Contacts of the helix formed by residues 22 - 46 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B SER* 1.4 67.0 + - - +
24B ASP* 3.2 2.7 - - - -
25B PRO* 3.9 30.3 - - - +
26B LEU* 3.1 38.2 + - - +
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Residues in contact with SER 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B SER* 1.4 75.1 - - - +
24B ASP* 1.4 60.1 + - - +
26B LEU* 4.6 7.7 - - - +
27B VAL* 3.7 23.0 + - - +
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Residues in contact with ASP 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B SER* 3.2 1.9 - - - -
23B SER* 1.4 75.4 - - - +
25B PRO* 1.3 74.2 - - + +
26B LEU 3.4 0.9 + - - -
27B VAL* 3.4 13.2 + - - +
28B VAL* 3.7 15.0 + - - +
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Residues in contact with PRO 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B SER* 3.7 30.3 - - - +
24B ASP* 1.3 99.4 - - + +
26B LEU* 1.4 58.6 + - + +
28B VAL* 3.5 9.6 + - + +
29B ALA* 3.0 26.9 + - - +
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Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B SER* 3.1 33.5 + - - +
23B SER* 4.6 6.7 - - - +
25B PRO* 1.4 76.3 - - + +
27B VAL* 1.4 64.6 + - + +
29B ALA* 3.2 10.7 + - + +
30B ALA* 3.1 23.9 + - - +
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Residues in contact with VAL 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B SER 3.7 15.4 + - - +
24B ASP* 3.4 9.2 + - - +
25B PRO 3.4 0.6 - - - -
26B LEU* 1.4 77.0 - - + +
28B VAL* 1.4 63.0 + - + +
30B ALA* 3.5 7.0 + - - +
31B SER* 3.0 30.0 + - - +
28D VAL* 5.3 19.7 - - + -
31D SER* 5.8 9.0 - - - -
32D ILE* 5.7 7.6 - - + -
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Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ASP* 3.7 12.2 + - - +
25B PRO* 3.5 11.1 + - + +
26B LEU 3.4 0.4 - - - -
27B VAL* 1.4 77.7 - - + +
29B ALA* 1.4 64.0 + - - +
31B SER* 3.2 9.6 + - - +
32B ILE* 3.1 39.8 + - + +
27C VAL* 5.3 18.6 - - + -
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Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PRO 3.0 14.3 + - - +
26B LEU* 3.2 17.5 + - + +
28B VAL* 1.4 77.0 - - - +
30B ALA* 1.3 58.8 + - - +
32B ILE* 3.5 13.4 + - - +
33B ILE* 3.3 27.2 + - - +
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Residues in contact with ALA 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU 3.1 15.3 + - - +
27B VAL* 3.8 8.3 - - - +
28B VAL 3.4 0.2 - - - -
29B ALA* 1.3 72.6 - - - +
31B SER* 1.3 60.7 + - - +
33B ILE* 3.4 7.4 + - - +
34B GLY 3.3 9.7 + - - -
35D ILE* 1.7 71.6 - - + +
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Residues in contact with SER 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A 308 3.9 31.0 + - - +
27B VAL* 3.0 20.2 + - - +
28B VAL* 3.2 13.5 + - - -
30B ALA* 1.3 73.8 - - - +
32B ILE* 1.4 63.1 + - - +
34B GLY* 3.3 2.8 + - - -
35B ILE* 3.2 27.7 + - - +
27C VAL* 5.7 9.6 - - - -
31C SER* 6.0 1.8 - - - -
31D SER* 6.0 1.2 - - - -
35D ILE* 3.2 4.1 - - - +
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Residues in contact with ILE 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 3.1 35.5 + - + +
29B ALA* 3.7 11.0 - - - +
31B SER* 1.4 71.4 - - - +
33B ILE* 1.3 67.1 + - + +
35B ILE* 3.4 9.0 + - - +
36B LEU* 3.1 38.5 + - + +
27C VAL* 5.7 8.1 - - + -
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Residues in contact with ILE 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ALA 3.3 14.7 + - - +
30B ALA* 3.7 11.7 - - - +
31B SER 3.3 0.4 - - - -
32B ILE* 1.3 81.4 - - + +
34B GLY* 1.3 56.3 + - - +
36B LEU* 3.3 15.3 + - + +
37B HIS* 3.0 26.7 + - - +
35D ILE* 5.1 2.5 - - + -
38D LEU* 4.2 21.1 - - + -
39D ILE* 4.7 23.1 - - + -
42D ILE* 4.9 12.1 - - + +
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Residues in contact with GLY 34 (chain B).
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 3.3 11.4 + - - -
31B SER 3.3 5.1 + - - -
33B ILE* 1.3 75.3 - - - +
35B ILE* 1.4 58.5 + - - +
37B HIS 3.6 0.3 + - - -
38B LEU* 2.9 37.5 + - - +
35D ILE* 4.8 0.2 - - - -
38D LEU* 3.0 33.1 - - - +
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Residues in contact with ILE 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A 308 5.2 4.5 - - + -
31B SER* 3.2 15.2 + - - +
32B ILE* 3.7 10.1 - - - +
33B ILE 3.3 0.2 - - - -
34B GLY* 1.4 73.1 - - - +
36B LEU* 1.4 60.7 + - + +
38B LEU* 3.3 16.4 + - + +
39B ILE* 3.0 52.0 + - + +
30C ALA* 1.7 73.8 - - + +
31C SER* 3.2 5.2 - - - +
33C ILE* 4.8 4.5 - - + -
34C GLY* 4.2 0.9 - - - +
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Residues in contact with LEU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ILE* 3.1 31.7 + - + +
33B ILE* 3.3 15.2 + - + +
35B ILE* 1.4 75.8 - - + +
37B HIS* 1.4 61.7 + - - +
39B ILE* 3.5 18.5 + - + +
40B ALA* 3.2 22.7 + - - +
42D ILE* 5.6 4.3 - - + -
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Residues in contact with HIS 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE 3.0 10.9 + - - +
36B LEU* 1.4 76.1 - - - +
38B LEU* 1.4 59.0 + - + +
40B ALA 3.5 1.4 + - - -
41B TRP* 3.3 20.7 + - + +
37C HIS* 5.7 4.5 - + - -
37D HIS* 5.0 6.7 - + - -
38D LEU* 2.6 46.7 - - + +
41D TRP* 2.0 100.6 + + + -
42D ILE* 4.5 7.1 - - + +
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Residues in contact with LEU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A 308 4.6 8.7 - - + -
34B GLY* 2.9 31.3 + - - +
35B ILE* 3.3 13.2 + - + +
37B HIS* 1.4 71.8 - - + +
39B ILE* 1.3 59.9 + - - +
41B TRP* 3.3 3.1 + - - +
42B ILE* 3.0 34.1 + - - +
33C ILE* 4.2 12.6 - - + -
34C GLY* 3.0 34.3 - - - +
37C HIS* 2.7 48.0 + - + +
38C LEU* 4.8 7.9 - - + +
38D LEU* 5.0 7.0 - - + -
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Residues in contact with ILE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ILE* 3.0 44.1 + - + +
36B LEU* 3.6 19.5 - - + +
38B LEU* 1.3 74.5 - - - +
40B ALA* 1.4 62.8 + - - +
42B ILE* 3.4 8.5 + - - +
43B LEU* 3.0 26.3 + - + +
33C ILE* 4.7 19.5 - - + -
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Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LEU 3.2 11.8 + - - +
37B HIS* 3.7 8.1 - - - +
39B ILE* 1.4 79.2 - - - +
41B TRP* 1.3 60.2 + - - +
43B LEU* 3.3 11.9 + - - +
44B ASP* 3.0 32.1 + - - +
41D TRP* 3.8 18.4 - - + -
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Residues in contact with TRP 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B HIS* 3.3 11.4 + - + +
38B LEU 3.3 4.2 + - - +
40B ALA* 1.3 77.1 - - - +
42B ILE* 1.4 90.5 + - + +
44B ASP* 3.2 13.2 + - + +
45B ARG* 3.0 75.0 + - + +
37C HIS* 2.0 73.9 + + + -
40C ALA* 3.9 17.9 - - + -
41C TRP* 4.8 14.9 - + + -
44C ASP* 5.3 0.9 - - - -
41D TRP* 4.7 16.0 - + + -
45D ARG* 5.8 4.7 - - - +
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Residues in contact with ILE 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B LEU 3.0 22.6 + - - +
39B ILE* 3.7 7.6 - - - +
41B TRP* 1.4 101.4 - - + +
43B LEU* 1.4 62.2 + - - +
45B ARG* 3.3 7.0 + - + +
46B LEU* 3.1 26.8 + - + +
33C ILE* 4.9 12.3 - - + +
36C LEU* 5.7 2.9 - - + -
37C HIS* 4.4 12.6 - - + +
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ILE* 3.0 17.2 + - + +
40B ALA* 3.5 13.7 - - - +
42B ILE* 1.4 76.1 - - - +
44B ASP* 1.3 61.3 + - - +
46B LEU* 3.3 34.9 + - + +
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Residues in contact with ASP 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ALA* 3.0 27.5 + - - +
41B TRP* 3.2 12.1 + - + +
43B LEU* 1.3 78.0 - - - +
45B ARG* 1.4 60.5 + - + +
46B LEU* 3.5 5.4 + - - +
41D TRP* 5.3 1.2 - - - -
45D ARG* 4.2 23.3 + - - -
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Residues in contact with ARG 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B TRP* 3.0 64.9 + - + +
42B ILE* 3.3 11.6 + - + +
44B ASP* 1.4 75.4 - - + +
46B LEU* 1.3 61.7 + - - +
41C TRP* 5.7 5.3 - - - -
44C ASP* 4.3 19.5 + - - +
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Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 3.1 20.1 + - + +
43B LEU* 3.3 30.3 - - + +
44B ASP 3.3 4.6 - - - +
45B ARG* 1.3 79.3 - - - +
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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) + - + + + + + -
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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