Contacts of the helix formed by residues 29 - 45 (chain B) in PDB entry 2KXH
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 ASP 29 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B VAL* 4.9 1.9 - - - +
28B ASN* 1.3 90.3 + - - +
30B ALA* 1.3 79.9 + - - +
31B PHE 3.3 0.2 - - - -
32B LYS* 3.1 5.6 + - - +
33B ASP* 2.8 30.4 + - - +
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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
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231A ALA* 3.6 20.9 - - - +
232A PHE* 3.5 18.1 - - - +
27B VAL* 3.8 24.8 - - + +
29B ASP* 1.3 85.7 + - - +
31B PHE* 1.3 58.5 + - - +
33B ASP* 3.3 8.2 - - - +
34B ALA* 2.9 24.4 + - - +
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Residues in contact with PHE 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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228A VAL* 5.0 1.3 - - + -
232A PHE* 3.3 27.6 - + + -
269A SER* 3.3 37.9 - - - -
270A MET* 5.0 1.6 - - - -
272A LEU* 3.9 24.5 - - + -
273A PHE* 4.8 4.0 - - - -
27B VAL* 3.5 32.2 + - + +
28B ASN 5.0 0.4 - - - +
29B ASP 3.3 0.6 - - - -
30B ALA* 1.3 76.3 - - - +
32B LYS* 1.3 62.6 + - + +
34B ALA* 3.0 17.0 - - + +
35B LEU* 3.1 48.7 + - + +
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Residues in contact with LYS 32 (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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28B ASN* 2.9 36.7 + - - +
29B ASP* 3.1 6.1 + - - +
31B PHE* 1.3 79.0 - - + +
33B ASP* 1.3 63.5 + - - +
34B ALA 3.1 0.2 - - - -
35B LEU* 3.3 5.8 + - + +
36B GLN* 3.0 39.3 + - + +
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Residues in contact with ASP 33 (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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231A ALA* 4.0 7.5 - - + +
29B ASP 2.8 13.5 + - - +
30B ALA* 3.3 13.5 - - - +
32B LYS* 1.3 76.6 - - - +
34B ALA* 1.3 63.3 + - - +
36B GLN* 3.5 10.6 + - - +
37B ARG* 2.8 63.2 + - - +
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Residues in contact with ALA 34 (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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227A SER* 3.8 1.2 - - - -
228A VAL* 3.3 26.0 - - + +
231A ALA* 3.5 10.9 - - + +
232A PHE* 3.0 35.0 - - + -
30B ALA 2.9 5.9 + - - -
31B PHE* 3.0 14.4 - - + +
33B ASP* 1.3 78.2 - - - +
35B LEU* 1.3 51.0 + - - +
37B ARG* 3.2 5.9 - - - +
38B ALA* 2.7 30.1 + - - +
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Residues in contact with LEU 35 (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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228A VAL* 3.5 19.3 - - + -
272A LEU 5.5 3.8 - - - +
273A PHE* 4.1 9.2 - - + -
274A ASP* 5.5 6.3 - - + +
31B PHE* 3.1 56.7 + - + +
32B LYS* 3.3 6.2 + - + +
34B ALA* 1.3 74.7 - - - +
36B GLN* 1.3 61.0 + - + +
37B ARG 3.1 1.1 - - - -
38B ALA* 3.3 9.9 - - + -
39B ARG* 2.8 31.0 + - + +
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Residues in contact with GLN 36 (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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32B LYS* 3.0 27.9 + - + +
33B ASP* 3.9 9.1 - - - +
34B ALA 3.4 0.2 - - - -
35B LEU* 1.3 76.0 - - + +
37B ARG* 1.3 60.0 + - + +
39B ARG* 5.2 0.6 - - - +
40B GLN* 3.1 25.7 + - - +
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Residues in contact with ARG 37 (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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227A SER* 3.2 42.7 + - - +
230A GLU* 4.7 15.0 + - - +
231A ALA* 3.8 19.3 - - - +
33B ASP* 2.8 49.8 + - - +
34B ALA 3.2 2.5 - - - +
35B LEU 3.1 0.2 - - - -
36B GLN* 1.3 79.4 - - + +
38B ALA* 1.3 51.9 + - - +
40B GLN* 3.1 17.5 - - - +
41B ILE* 2.8 39.2 + - - +
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Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A VAL* 3.4 4.5 - - + -
273A PHE* 3.2 29.2 - - + -
274A ASP 5.3 2.2 - - - +
275A LEU* 3.9 4.7 - - + +
34B ALA 2.7 18.8 + - - +
35B LEU* 3.0 20.6 + - + +
37B ARG* 1.3 74.2 - - - +
39B ARG* 1.3 60.3 + - + +
41B ILE* 2.7 32.6 - - - +
42B ALA* 3.2 9.0 + - - +
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Residues in contact with ARG 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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274A ASP* 2.7 46.1 + - - +
276A GLY* 4.2 10.8 - - - +
277A GLY* 4.1 10.3 - - - +
35B LEU* 2.8 16.7 + - + +
36B GLN 5.2 0.4 - - - +
38B ALA* 1.3 73.8 - - + +
40B GLN* 1.3 56.7 + - - +
41B ILE 3.2 0.2 - - - -
42B ALA* 3.4 13.3 - - + +
43B ALA* 2.7 36.1 + - - +
47B GLY 5.7 2.6 + - - -
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Residues in contact with GLN 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 GLN 3.1 17.6 + - - +
37B ARG* 3.1 25.0 - - - +
39B ARG* 1.3 76.3 - - - +
41B ILE* 1.3 64.9 + - + +
43B ALA* 3.1 21.9 + - - +
44B LYS* 3.4 9.4 + - - +
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Residues in contact with ILE 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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220A LEU* 3.4 26.9 - - + +
224A ASP* 2.9 48.9 - - + +
227A SER* 3.0 19.5 - - - +
273A PHE* 3.8 7.4 - - + -
37B ARG* 2.8 14.9 + - - +
38B ALA* 2.7 38.8 - - - +
40B GLN* 1.3 77.0 - - + +
42B ALA* 1.3 57.1 + - - +
44B LYS* 3.0 28.6 - - - +
45B ILE* 3.2 15.6 - - - +
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Residues in contact with ALA 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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220A LEU* 3.5 13.2 - - + -
275A LEU* 4.2 11.7 - - + -
276A GLY* 5.2 3.8 - - - +
38B ALA 3.2 13.6 + - - +
39B ARG* 3.2 19.0 + - + +
41B ILE* 1.3 79.2 - - - +
43B ALA* 1.3 63.1 + - - +
44B LYS 3.3 0.2 - - - -
45B ILE 3.1 14.8 - - - +
46B GLY* 4.8 1.6 - - - -
47B GLY* 2.8 36.1 + - - +
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Residues in contact with ALA 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 ARG 2.7 20.3 + - - +
40B GLN* 3.1 11.8 + - - +
42B ALA* 1.3 75.7 - - - +
44B LYS* 1.3 61.5 + - - +
47B GLY 3.5 10.5 - - - +
48B ASP* 3.7 27.4 + - - +
49B ALA* 5.1 10.1 - - + +
51B THR 5.5 2.9 - - - +
52B SER* 5.3 15.0 - - - +
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Residues in contact with LYS 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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221A SER* 5.8 0.2 - - - -
224A ASP* 2.6 38.2 + - - -
40B GLN 3.4 5.9 + - - +
41B ILE* 3.0 30.3 - - - +
43B ALA* 1.3 82.0 - - - +
45B ILE* 1.3 79.3 + - + +
46B GLY 4.3 0.2 - - - -
48B ASP* 6.0 0.3 - - - +
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Residues in contact with ILE 45 (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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219A ASP* 3.2 47.4 - - + +
220A LEU* 3.5 7.7 - - - +
221A SER* 4.0 5.2 - - - +
224A ASP* 3.4 20.2 - - - +
41B ILE 3.2 12.2 + - - +
42B ALA* 3.1 18.5 - - - +
44B LYS* 1.3 99.1 - - + +
46B GLY* 1.3 57.8 + - - +
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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