Contacts of the helix formed by residues 43 - 65 (chain B) in PDB entry 1KKC
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 LYS 43 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ASN* 3.4 45.3 - - + +
39B LEU* 2.8 35.2 + - + +
42B LYS* 1.3 82.9 - - + +
44B HIS* 1.3 60.7 + - - +
45B HIS 3.5 0.4 - - - -
46B GLN* 3.4 1.9 + - - +
47B THR* 2.9 37.3 + - - +
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Residues in contact with HIS 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A GLU* 3.9 4.3 - - - -
181A TYR* 2.7 36.8 + + - -
186A ASN* 3.6 25.6 - - + +
39B LEU 3.1 15.6 + - - -
40B HIS* 3.4 25.4 - - + +
43B LYS* 1.3 78.7 - - - +
45B HIS* 1.3 64.7 + - - +
47B THR* 3.2 8.9 + - - -
48B TYR* 3.1 35.3 + - + -
178B HIS* 3.6 39.2 + + + +
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Residues in contact with HIS 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 3.4 8.2 - - + +
19B PRO* 3.6 19.5 - - + -
40B HIS 2.9 17.6 + - - +
41B HIS* 3.4 14.6 - - - +
43B LYS 3.5 0.2 - - - -
44B HIS* 1.3 73.7 - - - +
46B GLN* 1.3 64.2 + - - +
48B TYR* 3.0 9.3 + - + +
49B VAL* 3.0 28.7 + - + +
84B GLY 4.5 1.1 - - - -
85B HIS* 3.0 35.3 + + - -
88B HIS* 3.6 13.8 - - + +
89B SER* 3.5 24.4 + - - -
92B TRP* 2.8 32.3 + - + -
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Residues in contact with GLN 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 3.3 38.6 - - - +
41B HIS 3.3 5.3 + - - +
42B LYS 3.0 28.9 - - - +
43B LYS 3.6 1.8 - - - +
44B HIS 3.3 0.2 - - - -
45B HIS* 1.3 76.8 - - - +
47B THR* 1.3 59.8 + - - +
49B VAL* 3.0 12.2 + - - +
50B ASN* 2.9 65.3 + - - +
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Residues in contact with THR 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LYS* 2.9 25.5 + - - +
44B HIS* 3.4 7.6 - - - -
45B HIS 3.2 0.2 - - - -
46B GLN* 1.3 77.2 - - - +
48B TYR* 1.3 65.9 + - + +
50B ASN* 3.2 9.3 + - + +
51B GLY* 2.8 27.9 + - - -
80B PHE* 6.5 0.4 - - + -
81B ASN* 3.9 3.2 + - - +
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Residues in contact with TYR 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B HIS* 3.1 31.9 + - + -
45B HIS* 3.0 7.9 + - - +
47B THR* 1.3 83.4 - - + +
49B VAL* 1.3 57.9 + - - +
52B LEU* 2.9 30.7 + - - +
80B PHE* 3.5 27.3 - + - -
81B ASN* 3.3 38.2 - - - +
84B GLY* 3.9 10.5 - - - -
85B HIS* 4.0 9.6 - - - +
88B HIS* 3.4 35.2 - + - -
161B GLN* 3.1 22.9 + - + -
176B TRP* 3.5 21.0 - - - -
178B HIS* 4.1 6.2 - + - -
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Residues in contact with VAL 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TYR* 3.5 28.9 - - + +
17B THR* 3.8 13.9 - - - -
18B LEU* 3.9 15.5 - - + +
45B HIS* 3.0 36.8 + - + +
46B GLN* 3.2 17.5 - - - +
48B TYR* 1.3 74.9 - - - +
50B ASN* 1.3 65.9 + - - +
52B LEU* 3.4 6.7 + - - +
53B ASN* 3.1 30.2 + - - +
85B HIS* 3.7 20.6 - - + +
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Residues in contact with ASN 50 (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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46B GLN* 2.9 49.3 + - - +
47B THR* 3.7 6.8 - - + +
49B VAL* 1.3 78.3 - - - +
51B GLY* 1.3 64.6 + - - +
52B LEU 3.3 0.2 + - - -
53B ASN* 3.4 9.7 + - - +
54B ALA* 3.1 24.3 + - - +
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Residues in contact with GLY 51 (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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47B THR* 2.8 12.6 + - - -
50B ASN* 1.3 76.7 - - - +
52B LEU* 1.3 56.6 + - - +
54B ALA* 3.9 5.4 - - - +
55B ALA* 2.9 30.7 + - - +
77B ALA* 5.2 0.2 - - - +
81B ASN* 3.5 26.9 - - - +
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Residues in contact with LEU 52 (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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16B TYR* 3.7 32.8 - - + -
48B TYR 2.9 18.8 + - - +
49B VAL* 3.6 4.7 - - - +
50B ASN 3.2 0.2 - - - -
51B GLY* 1.3 74.7 - - - +
53B ASN* 1.3 66.9 + - - +
55B ALA* 3.1 2.6 + - - +
56B LEU* 2.9 41.9 + - + +
78B ILE* 4.4 13.2 - - + +
81B ASN* 3.4 10.3 - - + +
82B GLY* 3.9 28.5 - - - +
85B HIS* 3.7 25.1 - - + +
68Y VAL* 4.3 9.9 - - + -
71Y LEU* 5.6 1.1 - - + -
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Residues in contact with ASN 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLN* 3.3 35.7 + - - +
16B TYR* 2.6 58.5 + - - +
49B VAL* 3.1 22.0 + - - +
50B ASN* 3.8 8.4 - - - +
52B LEU* 1.3 78.2 - - - +
54B ALA* 1.3 64.4 + - - +
56B LEU* 3.3 5.5 + - - +
57B GLU* 3.0 23.6 + - - +
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Residues in contact with ALA 54 (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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50B ASN 3.1 17.0 + - - +
51B GLY* 4.0 5.8 - - - +
53B ASN* 1.3 78.1 - - - +
55B ALA* 1.3 61.0 + - - +
57B GLU* 3.5 9.2 + - - +
58B ALA* 3.3 20.4 + - - +
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Residues in contact with ALA 55 (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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51B GLY 2.9 20.3 + - - +
52B LEU 3.1 5.6 + - - +
54B ALA* 1.3 75.8 - - - +
56B LEU* 1.3 65.9 + - - +
58B ALA* 3.1 10.8 + - - -
59B GLN* 3.1 4.0 + - - +
74B VAL* 3.1 23.1 - - + +
77B ALA* 3.8 24.7 - - + +
78B ILE* 3.8 24.0 - - + +
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Residues in contact with LEU 56 (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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16B TYR* 3.5 34.1 - - + -
52B LEU* 2.9 31.0 + - + +
53B ASN* 3.9 4.5 - - - +
55B ALA* 1.3 76.0 - - - +
57B GLU* 1.3 62.3 + - - +
59B GLN* 3.5 4.4 + - + +
60B LYS* 3.1 23.4 + - - +
78B ILE* 3.9 25.8 - - + -
59Y GLN* 4.6 9.0 - - - +
63Y ALA* 5.3 5.6 - - + -
71Y LEU* 3.7 35.2 - - + -
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Residues in contact with GLU 57 (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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15B GLN* 5.1 9.2 + - - +
53B ASN 3.0 18.1 + - - +
54B ALA* 3.5 10.3 - - - +
55B ALA 3.1 0.2 - - - -
56B LEU* 1.3 78.2 - - - +
58B ALA* 1.3 62.0 + - - +
60B LYS* 3.3 17.4 + - - +
61B LYS* 3.3 44.7 + - + +
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Residues in contact with ALA 58 (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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54B ALA 3.3 8.8 + - - +
55B ALA* 3.1 10.6 + - - +
57B GLU* 1.3 75.7 - - - +
59B GLN* 1.3 60.2 + - - +
60B LYS 3.0 1.3 - - - -
61B LYS* 3.4 3.9 + - - +
62B ALA* 2.8 34.7 + - - +
70B LYS* 5.3 13.6 - - + +
74B VAL* 3.8 15.9 - - + -
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Residues in contact with GLN 59 (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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55B ALA 3.1 3.6 + - - -
56B LEU* 3.9 7.1 - - - +
57B GLU 3.4 0.4 - - - -
58B ALA* 1.3 78.8 - - - +
60B LYS* 1.3 56.6 + - - +
62B ALA* 4.2 4.5 - - - -
63B ALA* 3.1 27.7 + - + +
71B LEU* 3.3 26.7 - - + +
74B VAL* 3.2 31.3 - - + +
78B ILE* 3.4 17.1 - - + +
59Y GLN* 3.0 40.5 + - - +
75Y GLN* 2.8 35.4 + - - -
78Y ILE* 3.6 8.0 - - - +
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Residues in contact with LYS 60 (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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56B LEU 3.1 13.3 + - - +
57B GLU* 3.4 22.2 - - - +
58B ALA 3.0 0.6 - - - -
59B GLN* 1.3 73.9 - - - +
61B LYS* 1.3 99.6 + - - +
63B ALA* 3.0 14.2 + - - +
64B GLU* 2.9 57.0 + - + +
59Y GLN* 5.5 2.0 + - - -
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Residues in contact with LYS 61 (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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57B GLU* 3.3 29.4 + - + +
58B ALA* 4.1 3.1 - - - +
60B LYS* 1.3 107.0 - - - +
62B ALA* 1.3 62.1 + - - +
64B GLU* 3.3 14.0 + - - +
65B ALA* 3.0 26.1 + - - +
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Residues in contact with ALA 62 (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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58B ALA 2.8 21.4 + - - +
59B GLN* 3.9 5.4 - - - +
61B LYS* 1.3 78.0 - - - +
63B ALA* 1.3 58.5 + - - +
65B ALA* 3.4 4.7 + - - -
66B THR 3.3 2.9 + - - -
67B ASP* 3.0 33.2 + - - +
70B LYS* 3.8 34.3 - - + -
71B LEU* 4.0 14.8 - - + +
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Residues in contact with ALA 63 (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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59B GLN* 3.1 18.8 + - + +
60B LYS* 3.0 6.5 + - - +
62B ALA* 1.3 73.6 - - - +
64B GLU* 1.3 58.6 + - + +
65B ALA 3.0 5.2 - - - -
66B THR* 3.0 19.1 + - - -
71B LEU* 3.7 23.8 - - + +
14Y GLN 5.9 1.2 + - - -
16Y TYR* 4.5 2.6 + - - -
56Y LEU* 4.9 7.9 - - + -
59Y GLN* 5.9 3.1 - - - +
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Residues in contact with GLU 64 (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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60B LYS* 2.9 55.8 + - + +
61B LYS* 3.5 19.2 + - - +
63B ALA* 1.3 76.5 - - + +
65B ALA* 1.3 57.7 + - - +
66B THR* 3.4 4.2 + - - -
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Residues in contact with ALA 65 (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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61B LYS 3.0 16.4 + - - +
62B ALA* 3.7 7.0 - - - +
63B ALA 3.0 0.8 - - - -
64B GLU* 1.3 78.4 - - - +
66B THR* 1.3 72.2 + - - +
67B ASP* 3.2 10.8 + - + +
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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
------------------------------------------------------------
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