* 4.6 7.3 - - - +
27D VAL* 3.7 23.6 + - - +
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Residues in contact with ASP 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D SER* 3.2 1.2 - - - -
23D SER* 1.4 76.0 - - - +
25D PRO* 1.3 77.1 - - + +
26D LEU 3.4 0.5 + - - -
27D VAL* 3.4 13.6 + - - +
28D VAL* 3.7 14.6 + - - +
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Residues in contact with PRO 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D SER* 3.7 30.5 - - - +
24D ASP* 1.3 99.3 - - + +
26D LEU* 1.4 58.6 + - + +
28D VAL* 3.5 9.8 + - + +
29D ALA* 3.0 27.1 + - - +
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Residues in contact with LEU 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D SER* 3.1 32.7 + - - +
23D SER* 4.6 7.2 - - - +
24D ASP 3.4 0.2 + - - -
25D PRO* 1.4 75.3 - - + +
27D VAL* 1.4 62.8 + - + +
29D ALA* 3.2 10.0 + - + +
30D ALA* 3.1 24.6 + - - +
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Residues in contact with VAL 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 5.3 20.6 - - + -
31A SER* 5.8 7.9 - - - -
32A ILE* 5.7 8.3 - - + -
23D SER 3.7 14.8 + - - +
24D ASP* 3.4 9.2 + - - +
25D PRO 3.4 0.8 - - - -
26D LEU* 1.4 77.0 - - + +
28D VAL* 1.4 63.2 + - + +
30D ALA* 3.5 6.5 + - - +
31D SER* 3.0 30.3 + - - +
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Residues in contact with VAL 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL* 5.3 18.8 - - + -
24D ASP* 3.7 11.8 + - - +
25D PRO* 3.5 10.9 + - + +
26D LEU 3.4 0.4 - - - -
27D VAL* 1.4 76.6 - - + +
29D ALA* 1.4 63.4 + - - +
31D SER* 3.2 9.2 + - - +
32D ILE* 3.1 40.1 + - + +
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Residues in contact with ALA 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D PRO 3.0 14.7 + - - +
26D LEU* 3.2 18.1 + - + +
28D VAL* 1.4 75.5 - - - +
30D ALA* 1.3 58.9 + - - +
32D ILE* 3.5 13.1 + - - +
33D ILE* 3.3 28.5 + - + +
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Residues in contact with ALA 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ILE* 6.2 0.2 - - - -
35A ILE* 1.7 71.7 - - + +
26D LEU 3.1 15.3 + - - +
27D VAL* 3.8 7.6 - - - +
28D VAL 3.4 0.2 - - - -
29D ALA* 1.3 72.8 - - - +
31D SER* 1.3 59.7 + - - +
33D ILE* 3.4 5.8 + - - +
34D GLY 3.3 9.9 + - - -
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Residues in contact with SER 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A 308 3.8 33.2 + - - +
31A SER* 6.0 0.3 - - - -
35A ILE* 3.2 4.6 - - - +
27B VAL* 5.8 9.0 - - - -
31B SER* 6.0 1.1 - - - -
27D VAL* 3.0 19.5 + - - +
28D VAL* 3.2 12.6 + - - -
30D ALA* 1.3 72.5 - - - +
32D ILE* 1.4 63.7 + - - +
34D GLY* 3.3 3.3 + - - +
35D ILE* 3.2 27.5 + - - +
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Residues in contact with ILE 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL* 5.7 8.3 - - + -
28D VAL* 3.1 35.5 + - + +
29D ALA* 3.7 11.7 - - - +
31D SER* 1.4 72.6 - - - +
33D ILE* 1.3 67.1 + - + +
35D ILE* 3.4 9.3 + - - +
36D LEU* 3.1 37.9 + - + +
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Residues in contact with ILE 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 5.1 2.0 - - + -
38A LEU* 4.2 19.7 - - + -
39A ILE* 4.6 25.4 - - + +
42A ILE* 4.9 11.5 - - + +
29D ALA* 3.3 14.8 + - + +
30D ALA* 3.7 11.4 - - - +
31D SER 3.3 0.4 - - - -
32D ILE* 1.3 80.7 - - + +
34D GLY* 1.4 56.5 + - - +
36D LEU* 3.3 14.7 + - + +
37D HIS* 3.0 27.4 + - - +
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Residues in contact with GLY 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A 308 4.5 6.7 - - - -
38A LEU* 3.0 33.9 - - - +
30D ALA 3.3 11.6 + - - -
31D SER 3.3 5.3 + - - -
33D ILE* 1.4 74.8 - - - +
35D ILE* 1.3 59.1 + - - +
37D HIS 3.6 0.3 + - - -
38D LEU* 2.9 37.1 + - - +
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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
----------------------------------------------------------
1A 308 5.1 5.8 - - + -
30B ALA* 1.7 74.5 - - + +
31B SER* 3.2 4.9 - - - +
33B ILE* 4.8 4.9 - - + +
34B GLY* 4.2 0.9 - - - +
31D SER* 3.2 14.7 + - - +
32D ILE* 3.7 10.1 - - - +
33D ILE 3.3 0.2 - - - -
34D GLY* 1.3 72.7 - - - +
36D LEU* 1.4 60.2 + - + +
38D LEU* 3.3 16.0 + - + +
39D ILE* 3.0 52.2 + - + +
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Residues in contact with LEU 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE* 5.6 3.6 - - + -
32D ILE* 3.1 30.6 + - + +
33D ILE* 3.3 14.6 + - + +
35D ILE* 1.4 76.2 - - + +
37D HIS* 1.4 62.8 + - - +
39D ILE* 3.5 18.4 + - + +
40D ALA* 3.2 22.9 + - - +
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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
----------------------------------------------------------
37A HIS* 5.0 6.7 - + - -
38A LEU* 2.6 48.6 - - + +
41A TRP* 2.0 99.1 + + + -
42A ILE* 4.4 7.3 - - + +
37B HIS* 5.6 5.0 - + - -
33D ILE 3.0 11.6 + - - +
34D GLY 3.8 0.2 - - - +
35D ILE 3.4 0.2 - - - -
36D LEU* 1.4 77.0 - - - +
38D LEU* 1.4 58.7 + - - +
40D ALA 3.5 1.2 + - - -
41D TRP* 3.3 20.7 + - + +
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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
----------------------------------------------------------
1A 308 4.9 9.2 - - + -
38A LEU* 5.0 6.5 - - + -
33B ILE* 4.2 13.0 - - + -
34B GLY* 3.0 34.8 - - - +
37B HIS* 2.6 48.6 + - + +
38B LEU* 4.8 7.0 - - + +
34D GLY* 2.9 32.0 + - - +
35D ILE* 3.7 12.3 - - + +
37D HIS* 1.4 72.0 - - + +
39D ILE* 1.4 59.5 + - - +
41D TRP* 3.3 3.1 + - - +
42D ILE* 3.0 34.1 + - - +
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Residues in contact with ILE 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 4.7 20.2 - - + -
35D ILE* 3.0 43.3 + - + +
36D LEU* 3.6 18.6 - - + +
37D HIS 3.4 0.2 - - - -
38D LEU* 1.4 75.3 - - - +
40D ALA* 1.4 62.7 + - - +
42D ILE* 3.4 8.1 + - - +
43D LEU* 3.0 26.5 + - + +
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Residues in contact with ALA 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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41A TRP* 3.9 17.3 - - + -
42A ILE* 6.3 0.2 - - + -
36D LEU 3.2 11.2 + - - +
37D HIS 3.7 8.1 - - - +
38D LEU 3.4 0.2 - - - -
39D ILE* 1.4 78.9 - - - +
41D TRP* 1.3 60.2 + - - +
43D LEU* 3.3 11.2 + - - +
44D ASP* 3.0 31.8 + - - +
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Residues in contact with TRP 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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41A TRP* 4.7 14.9 - + + -
45A ARG* 5.8 4.5 - - - +
37B HIS* 2.0 74.1 + + + -
40B ALA* 3.8 18.2 - - + -
41B TRP* 4.8 14.5 - + + -
44B ASP* 5.3 1.3 - - - -
37D HIS* 3.3 9.8 + - + +
38D LEU 3.3 3.8 + - - +
40D ALA* 1.3 77.7 - - - +
42D ILE* 1.4 90.1 + - + +
44D ASP* 3.2 12.5 + - + +
45D ARG* 3.0 73.2 + - + +
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Residues in contact with ILE 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 4.9 11.7 - - + +
36B LEU* 5.6 3.4 - - + -
37B HIS* 4.5 12.6 - - + +
38D LEU 3.0 22.4 + - - +
39D ILE* 3.7 7.4 - - - +
41D TRP* 1.4 101.6 - - + +
43D LEU* 1.4 61.9 + - - +
45D ARG* 3.3 7.4 + - + +
46D LEU* 3.1 26.5 + - + +
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Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D ILE* 3.0 17.9 + - + +
40D ALA* 3.3 14.6 + - - +
42D ILE* 1.4 75.4 - - - +
44D ASP* 1.3 62.5 + - - +
46D LEU* 3.3 34.6 + - + +
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Residues in contact with ASP 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TRP* 5.3 1.7 - - - -
45A ARG* 4.3 22.3 + - - +
40D ALA* 3.0 27.5 + - - +
41D TRP* 3.2 11.7 + - + +
43D LEU* 1.3 78.0 - - - +
45D ARG* 1.4 61.6 + - + +
46D LEU* 3.5 5.4 + - - +
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Residues in contact with ARG 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B TRP* 5.8 4.9 - - - -
44B ASP* 4.2 20.3 + - - +
41D TRP* 3.0 64.5 + - + +
42D ILE* 3.3 11.0 + - + +
44D ASP* 1.4 76.7 - - + +
46D LEU* 1.3 61.3 + - - +
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Residues in contact with LEU 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ILE* 3.1 18.7 + - + +
43D LEU* 3.3 30.1 - - + +
44D ASP 3.3 5.5 - - - +
45D ARG* 1.3 79.7 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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